Once you have an assignment, you need to grade it. Canvas has a tool called the speed grader that really does live up to its name. The quickest way to get to the speed grader is to click the assignment in the to-do list on your home page. It tells me that there are students who need their assignments graded. The first person who needs their assignment graded is Raquel Corcoles. Since she used the text entry to do her assignment, you can see what she typed. You can give it a grade. This one's worth 10 points out of 10, and you can leave a comment for the student to read. If you want, you can attach files in the comments for students to download if you need to make longer comments.  You can use the left and right arrows here at the top of the screen to go from one student to the next. Or you can use this drop-down menu to see a list of students and whose submissions need grading. The orange dot means that it hasn't been graded yet. Let's look at Georges Remy's assignment. Georges uploaded a word processing document, and you can see the preview of it here. You can annotate the document here and leave a comment. You forgot question two. Or you can use the highlighter, highlight part of the text, and make a comment. Good use of correct punctuation. You can have text annotation or area annotation. Let's make an area annotation in red and say, this should probably be right aligned. All of your annotations will be visible to students when they look at the grading for the assignment. And now, give it a grade. You can give fractional points in Canvas. We'll say that this one is worth 8.5 out of 10. And again, if you want, you can leave comments with the assignment. When you finish grading, you can go back to the assignment, or you can go to the gradebook. Let's go to the gradebook and see what it looks like. We'll investigate the gradebook a bit more in another video.


Good morning and welcome to this FDP on pedagogies for effective teaching learning using online and blended modes. The introduction was actually supposed to be done by Professor Fatak who is currently in Rajasthan in Udaipur in Padmopat Singhanya College. But there seems to be some problem with transmission from their end and the audio is not coming out clearly. So we thought rather than delay the start of the session we will just go ahead and start with the session and later on when he is able to connect we will also have him participate in the session. So many of you would have done the previous FDP and we are happy that there is such a large amount of participation. What we will be seeing in this one in the previous FDP you would have seen various technologies and what we will be seeing in this one is how to use these technologies effectively both in the classroom as well as online as well as blended modes. So some of these technologies are what we call as learner centered technologies. So over the next two days we will be having interactions to talk about how do we do peer instruction using such technologies, how do we do peer assessment, how to move from being a 20th century teacher where the focus was mostly on one's own delivery, how well am I lecturing to moving to a 21st century teacher where the focus is on how well are my students learning, what activities can I create for the students to learn well, how can I promote collaboration and things like that. And in tomorrow's session what we will be doing are some strategies for how do we use visualizations effectively both in the classroom and online mode, how do we integrate active learning with visualization and also we will be talking about creation of open education resources, how everybody can participate to create a large number of open education resources. So that is basically the agenda for the live interaction for these two days. So with that I will invite Dr. Jay Krishnan to take over the session. Good morning everyone and thank you Professor Sridhar. So the key points for the coming two days or the key focus in the coming two days is how to use technology effectively, the pedagogy behind it and how to make the entire teaching learning process more learner centered than so the idea of moving from the 20th century teacher who is the in the information transmission mode to a 21st century teacher who is actually a facilitator within the classroom that is what we will be focusing on in the coming two days. Now some quick what do you say updates about FDP 101x. So in FDP 101x we had around 7700 registered participants and at the end of the faculty development program the initial grade cut off was 50 percentage. So around 4900 participants had qualified with more than 50 percentage marks. However we have I mean as you would be familiar lot of technical issues were faced by both the participants and IIT Bombay which had made it a which had made a lot of problems during the entire FDP 101x. There were also very genuine reasons due to which some of the participants were not able to completely participate or were not able to complete lot of the activities in the FDP 101x the graded activities. So keeping this in mind and since this was a foundation course where we were expecting the if you look at the learning objectives the idea was to expose participants to the various technologies that are being having and ensure that they use it in one form or the other. So what we had done in FDP 101x was that we had modified the grade cut off to 35 percent so that which allowed around 498 more participants to qualify for FDP 201x. So now we have a total of 5300 participants in this particular FDP where they will all be exposed to how to use the technology. So each of we had three main technologies in the previous FDP wordpress as a content management system, Moodle as a learning management system and screen casting software like CAM Studio and Screencast-O-Matic so that faculty can create their own audio-video resources. These three skills will be used extensively in this particular FDP so that all faculty will create effective teaching learning designs or teaching learning plans for their own courses. So for example, let us say I am teaching computer science, let us say programming. So as a teacher what would work while doing FDP 201x is that you take up topics that you are going to teach in the upcoming weeks. Let us say I am teaching loops in computer programming on 21st that means the coming Thursday. So for the flip classroom practice you can just use some topics within this loops, let us say it is a for loop. You can create a small screencast on the for loop, the contents on for loop and then see whether you can do a structured discussion within the classroom or do some activities like think-pair-share or the peer instruction that you will be doing today and tomorrow and see what is the change happening within your own classroom, how the learners are responding. So this would be an ideal way of doing the FDP 201x. So once again repeating take a topic that you are going to teach in the upcoming weeks and for all the activities as practice you create resources based on these topics. We are going to just check with RC 1132 where Professor Fartak is present and he will be addressing all of you for the first introduction session. Over to Professor Fartak. So first of all I apologize for the delay in starting the session, much of it was because of me, I did not teach here in time and the connectivity took some issues to be resolved. I am very happy to be personally present in Padampat Singhanya University where I see a lot of enthusiastic people here. Tomorrow I will be addressing all of you from Mewar University Chittorga. I wish to take up a couple of points today. The first and the most important probably is to emphasize active learning. People are familiar with the term active learning but often it is not very well understood. Active learning is where learners act and learn by doing. You are already familiar with some of the exercises in FDP 1 where you actually encourage the learners to participate by action. But here we are talking about active learning in a classroom. Traditionally classroom is used only for delivering lectures. However in the active learning mode when we use the flip classroom we typically ask the learners to study the video sequences elsewhere typically from their homes and when they come to the classroom we engage them in activity. Now that is the common sense interpretation. However to prepare for the flip classroom is not an easy task. It is not a random activity that we wish learners to undertake but a very focused and planned activity. Let me emphasize that the concept of flip classroom was not feasible more than 20 years ago. There was no internet, there were no pre-recorded videos available and accessible easily to people and therefore the teachers had to give the lectures in person. And of course as we all know we cannot rewind a physical lecture being given unless of course we stop the teacher and ask him to explain something again. And that was the time for everyone. Basically pre-recorded lectures, short lectures permit learners to view these at their homes, at their leisure, at their chosen time. They can view these again and again if they have any difficulty hopefully they would have learned the basics by viewing these lecture clips. So when they come to the classroom essentially we convert the class into a large tutorial session. Perhaps it is best to take an example and explain how some of us attempt a flip classroom. Three years ago my colleague Mr. Suprati and I taught the first course called CS 101. It is a first year programming course. All the participating teachers would be familiar with this course. Some of you would be teaching this course and others would have done a similar course when studying their undergraduate degree. I believe all of you are familiar with basic programming. Now the way the programming was traditionally taught is usually the lectures are given and in the labs you attempt some programming problems. Some assignments are given which you work at home. But in a flip classroom what Suprati and I tried was we actually converted the entire one hour session into a problem solving session. Typically we made groups of students sitting in the class which were aligned to their lab groups where they will be working in the labs later in the afternoon sessions. Now each session began with a problem being presented on the screen and that problem a programming problem was to be attempted by all individuals first. We would give them five to seven minutes to write their programs and then we would ask them to exchange their answers with the neighbors. What I learned from my colleague Professor Sridharayar and Prasanna Murthy, what they call the think-pair-share method, whether I have worked out a solution, my neighbor has worked out a solution, we both exchange the solutions and comment on each other's solution. There is supposed to be a small discussion in which I try to convince my neighbor how my solution is right and the neighbor does exactly the same thing. After giving three or four minutes for individuals to discuss, we extended this think-pair-share where we said the entire group of about eight to ten students typically sitting in a row in the class would work together in working out a better solution than the ones which were produced by all the individuals. They'll give them five more minutes to do so. In a class of 250 students, we had more than 25 to 30 groups of this kind. Each one would have a handwritten time ready with them at the end of the seven minutes. Then I decided to do a more fancy stuff. I would randomly pick out two or three solutions from these groups and take one solution and present it on the overhead project in the class. The entire class looks at the solution prepared by one group and then I ask the whole class, please find out errors in this program. As all of you know, we being humans, we are delighted to find errors in other people's work. The whole class very actively participated, making comments like this one is missing, the logic of the statement is wrong, something or the other. The point is because of this activity, the entire class without exception was engaged. The group whose solution was being presented was furiously taking notes and was trying to defend their solution. The rest of the class was busy in critically finding out errors in that program. The point is the whole class learned much more than what they would have learned through a 20 minute lecture on the same issue. Then we'll go to the second problem, do the same thing, go to the third problem. It is possible typically to solve three programming problems in this kind of individual and collaborative effort and engage the entire class in discussion and dissection of the solutions presented. Believe me, at the end of the semester, we both determined that our students had learned much more than what they would have learned in a normal course. Now, this one activity that I gave an example of was peculiar to a programming course.  That's why as I said, it is not something that one solution fits all. But active learning is the important element. And the active learning can be incorporated on a large scale throughout the semester only if you practice the flip classroom and for which you prepare very thoroughly by planning the actual actions that you will do. In IIT Bombay, we were privileged where we could experiment throughout the semester like this. However, when all of you are engaged in teaching conventional university, I believe it is next to impossible to try and do it for an entire course in a semester in the first instance, particularly the university compulsions, the rigid syllabus, the rigid follow-up, etc. But my suggestion is you could always choose one or two topics of your entire syllabus which are typically covered in one or two weeks in advance. And inform the students that for these two topics, you will be engaging them in a flip classroom. Prepare the lectures, prerecord them, you are welcome to use any open source lecture material on that subject wherever available. IIT Bombay itself will be setting up all these lecture resources of previous workshops in an OER repository. And you could use that and tell your students that look for these two weeks when you come to the class, you should have studied these lecture clips, come to the class prepared and we will be having only problem solving and discussion session to active learning. I am sure that if you practice this for just one or two weeks in one semester, you will have enough experience and expertise so that subsequently you can extend it for the entire semester for the whole course. I will like to inform you that for the first time when you do this, a whole lot of more effort is required. I remember Sukratik and I and two of my senior associates, Firuza Aibara and Nagesh Karmali used to spend 8 to 10 hours in designing for the problems for every session. But subsequent years it was possible to use variations of those problems and the effort required was much less but the impact on the students was much more. So in conclusion I would like to say that active learning of which flip classroom is one important but not the only element is the way going forward. You should promote this activity even outside the classroom and that is where we need to encourage collaboration among students, collaboration amongst teacher and the students but on which I will speak later tomorrow from Chittorgad but today I would like all of you to know that encouraging active learning by doing appropriate planning and execution of a flip classroom is a far better mechanism to ensure phenomenally higher levels of learning by all learners. Thank you so much. Over to you JK. Thank you Professor Fartal. That was really an inspiring message to all the teachers who are out there. So two important things that I will reiterate when you start off just do it for just one or two topics within your course and then slowly once you get a hang of the entire active learning strategies then start using it more frequently. So this is what we have been doing even in our if you look at the pedagogy of the course itself. So there is always these learning dialogues where the teacher uses reflection spots to make the learner engaged and which is immediately followed by a learning by doing activity. So as a teacher when you are practicing these kind of activities in your classroom it is very important that the practice is continuous. You take specific you design for the flip classrooms or any other active learning strategies well in advance and try it out on very few let us say two or three topics and then understand its effectiveness before trying out on an entire topic. So what we will do is in today's first session we will try out active learning strategies in a innovative manner. So I hope all of you are have used AVU interactions either with your mentor or now using the remote center interactions scheduled remote center interactions that we have. So within AVU there is a tab called questions. So what I would request all of you is post one question from each RC where you have a doubt regarding the wordpress, screencasting and moodle. So integrating wordpress, screencasting and moodle within your classroom. But we have to do it in a structured manner. So individually think what is one challenge that you face while integrating these technologies in your classroom. So within think phase I want the remote center coordinator to tell all the participants to think individually. So at this point think individually what is one challenge that they are going to face while integrating these technologies within their regular classroom. So you can take approximately one to two minute to think about this. Do not post anything in the questions tab now. This is a time where at the RC all the participants have to think. So remote center coordinators please ensure that everyone in the remote center is thinking about this question, challenges that they face while integrating moodle, screencastomatic and wordpress within their own teaching learning. So at the first point do not post anything in questions right now. Just think individually. So approximately one minute is over now comes the pair phase. Just turn to your neighbor share the challenge that you face and then together come up with solutions for the challenges that has been shared by the peer both you and peer. So in the pair phase I am repeating again remote center coordinator you can just ask the participants to share with their neighbor the person who is sitting just next to them these challenges and together come up with a solution for come up with one mechanism through which these challenges can be addressed. Once again do not post any questions in the questions tab right now there is going to be a time. In the pair phase you can take approximately two to three minutes to discuss the challenge and come up with a solutions for these challenges or ways in which you can tackle these challenges. Remote center coordinator please ensure that participants are discussing. Now we require the center to be very active there will be loud noises but it is acceptable. So take two to three minutes in discussing the challenges that you face and possible solutions to it. So once again requesting all the remote center coordinates not to post anything in the questions tab now because there is going to be a specific time for allotted for this but if you want to post just see what all questions have been raised first in the questions tab and upward questions that you are finding similar to the ones you are having. So supposing somebody had a question on let us say screencastomatic and there are some questions related to screencastomatic in the questions tab. So you can just go there check what the question is and upward it so that the instructor will know that more than one people are having the same question. So do not post the question again just wait for see whether that question is already there but in this pair phase continue with the pair phase find possible ways or mechanisms through which you can tackle these challenges that your peer has given you. So now the pair phase time is almost coming to an end we will now move towards share phase. So within RCs share all the so the remote center coordinator please take some time now and ask all the pairs to share the challenges that has not been answered or that for which mechanisms have not been found to tackle the problems within the RC. So for example there is a person there is a peer group one where two challenges were posted and only one for only for one challenge they were able to come up with a solution. So there is one challenge that has not been addressed. So as a remote center coordinator you should now take consolidate all these unaddressed challenges. So ask participant to share all these challenges for which you have not found solutions. So this should be now done at RC and all those problems which has not been addressed yet the remote center coordinator has to consolidate. So remote center coordinators you can it will approximately take around 5 to 10 minutes for the sharing activity which is fine consolidate all these queries at your end. Once again participants we are hoping that all of you are sharing the challenges to your remote center coordinator. So we are also from our end we are looking at what is happening in each RCs we are taking few RCs we are also seeing that some are discussing so now the share phase is supposed to happen please do not sit idle yeah. So I see that the remote center coordinator in few colleges are actively looking at making people discuss. So remote center coordinators please do not sit idle this is the time that you have to be more active make sure that participants all the challenges that that are been discussed by the participants are elicited. So now what we are going to do is if the consolidation is done we would request the remote center coordinators to raise a hand. So we will approximately visit around 10 remote centers now through a view interaction. So what we are going to do is now we will come to each remote center and the remote center coordinator has to post one challenge and share it to everyone and we will be getting possible solutions to this from we will be sharing these challenges to all the remote centers and we will see whether someone can come up with possible strategies or possible ways or mechanisms through which these challenges can be tackled. So now I will go and visit each remote center so do not post any questions as of now because that question posing activity is going to come immediately after that please raise your hand I mean within a view please use hand raise option and we will listen to the challenges that has been posted by different RCs. So we will go to approximately 10 RCs today in the first session but we will be coming to each and every RCs across different sessions and we will be collecting these kind of challenges and other we will be interacting with each RCs across the coming two days. So first I will now go to RC1015 the coordinator can you kindly let us know one challenge that has not been addressed within your remote center. Good morning sir. Good morning. Actually sir at the time of that RCA2, RCA1 was related to the WordPress and RCA2 was related to Moodle. And in RCA2 at the time of creating Moodle site we have created the Moodle site but while uploading the videos there we face some problems like if video is of say mp4 format it is not accepting. So we are not able to understand which kind of video we should upload and how we should go for it. Okay. So because of that most of us have not able to complete that particular assignment. Okay. The question that has been raised by RC1015 is they were not able to upload mp4 videos into Moodle directly. Now there could be multiple issues to it but what we are going to do now is so I want all the RCs to ask your participants how can somebody tackle this problem. So within each remote center rather than me answering now all the participants have to think about this problem. The problem is that it is difficult to upload videos directly to Moodle. How can this be tackled? So all the participants think about this question and if you have an answer post it in chat. So I want RC1015 to look at their chat window right now within Avue. Remote center coordinators from other remote center coordinators please ask the participants within your remote center. So the question is how can videos be uploaded in Moodle? What is an effective way of uploading videos in Moodle? Direct mp4 or other videos are not being supported in the Moodle site. So the question so I want all RCs to look into this question. So RC1015 if you look at the chat window one solution that has come from RC1063 D.Y. Partial Institute is to upload in YouTube and share link in Moodle. So somebody is saying use file upload or book upload reduce the size of video upload video in link upload the video in YouTube. So a common answer that is coming from all RCs is use upload the video in YouTube and share the link within the Moodle site. So RC1015 have you received the answer? Yes sir yes okay. So what you are just seeing right now is like just what Professor Fatak said wherever there are issues so it is not just one person who is there to answer this question. You have almost now 5000 colleagues 5000 peers with you with whom you can discuss and that is the leverage that this technology is giving you. So you should make optimum use of it and there are many people who have tried different things. So for example I so what I used to do is in the case of video uploads is I will use a activity known as label and I will embed the YouTube link in that particular label. So if you go to YouTube and when you click share you will see an option where you will get a link or you can embed it as an iframe. So I take this iframe link and I put it in the label using the HTML edit facility of the label. And once it comes so you will see the videos embedded in the Moodle page. Like what you see in learning extension resources you will see the video and there will be some text along with it and everything will be seen as a page. So let me now go to the next RC. So we will be using the same mechanism throughout rather than me answering it will be the participants from other RCs will be giving the first answer. So this is RC 1094 Lourdmada College Trivandrum. Our doubt is regarding Moodle. So we could create Moodle in Genomeo. We want to know how many users can be enrolled in a course. Is there any limit? So the question so the new question for all all participants. So remote center coordinators please note the question from RC 1094 is what is the number of users the limit of users that you can have in a Moodle course. You can check with all participants, consult it, the answer. So I see that lot of people are responding. So they are asking about Genomeo site. Genomeo site which is a Moodle hosting site what is the limit of users. So many are saying unlimited but I see conflicting answers. Somebody is saying so it is not Moodle cloud they are asking about Genomeo. So somebody is saying 350 somebody is saying there is no limit. So RC 1094 I think the answer that you would be looking at is I think Genomeo might be having an unlimited size I will just check from my end also. So if you look at the Genomeo website there is a section called capabilities and restrictions. So over there it is being said that there are no limits on bandwidth or disk space but our resources are somewhat limited. So I think it is safe to assume that you can have around 100 people within a Moodle course but the size problem you will have to check with the Genomeo but I think if you actually look at so there are some answers saying that you need to go for a paid plan because it is being said in the website also to support more resources it is important that you go for a paid plan within Genomeo. Then you can have more services from the Genomeo website. So this is how typically all Moodle hosting services work. So they are offering this technology or the software as a service and there will be some cap for which you can have it for free and for the others you have to get extended services you have to pay them. So this is a typical model in which many of these technology hosting platforms and other services work. So I hope Lujmata I hope you have received your answer. Yes sir, thank you sir. So once again what I am trying to do over here is the pedagogy. So I have a tool like AVew and I have around 5000 participants connected to me and what I am trying to use as a teacher is engage students both in the session and also use the facilities of the technology to leverage the knowledge sharing as well as leverage the way in which technology can be used in the classrooms. So let me now go to the next remote center RC 1063 DY Partil Institute Pimpry. Good morning sir. Good morning. So the solution what we used in our colleges we have a local model server and we have increased the capability of a video which can be uploaded from 16 MB to the desired size and since it is a local. So unfortunately they got disconnected due to some technical difficulties. So I will repeat their answer. So the answer that RC 1063 provided was they hosted so I have RC 1063 once again back. Yes sir, please continue with your answer. Locally as well as can be accessed outside so as far as the technical challenge of size limitation is concerned that can be overcome by changing the size from 16 MB to desired size so that desired video can be uploaded on our server. If we upload it on a YouTube then there is a another challenge what we face at our end that YouTube is most of the places not allowed in the college. So by using this solution we can upload desired size video on the model. Okay. Also do you have a challenge to post so I will repeat the answer that they provided. So apparently within their college there is a constraint that YouTube is blocked. So to overcome that what they also did was they increased the size limit of the files that can be uploaded in their model servers and faculties then restricted the size within that particular size limit and uploaded videos directly to model. So this was a solution that is proposed to the initial challenge that RC 1061 had posted. So RC 1063 thank you for the solution can you now give me the challenge that has been undersold within your remote center we will try to get okay. So unfortunately RC 1063 got disconnected but let us move to the next remote center. Mayvar University 1, 2, 3, 7. Sir our query is regarding Moodle like you told like there can be unlimited users and there can be more than 100 users. So my query is regarding like if I am having one course and in that course number of students are there who are enrolling. So for them how I can evaluate like quizzes because if I am enrolling each and every of them then I have to fill details like username and password should be different for all students like if it is 58 students class then 50 students username and password I have to create. So is there any other way around like it could be easy for me to evaluate quizzes for these types of courses so that I could have only made only one time username and password and I can evaluate the quizzes for different students like this anywhere easier way. So the query raised by RC 1237 is that currently for enrolling 50 students he has to manually add all the details of the students and which is taking too much of time. There has to be unique passwords and other things so how to overcome this. So please look into the chat window now I want all RCs to query the part ask the same question within to the participants and post the solutions. So do not post answers other than this so the query is how to reduce the effort of bulk upload of users. So there are lot of solutions coming in I think somebody has first said about manual enrollment. Second is bulk upload using a CSV file 1103 is saying that they create Excel file with username password email ID etcetera in a single file and then upload it self-enrollment is a better option self-enrollment by students. So if you actually look into your chat screen within a view you can see lot of solutions coming in. So these are some of the solutions so I will just summarize the solutions provided by different RCs first you can do manual enrollment so if you set the course in a self-enrollment mode all you have to do is give the course enrollment link to the students and they themselves can fill in these details and get enrolled in a course. So it is similar to how users register in IIT Bombay X for an open course. They register first in IIT Bombay X and then they browse the courses that are available and then they register for courses that are open what you are doing in your own courses that you are actually mapping doing an invitation only mode wherein you know the students and then you are yourself are creating all the different user names and passwords but if you want to do this a better option is that you provide an Excel file with the username and details that you will be having of students and then ensure that there is a force password change is enabled for all the users I mean make this setting within the Moodle site settings where the moment you can give a provide a dummy password initially to all students so the password can be same but when they log in using this password then Moodle asks these users to change the password and then access the course so over here what you will do is you will do a bulk upload or a CSV upload in a CSV file give the details of all the users that who are there so essential details like name email ID a first name last name email ID user name and password so username could be their role numbers also and then do a bulk upload and if the force password changes set then when they log in they will have to change the password and create a new password which is known only to them so RC 1 2 3 7 have you received your answer yes sir yes yeah we are really satisfied thank you thank you before moving on to the next RC please note what we have done in this in the previous question so the student first raised a question the learners first raised a question where we collected answers from other students and based on the other answers that the teacher instructor received instructor then gave some more additional possible solutions on top of it so this you can do within your own classroom as well so this strategy if you actually look look at it this can easily be implemented even in a single classroom let's say you teach a concept or a teacher lesson in a day and you keep the final 15 minutes of the class for discussions like these where you do a think-pair share activity so the think-pair share could be that first you ask the students to identify concepts that they did not understand in that particular lesson then you ask them to pair up and discuss between themselves to see whether there is anybody else who know the concept and they are whether they are able to explain that concept to the peer so there here the peer learning is happening at the first level and then in the share phase you can take concepts that has not been understood by both the peers like in this case it was the challenges that was undisolved you can take up these concept and address it in the share phase where you can first ask other students the whole class to first find a solution for the I mean explain the concept to the person and if there are some shortcomings you can just add on top of add your own explanation along with the students other students explanation so let me now go to the next remote center symbiosis Institute of computer science 1190 the question is regarding a video creation screencast software is used to create the video and the original size of the video was 9 MB but editing was required so opencast software were used to edit the video and an increase to 90 MB okay size of video has increased 10 times than the original one after editing okay so yeah so the what is your question so the size has increased so do you want the mechanisms to reduce the size 90 MB uploading on even if on the moodle or YouTube it's not advisable to reduce the size so that even for the downloading purpose also it is convenient for the users okay okay so if other remote centers have not heard the question so the question from RC 1190 is that they had created a screencast using screencast automatic and then they found that there needs to be some things added so they use the open short linear editor to add these particular missing things or edit the video and after editing the file which was initially 9 MB increased to 90 MB which is a 10 time increase so is there some way in which the size can be reduced while doing editing so I am asking my video team also the same question so my video team also is also preparing answers to it over here so the video team the question is when the linear edit the nonlinear editing is done through open short the size increased to 90 MB so remote centers now please discuss possible ways in which the size can be reduced so one solution that has come from 1319 is use any online format converter and reduce the size of file the one more solution is the file can be put in RAR and then no so RAR upload is not possible so RC 1348 the RAR upload so you can zip file and upload videos into YouTube online video compressors are available truncate option so some of the solutions that are coming are use of online compressors yes so there is somebody else managing quality of video in terms of pixels I think this solution is somewhere coming so can you think the person who has posted the pixel solution can you think a little bit more I think you are coming close to the solution so somebody is suggesting other editors so MPH to editor or Microsoft will do so there is a editor look into the response provided by RC 1346 there is an editor at additional editor zip software is will not work because they have to upload the video in YouTube split video into smaller size split video into so this is from RC 1005 split the video into smaller sizes use video compression software photo editor or Microsoft photo editor will not work because photo editors this is a video so just normal photo editors will not work so I will ask my studio team to give you one more expert answer so so you can use lot of these online editors that are available where you can get a better compression rate I will also ask my studio team who are currently doing these kind of things over here to provide one more solution yeah good morning to all so when you edit any video in the editing software so when you render the file there are some parameters you need to set and the size depends on the bit rate as well as the codec which you are going to use so there are so many parameters you can set just try out if you use the lowest bit rate then you will get a file in less size so try some of the experiment using the editing software there is no need to use any additional software to compress the file okay so the solution that is coming from over here is that you can within your editor itself look into the settings and experiment on it and see whether you can get a lower bit rate so setting the lowest bit rate is always advisable if you want to reduce the file size and also there are other so through this we also came to know that there are lot of these video compressing softwares that are available online also so if you want to explore that you can also do the compression over there or online editors are also available so I hope RC 1190 you have your answer yes sir we will try are you happy with the solutions that has been provided not fully we need to try it out first and let us see whether it works because online if I use the online editor when I need to upload a file of 98 the first on the online exactly so while so you can use the alternate suggestion that our studio team has provided try for lowest bit rates yes sir that we'll try about that work out on that practice on it if it is workable will inform you yeah let us try it first let me try it first and then we'll come back to you sir yeah sure thank you sir yeah thank you so let me now take the next RC which is RC 1128 I have one query like using a view or model like how to cope up with the issue of low or interrupted internet connectivity or speed like most of the resources like the colleges they are located in a remote center so how to cope up with this issue okay so the question that has been posted by RC 1128 is many a times it may so happen that the internet connectivity at different places are not what you say continuous or the bandwidth might be fluctuating so how to cope up with the issue of fluctuating bandwidth when when you are using either so I hope it is a view that you are referring to right yes sir yeah so while using a view how to cope up with the bandwidth issue while using a view for interactions with different RCs so first I am hoping that since most of the mentors and mentees had interacted through a view across two to three slots two slots that we have provided think about possible ways so this is a quite a challenging question the question is how to handle interrupted connections of various places while doing interaction in a view so I request remote center coordinators to collect answers from participants and post in the chat so there this challenge so I see that the remote center coordinator so this was really good so what he tried the remote center coordinator tried is collect answers from the participants within the remote center itself so and this is decided so this is what is decided that you increase the engagement so within remote centers why the synchronous interaction is kept is because you not you can have you have around let's say 40 to 50 users and experts with you you should first get solutions from them and then ask then move ahead and you have around 5000 people connected within a view where you can get more answers and finally there is instructor so this is what technology is actually supporting in any classes it is actually leveraging the power of the knowledge that is available within you and is as a teacher you should know how to facilitate this knowledge sharing then you will have more engaged students and more active students which is required while these concepts are being taught so I see lot of solutions practical solutions as well as coming up use chat option do not use busy hours use the non busy hours to solve the connectivity problem internet connection through wired or fiber optics is better use chat option set higher priority for video streaming data on your firewall clear cache so whenever there is a video disconnection you can use chat button you can post more answers so again over here I will request our studio team so one practical difficulty is that if the internet the entire a view software is built on this internet availability of internet but over there also they have ensured that you need only very minimum bandwidth even with many very minimum connectivity you could what do you say get the optimum use out of it but typically when you use video and you have lot more people connected then the bandwidth that is being used is going to be pretty high the high bandit is going to be consumed so in this option so one of the ways in which is let's say you decide that you will be sharing video and audio let's say for five minutes or you decide the slots at which video and audio is going to be shared use chat more frequently and ensure that there is at least minimum to Mbps connectivity at the places so other than that I don't think there are other valid solutions so yeah so what the studio team is also telling me is that there is a audio chat facility available in a view so if video is consuming larger bandwidth audio chat can also be utilized so it's like you are there for two or three so like you do a Skype or the Google Hangouts where you don't use videos use the audio portion of it so offline videos system updates yeah so basically these are some these are all some solutions that we have from our end so RC 1128 happy with the solutions yeah seems to sir but not not so completely but yeah yes I can hear some feedback not completely but yeah partially we are satisfied yeah please thank you sir yeah so I understand that let me just explain a little bit about usage of ICT so it is so some of these softwares like the virtual classrooms that we are using the video audio synchronous interaction mechanisms they are all they all consume high bandwidth and hence the access to the resources becomes very important but if you have let's say limited resources and you want to do some integrate technology into the classroom then the first and foremost thing that you have to ensure is that what are the essential learning purposes for which you want these technologies so for example video streaming and discussions I think one way of looking at it is let's say you have a recorded video of with some initial guidelines and other things and then you handle it through chat which is more text based and consumes lesser data bandwidth that would be a viable solution so let me now go to the next remote center so we'll be taking this this will be the final question for this particular session but what we will do now is before we end the session I would ask all remote center coordinators to consolidate this questions and post in the question tab now for all the participants all of you can see this questions in a view in the a view so look into this questions and as a remote center come up with solutions to the problems that has been posted by other RCs and towards the end of the day what we'll do is we'll try to see whether we can find a mechanism through which this can be shared so what I'll do now is I'll take the last question for this particular session this is RC 1247 school of management sciences technical campus Lucknow sir my question is regarding screen casting when we are recording a video often we get noises from suppose fan or sometimes dogs barking outside my house because I'm recording from my home or the household noises how can we reduce these noises software for that or any other special mic or something for that so the question is a very interesting one so the question from RC 1247 is that while recording screen cast at home there are lot of background noises that are coming in now is there some mechanism through which this background noises can be removed or reduced what can be done on this so one question one solution use audio from speaker option I'm not sure whether that would work completely because the noises will still come in so all the remote centers once again repeating the question question I think is a very something that many of you would be facing while recording the screen cast at home or at your institute there are lot of background noises that are coming in how to reduce the background noise so if you have answers 1136 is saying use noise filter software use noise removal application so one there are noise removal application available in software like Adobe CC okay one practical suggestion use quality mic and a separate room so there is a recorder du recorder and adobe audio screen that you can use construct a special room use noise removal option use soundproof classroom okay there is one practical suggestion to take care of noise prefer recording at night okay one more solution switch off fan and record okay use mixer to filter out noise I think there is lot of audio processing that you will have to do at the end if that is there but yeah using headphones with mic but over there also the noise will come practical suggestions record at night okay just to add on to the so you will see a lot of so remote center you can actually look into the chat window there are a lot of solutions that are coming from different remote centers just to add on to it something that is that you can do is there is something known as a unidirectional mic so when you record you have to use these unidirectional mics and also sorry directional mics and then so okay my studio team is correcting me do not use unidirectional but use directional mic and these so when you actually look into the audio driver of your system go to the control panel and check the audio drivers there is a setting that you can make where you reduce the noise that can be controlled within your audio drivers so these two together and preferably ensuring that there is some sort of when you are recording you are you close the room and ask switch off fan and other things and ask your family not to make too much of noise I think with all these three options you can have a better quality but using of directional mic and adjusting the audio settings within your laptop is some ways in which you can control it control the technology aspect of it and regarding the practical aspect yeah so if a dog is barking I mean unfortunately we can't do anything even in our own studio if a dog barks now you may hear it yeah so RC 1247 are you happy with the solution we will try out the solutions which you have suggested okay and see the results and then probably see what results yeah so yeah so do not just limit it to the solution that I am saying so if you actually look into the chat window you will see that there are a lot of solutions that are coming being posted by other remote center remote centers so these are coming from the experiences of participants from those remote centers so you can actually also look into all the solutions over there and based on the whatever you is fitting within your own context you can use those particular solutions yeah with this we have come to the end of the first session the introduction session where process part and process neither I hear first provided you with a broad agenda of the fdp and once again they reiterated the need for use of active learning methods within the classroom when you want to engage the students more in these kind of activities to ensure that they achieve the desired learning outcomes so what we also tried out over here is we tried an active learning strategy called thin pair share to elicit solutions and do a first level answering of these solutions at the remote center and finally when it was shared as an instructor as a facilitator what I did was I first went to other RCs to get the solution and then provided some extra solutions from my side or from the course teams side which could work out so if you actually look at this strategy the same is actually applicable in your own teaching learning settings as well so specifically with with the scenario of use of ICT your students would be more interested enthusiastic and active in finding out various mechanisms or experimenting out with technologies and that that you will have to use it for your advantage that make them do more activities engage them with the content and that is how the lesson designing has to happen to ensure that your students are also active and they are also in the meantime looking into the actual content that they want to know and by use of these ICT what you can also see is how they are applying it in the real life so make connections to real life where your concepts are required and give these kind of assignments to students these kind of activities to students where they will also get engaged so we will now go for a break and we will come back at 11.30 at 11.30 we will be discussing about peer review mechanism I understand that many have queries and cribs regarding peer review so Dr. Sameer Sahasrabudde will be joining us from Chennai and he will be taking a session on how to do this peer review the importance of it etc. so till 11th we will come back and assemble at 11.30 thank you


Okay, everyone. Welcome to the last talk session for the day. This is a series of success stories with Galaxy or a series of speakers being surprised when the bell rings earlier than they thought. We'll see how we go. I think we've got it sorted now. We might get cracking because we've got a series of short talks and a couple of long talks. As I said, success stories with Galaxy. Dan from the Cleveland clinic clinics going to talk to us a bit about what's that metagenomics. Thank you. Good morning or afternoon, I guess everyone. I'm going to be giving a talk that was originally supposed to be given by Bobby, but he unfortunately had some visa issues so he wasn't able to come but I get to go tell you about all this great work that he's been doing. So when I say we, I very much mean a lot of this work has primarily been done by Bobby. So, first I want to quickly just give a brief introduction to sort of what the microbiome is. So as you're aware, we have many, many cells within your own body, but there's actually a larger number of microorganisms that live inside of inside of your own body. That have large influences across metabolism.  The compounds that they're generating the metabolites.  And then so what can we do to sort of investigate these these microorganisms and and sort of better characterize them. So, I want to talk today about something called meta SBT. And so metagenomics allows us to study not only well characterized microbes, but also a large number of microorganisms that are not able to be cultured. Also, an increasingly large collection of meta genome assembled genomes, also known as mags, and these have sort of paved the way to get from, you know, higher order of taxonomies into individual species including strain level resolution of these microorganisms It's important to get down to these, these more precise categories, because, you know, it's really not just what microorganism is there but it's the genes that they have that are actually acting within your body with creating, you know, these compounds and metabolites and affecting your human health. So what what we're really missing now is a systematic procedure for organizing and processing hundreds to hundreds of thousands of these mags, along with all of these reference genomes that have been obtained from doing isolate sequencing. And then how can we then further go ahead and leverage these along with human health metadata, for example to to determine how we can assess and improve human health. What is meta SBT, this is a computational framework composed of several different modules, different sub routines. And so if we want to first think about the first one, this is the meta SBT index. And so what we can do is we can take us a collection of genomes along with their taxonomies, and we can build these for these in order to allow us to create a database that we can then take with our own sequencing data, our own mags that we've assembled, for example, to then go ahead and investigate this. So meta SBT, it leverages a tool called Howdy SBT, which is written by Bob Harris from from Penn State. And it's greatly improved upon from the Kingsford and Salomon 2016 approach for building the sequence bloom trees. It also includes check M to build with completeness contamination and so forth. So the index allows us to build the database, there's a boundaries function that then allows us to determine the common camers the minimum maximum of those, as well as the cameras between these different taxonomic levels and so when we're actually building these, we're building seven different SPT's from the different taxonomic levels from species, all the way up through to the kingdom. And the reason this is important that we do this screen went blank. The reason why it's important that we do this is because we will want to end up having an update process. So with the profiling what we can then do is we can provide our own sequence data, plug it into here and we can find out where along this taxonomic tree that our data results. The problems with the currently existing processes is that there's no way to update, but because we're actually building different sets of trees at different levels with meta SPT, we can actually have a update process where we can just update individual leaves by having to update the entire database. And this is important as we discover or sequence additional additional metagenomics mags and fully assembled genomes. So so far, what Fabio has been able to do is he's indexed all of the viral reference genomes, as well as a large set of mags from NCBI. We're using these with even more mags and as well as building bacteria archaea and fungi species into this. And we're currently investigating how to simplify this by building sketches representations of the genomes for these larger genomes because some of these some of these clustering steps and so forth are quite computationally intensive. So we have a Galaxy tool suite to do this to build the indexes that the databases to actually run profiling and then also to update. We're also, we have the genomes available that the databases available will be making available on CVMFS as well. So that everyone will be able to use them within galaxy or outside. I don't have time, but I also just want to briefly mention that. Okay, I'm out of time. Yep. Yeah, so if you want to go ahead and access these databases and the tools they're all open source they're available on GitHub. They're available on bio conda. There are galaxy tools that are also being released soon. So, thank you. We don't have time for questions at the moment, but next up we've got a talk from Linel and Alex about vertebrate genome project workflows within galaxy. I'm Linel and this is Alex and we're here to give an update about a vertebrate genomes project and the galaxy workflows you've been using to assemble a whole bunch of vertebrate genomes. So, the vertebrate genomes project as a bit of an introduction is a bit of a lofty goal of a project where we're aiming to sequence, as it says in the tin all 66,000 vertebrate species, but baby steps so we are shopping it up into phases the first one of which is sequencing a taxonomic representative from all orders, all vertebrate orders, and that amounts to about 260 species of which we are almost finished we have a little over 200 sequence in NCBI and curated NCBI ready for annotation. And on our, we have all of them publicly available as well this table just a screenshot from our public facing portal, where all the data is publicly accessible and viewable, as long as you're here to our data usage policies which you can email Eric about and not me. Aside from that, so these are the 51 genomes that have been done so far. Well, more since the 51 that are have been done and described in the paper that just came out and is on bio archive. It is currently in submission and nature biotech. Yay. But so it's 51 species assembled across the vertebrate tree of life. That's sharks, fish, mammals, reptiles, birds, and even works on some invertebrates we've used it on some spiders and some mosquitoes, because people don't read the lab name, but it works in a variety of genome complexity to from very homozygous critically endangered species from zoo populations to very heterozygous almost like strain crosses of zebra finches in a colony. Also genome size, it has worked on the 800 we get at a 800 megabase pear chub mackerel all the way to the eight gigabase pear carob refrog which crash every single note I tried to run it on. And about a third to half of these were run on galaxy EU using freely available public compute because it was before I was able to set up our local server and really utilize the compute my institution has and also stop giving Bjorn a headache. But the actual workflow itself is dependent on hi fi data to make context using hi fi asm, and we have a variety of different workflows available for if you have additional phasing data like trio parental data, or high C data which you can also use later on for scaffolding. Also, there's scaffolding pipeline for bio nano, and there's also expert workflows that help get all your reference quality genomes up and out into our genome arc where they are also freely publicly accessible. There's also an independently invoked mito some mito genome assembly pipeline that's available as a workflow to and yeah so progress updates were as I mentioned papers and submitted to nature biotech also and bio archive if you want to take a look at it. And it's 51 plus genomes assembled and available, and they're directly available from the data importer on major servers you can just click genomark and just navigate to your species you want, and there's more genomes that have been done since this was updated but I'll take it. And I give the update on the actual enhancements to galaxy that we've made for this so all of the workflows that are being used by the VGP are now available on docstore so you can pull them into a galaxy instance very easily and run them. If all of the tools are available on your instance. They're also all available from from the VGP page on docstore like I mentioned, everything is currently runnable on both org and EU and hoping to get it available on the Australian server soon. And those will have extensive training material available through the GTN, which will allow you to assemble your own genomes as well as to assemble any with that any data that is available in genomark, because again that is available from the importer now. We're hoping to obviously do some more genomes to increase pace by running it against multiple servers, as well as the VGLs compute increase automation, and just more places are running and as people become more aware of the VGP, they can start running their own and helping out the project themselves. We also want to be using some of the more some of the IWC enhancements so for example. There's an alternative workflow pass such so that a workflow depending on what data is available for any given species you can run a different version of the workflow from a single invocation. More will be discussed about that in posters that Tyler and I will be discussing later, as well as a talk on Wednesday. Furthermore, we want to start annotating the workflows that are being output so we're going to have some workflows on that as well as some availability on the Australian server. Thanks to everybody who has helped out on this project as well as some of our funders and love to have some questions. Thank you. Wait, sorry. One more thing for the update I forgot to mention very importantly related to genome sequencing hubs we've got some buy-in from local projects such as the Sidra HPC and the blue guitar which is set up a galaxy instance to sequence some species names is there and culturally important there and African bio genome project I'm also helping them set up their local instance which I think the compute is located in Johannesburg but I could be wrong. That's a fun update. So you said a lot of this was run on public infrastructure so approximately how much did you save by giving Bjorn a headache versus using AWS. You mean like money if you had to pay for that computer or if you had to pay for the compute with AWS right. How much money did I save. Yeah, I haven't run the numbers and I don't think I will. Okay, but it's a good question. It is in the metrics I could tally it up on the metrics according to you but I won't. Probably still worth Bjorn's headache. It's there. It's in the metrics. They're just not counting where I was troubleshooting some of the stuff as well. Thank you. There's there's we got enough time for one question. I will do a shout out to Anna Simon is going to wave at the back. You two should talk to Anna Simon about getting the VGP pipelines on to Galaxy AU because Anna's already started that way. All right, time for a 30 second question. What's the annotation workflow going to do and how heavy is it in compute. I don't know. I am new to genome annotations it will be deferring to like Anthony and a couple other experts for that, because we have been usually just waiting for NCBI to annotate it once we get our RNA seek and I said seek data uploaded. It's nice to have also like a quick and dirty annotation of just like maybe repeat content of the finish assemblies, but TV determine it and if you want to help make that happen. And also, what about the transcriptome like is that something that will also be done like a separate transcriptomic assembly worker. I don't know if we generate enough data for that usually as part of ours. And really quick plug before we walk away we have a post we didn't really get to get into actually the nitty gritty of the pipeline so if you want to talk to us about that we have a poster on Wednesday and you can come to the VGP training on Thursday. Let me start with. Thank you again. Thank you for organizing us to getting us there is a great opportunity to see the great country. But oh my gosh to get here. I write today 5am after 26 hours trip so if I fall asleep don't blame me please. I'll try to do it quickly so that's a short slide for motivation and traduction so basically we have this great compute resources in our lab compute supercomputer number one on the wall supercomputer number five on the wall. We have great experimental facilities great scientists but the part which is missing is the one that glues all the stuff together that basically a lot of work has to be done manually. What we thought this morning call so that the science I don't want probably maybe to focus on infrastructure on coping data on starting stuff they want to concentrate on their work. That's why we started looking into galaxy we're lucky that we found galaxy basically our job what we've been doing since a year or so it's adjusting galaxy or part of the work is adjusting galaxy to our structure. It's erratically if you read tutorials whatever galaxy can run everywhere laptop cloud HPC Kubernetes. That's true but still to make it work some some efforts are quite and we've been doing that we have multiple resources which are available for users. We have experimental analysis cluster some cloud machines HPC in cloud HDGX nodes and we have this big machine summit and frontier. So, I split it into three parts what we what has to be done basically we have to to make sure that we can use this multi cluster multiple computers also. There's HPC cluster cloud, whatever, but this all kind of multiple isolated islands of computer resources and what we want to do to make it transparent for galaxy user. Then you have this authentication authorization problem and the same you have different islands with different security requirements on HPC should be the fact authentication on cloud that should be some other authentication analysis cluster we can have external users we can have internal users and how idea our goal again to make it transparent for galaxy users so that we use galaxy and don't care about authentication. And also require that the job should run behalf of the user we can just have some service account trans galaxy jobs because of the accounting of the data access and so on. The short part may be probably the most complicated violence. Again, we have multiple islands of storage multiple islands of data, have data in HPC we have data coming from experiment data stored in the cloud. It's definitely even access more to this data is all open data data data and again we want that to be also transparent for the galaxy user. And here the condition is that we don't want to basically we cannot duplicate the experiment produce petabytes of data and we cannot just create another object storing galaxy and copy data there so galaxy ideally should stay in place. So how we implemented all these computers relatively easy. Thanks for galaxy we have pulsar galaxy rabbit in combination of this free basically did the work for us. You have these different islands and we start pulsar on the island and then galaxies and jobs to pull south for a bit and pure a bit and pure is very useful for the changing direction of the flaws to deal with firewalls. On how access summit we have this Kubernetes cluster which is basically you can start a port on this class and this class to have connection to summit and submit job to summit. So we also start pulsar and Kubernetes and then it can accept jobs from them. That's easy. With more difficult identification authorization what we did using code to see tokens that was also available in galaxy. We don't have galaxy user like and database or central identity provider and galaxy user can log in for this provider and then we receive the open ID. And we start passing this talking to all resources where we run galaxy jobs and using this token using different authorization mechanism allow or not allow to start the job allow or disallow access to the data. For this he had to do some changes to galaxy and pulsar first one was to auto refresh this token because previously when you receive this token when you look into galaxy get this token was stored on database basically never updated there. So now we do this auto refresh and we expose this token is galaxy endpoint for pulsar so that the job running and for pulsar couldn't get this token fresh token from galaxy and use it. Also implemented an option to run Docker container as a user because currently you can hard code and configuration. A user to run Docker container but we want to be dynamically so also use this token with check have this parameters for the destination and you can extract them. And then check the token and run this Docker container as a user. Also created a couple pulsar plugins to authenticate authorize job on the user base currently pulsar does not know actually which user submitted the job which I can check the tool if the tool for the destination of here not. We also implemented it can have a look into the token again extract the user name and using different plugins decide if this user allowed to run the jobs or not. This briefly about authorization data management. Just a reminder what we have what we want to do. So, again galaxy has this object store. You can use the object store and we use it and we use it to put data and get data from galaxy and we also use in from pulsar site to get data from object store before you submit the job. And put out put data set. But I'm saying here put and get instead of upload download because if you don't want to move data, or it's not necessary so in some cases we just keep data in place and just work with metadata. So, this galaxy object store should be able to work with these different islands of data and have implemented here using crucial plug in Russia is a distributed management data management solution. I'm from somewhere they use it to store data and different tears around the globe. We created this Russia plug in for galaxy object store so basically galaxy only talks to Russia plug in using a couple of functions and then Russia is configured to talk with different islands of data. There's a little bit more about implementation so basically for Russia you have to configure this Russia storage element and for different for all of this data. There's a lot of different resources for HPC for example cloud and experiment in this page in this slide. And then you can configure different protocols which this storage element can use to deliver to upload download basically date and then depending on the location where you want where you run where you run, you can use different protocols to get this data so basically if you're on the pool side that run on HPC for example you ask Russia to download file or Russia as an answer just gives you some protocol. Some some protocol, it could be politics it could be as free it could be it's also everything is configurable so ask Russia I want to download file as a use protocol and then you go to the storage and using this protocol. You get your data and one of the protocol could be the same link where you really don't copy data and just if your job is located close to this data storage then you don't have to move the data and the protocol which Russia would give you allows you know to move in the data just to get the same link. Or simple copy whatever but if you're somewhere away from this storage if you're in cloud and want to get data from HPC, then the Russia would return or some different protocol seemingly would not work if you give you as free or custom protocol to get this data. Naturalization dedication also working with these tokens. And also what implement as I said this in place ingest we don't want to download we don't want to move the data so we created a tool and this protocol and change to the Russian plug in so you can just ingest the data to the galaxy to Russia basically your galaxy says I want to. The galaxy still executes this calls this upload method but then Russia know that it should not do upload or just ingest the metadata. Yeah, and the nice feature that galaxy still sees this data set as a normal one you can click on an eye you can see this date it will be downloaded the data is not close to galaxy. So, as we said for for users that transparent and behind the scenes that's all this data movement happens or not happens. Some changes has to be done first of all this Russia plug in we created quite similar to I wrote since three plug in that I've done still has to be refactor because I learned today, you'll do refactor the other plug in. Another feature that we had to use this set meta from Pulsar not as a part of the job because normally when you submit a job to Pulsar and the job script job or us and at the end of the script. We execute basically sending metadata and uploading file somewhere to object store. We did not or we could not use it because the job can be executed on some summit note and we don't have control there we cannot install galaxy dependencies that we have to change it to introduce an option that after job has finished Pulsar calls basically the same script to upload the data. Download from object store only when needed again as has it was implemented before. As soon as you touch this get file name function the data has been downloaded from object store into the galaxy cache. You can also split this functionality so until you clicked an eye button the galaxy data would never leave its original location and in many cases you don't need it if you run workflow steps on different resources I don't. So then there was no data copy to it's not different resources then data will be copied between these resources but it will not be copied unnecessary copied to galaxy until you want to really see the download from your client. And a small one displaying binary file instead of downloading. Some PRs are accepted a couple or one is pending and we still have to do a lot of them. So that's basically the final architecture. Altogether we have galaxy clients the authorized for the density provider we send the job for a bit and cute. Pulsar Pulsar talks objects store gets the data submit the job and push the data or register the data back. Work in progress. My DS recently implemented this live job output that's what our users wanted when you run some tool you actually don't see the output and tool has been implemented that you can have this live viewing galaxy. It's pretty nice interactive tools on remote resource that I discussed with Nate it's already working, but for us did not work when we started for Pulsar it starts interactive tool somewhere but we don't get the feedback to galaxy. We have to see how that works. Generic tools for HPC jobs also we had to do quite a lot of hard coding inside the tool itself to make it run on summit. We don't like it discussing how to make it better. Another one this workflow stop restarts. I'm not really sure if we like it but our user sometimes asked for it so they start that job. We have now this live job out but then they see oh it's already finished or conversion good enough or something like this or not. They want to stop it but they want to kill and delete all data. And if it's workflow maybe then restart the next step of the workflow using this results. It's kind of break this reproducibility so that's why we don't read Michael. If considered as a kind of interactive part of the work while using still investigating that might be a nice feature as well. And we owe a lot of PRs to main galaxy repo. We should be working on it and we will do. That's basically it. Thank you for attention. I have to mention that's only the first part tomorrow. We'll do the second part basically how we use all of this. Got got time for one question up the back here. It's for the zoom folks we need. Yeah. Really. I mean I'm amazing talk. I remember you came last year and you were starting out and like you have a fantastic vision there. I think it's not a question. I mean it's just I mean really really really good job. I do want to say like all the things you've listed these are really solid changes should have done them already for other projects in the community. Please please do also open the list of things you want to see. But if you say everything you said makes a whole lot of sense the architecture is really good. Let's do it. I mean really really happy how you've done this also your contributions are amazing. Keep going. I mean really good. Thank you. We do our best. I think that that's because we try to get a feedback from our user and we're lucky that we have several users and we work with them. We ask them permanently what do you need. But I agree what I want to want to say we need to collaborate with you guys more because I learned that you did something that we were already doing for maybe there's already some solution. And then the bicycle the second time they want to change it. But thank you. Thanks again. Thanks again. Up next we've got. I think I'm going to use your your nickname is going to talk about gene polymorphism and the links to Parkinson's disease and how you've investigated that in Galaxy. Thank you very much. Thanks for inviting me and this is great opportunity so I could extend this thanks to Galaxy for extending. This support to us regular biological scientists who are sometimes stuck in the world of bioinformatics. So well done guys. I think the galaxy is improving from yeah every year. Yeah it's better and better so I will definitely recommend my students use that more. So I will probably talk a little bit completely different than what Sergei was talking so it could be closer to some hearts or further I'm not sure. So it's about superoxide dismutase and how the polymorphism in this gene could impact basically certain diseases in this case its main focus is on Parkinson's disease. But just before I start sorry, I have a tendency to talk too long so it's seven minutes I realize I will have to be. I am honestly yes. I know. So, just to mention that big thank you for a number of people that are enlisted here my student Mia she did majority of work and there are other colleagues involved in the project so I'm just thanking them for all support here. And just regarding now the impact of a certain genetic background on Parkinson's disease so I don't know if you watch back to the future maybe anyone watch back to the future so I did. Hence, maybe younger generation not yet. So majority people did actually so if you know Michael J. Fox famous actor. He got Parkinson's disease quite early so that's a very unusual and it's mostly impacting population who are above 70 but there are some people who are impacted very early like Michael J. Fox and in the case of Parkinson's disease. There are a number of interesting things that I will try to make short just overview if, if you don't know, many of people impacted by Parkinson's disease are having a bit of shaking movement. They are having that trap so called like clinical picture so rigidity stiffness. They are also having impairments in voluntary movements so there are lots of involuntary movement and a bit of posture issue so I have even family member being impacted so it's for me close to my heart, working on this. Area so this is a little bit of overview because there are some certain molecular markers that are overlapping with dementia and Parkinson's but because of time I will not go further. There are some loose bodies that are found to be present in certain people with Parkinson's and regarding the development of the disease. It's complex multiple factorial disease because there are a number of factors that do have make a like impact on this disease. Today focusing on genetics but just bear in mind that there are of course there are other factors like environmental exposure and even gut microbiome so it was good really talk because there is a very synergy about that microbiome and predisposition so into lots of fibers if I could say keep your gut healthy. So, today we are focusing on genetics and just super oxide this with days is one of these genes that are enlisted to be potentially important here. So, they are around 5 to 10% they say now even more people that with genetic predisposition which is very likely in the case of Michael J. Fox actually, as he developed that very early. So, we will focus on that aspect regarding genetic polymorphism of super oxide this with days and how this polymorphism increase actually oxidative stress and has a very good hypothetical chance to develop to lead to development of Parkinson's disease. So, that was the goal of just an overview quickly and what we did we applied galaxy tools there are multiple other tools I'm aware that we should extend our use of galaxy even further so will definitely more now be inclined to use galaxy for even other databases and to access it so the poster is tomorrow so if you have a specific questions and if I miss something to say please come tomorrow to but there was a sequences that were retrieved from databases and they were then filtered. Okay, very close. So anyway, so we use galaxy. I will give you an overview here so database were used to get sequences then we did a bit of filtering using certain tools, such as SNP AFF and we then did all this process to get towards the laterious variance so it was. Yeah, long talk for seven minutes. So, but we ended up with seven variants, which were selected through this pipeline workflow. And so we'll just go here so SNP AFF was used plus the NCBI clinical significance tool for finding out which potentially of these variants would have impact because they are over, you know, 334,000 even more. Yes, variance so you needed to filter really closely on where where is significance and which sequences could have impact so multiple tools were used multiple sequence alignment and then protein modeling and identification of domains to see and quantify what impact is on the functionality of protein. So, to make story short. So we basically further extended knowledge regarding genetic so polymorphism by exploring genetic variation and how they could have implication on functional domains. And we identify seven very likely harmful so variance. And that's basically it future studies are to come. Thank you very much and just wanted to say that I'm editor for this journal marine drugs so you are really welcome to potentially submit your paper. So one of my papers was published there recently on genome mining so I think galaxy users could look towards that in the future. Thank you very much for your time. Thanks. Thank you. We don't have time for question the time for questions but a great great example of galaxy success stories. Thank you. Last but not least we're going to have a change of a change of pace and move away from molecular biology towards ecology and hear about the galaxy for ecology and galaxy project. So I'm very juicy from the National Center of scientific research of friends. So I will speak about galaxy for our system and biodiversity and about the various project on how to how the project want to create another network using your galaxy. So first I will talk about galaxy ecology. How is it how it's an inspiration for the galaxy Earth system. Then what is the system model and finally what's a nationality club. So galaxy ecology was created in 2018 by the French biodiversity data infrastructure is a transnational initiative for the analysis of biodiversity data in research and expertise. It's a European instance. So I will talk about some of two of the workflows that are already on galaxy. And I will talk more about galaxy ecology tomorrow during an update. So one of the workflow on galaxy that was implemented yesterday is using satellite data to create biodiversity indicators so you can download data from the company or the European Spatial Agency or the platform. And from this sentinel to data you can process them and have a raster bill format that will can then that can then be used for biodiversity to create biodiversity indicators. So you have different kind of biodiversity indicators that you can compute. The first one is the identification of biodiversity hotspots with indicator just Shannon Simpson and others. Then once you have the hotspot you can do biodiversity indicators only for the canopy with alpha beta and functional analysis. So for instance here you have a map of the alpha biodiversity indicators and here a tabula of the breaker chess table. Then you can also do a an analysis on the spectral and not I spectral on spectral indices that allow you to see the well being of the vegetation so for instance you have the nominal day different vegetation index or the canopy quality content index. So everything on this workflow that goes from the sentinel to data to biodiversity indicators are explained on galaxy training networks. So this new workflow is a first step toward having an analysis on the earth critical zone so the land degradation. Another set of tools that is available on galaxy ecology is focused on the biodiversity of the ocean. So for that ocean biodiversity biographic information system which is a global open access data and information clearing house on marine biodiversity for science conservation and sustainable development. So in order to visualize the marine data obviously created the package of this indicators which I use to create a galaxy tool that allows you to to compute these five indicators and so here you have an example of the output as a map for the channel index. So this set of tools allows you to have some information about the marine omics. So I'm speaking about land degradation and marine omics because these are two topics of the ferries earth system model. So the system models describe the atmospheric and ocean circulation and thermodynamics the biological and chemical processes that pick back on the physics of climate and grid over the surface of the earth and underneath the surface of the oceans. So we have two main topics here. The earth critical zone with the land degradation using Sentinel to data that we had that I explained just before and marine omics with obvious indicators. So these two topics are among the topics of ferries that that was designed to have another system model. So we have five main topics ocean biogeochemical observations. Then we have coastal water dynamics, the earth critical zone, volcano space observatory and marine omics observations for these five topics are for the ferries project. Project a an assist are creating a system model. This project is a European open science clock project it's a new approach to observation and modeling of the earth system environment and biodiversity. It ends at getting interdisciplinary data discovery and access service and to create another little analytic lab and data lake. It's for policy makers resource providers civil society and general public for scientific users community and operational forecast services. So we will focus on the earth and I think lab as we want to try to create one with galaxy. So authentic an authentic lab is an easy way to visualize analyze and process environmental data on demand. So here one of the solution is galaxy to crew the idea is to create a galaxy instance with a set of tools for our system environmental and biodiversity data. So that way we can use multiple data set to process them and change them in one environment. So to do so we were inspired by galaxy ecology and galaxy climate. So, from the galaxy ecology instance we have tools for accessing data, for instance, the occurrence tool from the occurrence tools that can retrieve data from GBs or obese. We also have from the galaxy climate the common is the Copernicus climate and atmospheric stores tools that allow you to retrieve data on climate. So as I told you earlier you have the biodiversity analysis tools that are that we can rely on to start our work on different topics. So for instance, the Sentinel to about biodiversity. So when integrated tools for the earth system I use the pendulum ecosystem tools with Jupiter notebooks and interactive tools as an inspiration. And finally, I reuse all the galaxy 20 networks that are available from these two instances. One of the main issue here is that we have multiple topics with multiple kind of data sets so it's a real challenge. So Ferris wants to open gateways for the field of earth and environmental sciences by addressing the limitations of the current digital architecture. One of the reasons that everybody is asking nowadays is where the data how to store them how to access them and is the data like the medical answer. So for now we don't really have an answer to that, but we know what kind of data that we want. So we have for the coastal water dynamic the data on river discharge meteorological and oceanographic condition data from satellite sensors for the earth critical zone. We also have satellite data such as Sentinel one or Sentinel two, we need the data for the soil databases and national and regional earth critical zone data sets for the volcano topics also need remote sensing measurements and more, more furthermore we need access to the Copernicus Sentinel open data hub. And for the two other topics, it's quite the same we need in situ data access to them and remote sensing data for marineomics, however, we already have some of the tools on galaxy ecology that we can use. For instance, with the global biodiversity information facility so the occurrence tools that I talked about earlier, that allow us to access data from from the gym. So, once we talk about data access we need to process this data. So for the coastal water dynamics workflow, it focuses on the coastal marine environment near river estuaries. So it wants the aim is to follow the evolution of plankton blooms or the transverse and fate of neutral of nutrients, carbon and contaminants. So here to create this coastal water dynamic workflow with the aim is to change three tools using net CDF files as inputs and outputs so to do so we have, we will have three interactive tools. So we already want have one divinely that performs and in the end dimensional variation national analysis greeting of habitually located observations. So this is a Jupiter notebook tools that is already available on galaxy Europe. So this tool allow the user to browse among all the notebooks available for this for this kind of analysis and can input and output net CDF file that can be then used in for instance ocean data view, which is a desktop interactive tool for exploration analysis and visualization of oceanographic and other georeference profile time series trajectory or sequence data. So this tool is also available on galaxy Europe. And then the final aim is to change this to tools with source, which can, which will be a Jupiter notebook tool also that can calibrate and validate ocean model within a selected special domain using in situ observations. So this is the workflow that we work to do on the most on and will soon be complete, I hope. We have earth critical zone aims so the sustainable development goals created a target to combat the certification from this target indicators to monitor the poor portion of land that is degraded over total land area was implemented and from this indicator three sub indicators were chosen so the vegetation productivity the land cover changes and the salt organic carbon chances. So these three sub indicators are calculated by to the trends of software which possessive raster data set and allows a pixel based qualitative index of potential degradation. This software is a QGIS plugin. I'm trying right now to take the script out script out and create three different batch tools that can process the data and have vegetation productivity and the three steps indicators. For now I'm having Google access issues with that so if anyone has some idea about that I'm all ears. For the volcano topics they propose to join and to make a joint analysis of heterogeneous remote sensing observation for the monitoring of global volcanic activity allowing the focus on any major volcanic eruption worldwide. And for the final two topics we have biogeochemical that wants to provide a common platform to data scientists in order to qualify calibrate validate bgc data from sensors deployed on various platforms so we want to use galaxy for that. And finally we have marinomics, which wants a platform that can provide the ability to analyze spatial and time comparable marine makeable metagenomics data sets for the exploration of biodiversity and its collaboration with environmental quality. So for all these topics there is multiple data set and multiple workflow that overlaps and so we want to reuse these different workflows and Dexter in other kind of process. So to do so, we have a collaboration with the project for our science gateway. So the partners and the colleagues from our science gateway came in France to make a two days galaxy training where they were helping to teach the ferris partner how to use and why use galaxy. We had one day of hands on to integrate tools with the attendant, we were able to integrate five tools at the end. So two of these tools were LGF viewer and scoop which check the quality of oceanographic data. So the collaboration of the two years project can get efficient cross discipline workflow by creating sharing and reusing tools and workflows on galaxy. And so this collaboration is here to help us to integrate all of this system topics on galaxy and create. We hope at the end her system use galaxy. Thank you for your attention. And if you have any advice comments and other remarks, I'm all ears. Thank you, Marie. We have time for one question. Great talk, Marie. Thanks a lot. Can you tell us a little bit about the problematic or maybe it's not problematic aspect that your tools are more or less running as either Jupiter notebooks right or even desktop applications in the cloud. Is that a specific and more complicated problem than just integrating galaxy tool. So where do you see problems that we might or can help you to make that easier to run those. Yeah, VR is virtual research environments for you. Right now for the tools that are already on galaxy. I don't think there is any kind of troubles but I think that some of the asset topics that the partners of Paris would like a persistent service where we don't have a tool that stopped at one point and keeps running. So I don't know how to say that exactly but if galaxy the aim is to use galaxy also, it would be great to use galaxy also as a service and not just as tools that will one day stop. And we have to relaunch them and use them so that's one part. And then we have, I think, a lot of tools that will be coming on galaxy and some of them. They are using multiple kind of language and the huge kind of data access and that's some stuff that we will be needed help. I don't know if I'm really clear or not. Great. Thanks again, Larry.


T. F. N. N. headline news update. Good afternoon everybody I'm Tommy O'Brien coming to you live from T. F. N. headquarters in St. Petersburg Florida 12 noon Eastern time on Wednesday middle of the trading day and we got markets in positive territory somewhat off the highs though S&Ps up nine points at thirty three twenty nine get the Dow Jones up twenty five trading twenty nine thousand two twenty one NASDAQ up forty five points trading at ninety four sixteen gold contract today right now off one dollar and eighty cents at fifteen fifty six oil having some negative action below fifty seven dollars off a buck forty eight at fifty six eighty nine notes and bonds pretty muted day ten year negative two ticks one twenty nine sixteen the thirty year bond positive five ticks at one fifty eight twenty four and the dollar index up forty three ticks at ninety seven five seventy five start things off let's jump over to the charts we'll start off with the Dow so even just if we back things up from ten forty five we got a little bit of a sell-off there these are I believe fifteen minute yes fifteen minute bars we got a little bit of a sell-off in the Dow at ten forty five you trade from twenty nine thousand two seventy one down to twenty nine thousand one fifty we're just above that level at twenty nine thousand one seventy NASDAQ one hundred little bit of a different story though ninety two twenty nine just off the highs about twenty points from the high of ninety two fifty three S&P five hundred a little bit of a sell-off as well at ten forty five towards the end of the bull bear hour we were up as high as thirty three thirty seven in the S&P is for an all time high about ten points off of that level of thirty three twenty seven crude oil talk about an acceleration to lower prices Tuesday at about one o'clock we're trading at fifty eight seventy seven we're now down almost two dollars from that price trading at fifty six eighty six there's your gold contract trading at fifty and fifty six and the euro US dollar train at one ten eighty four terms of what else you have happening gotta mention Tesla quite a day as the run continues Tesla hitting a high of five hundred and ninety four dollars and fifty cents up seven point five percent right now on the day to put things in context we're just going to back this up let's put it on an hour hourly chart going back twenty days my goodness folks you back that up to December 20th and we were at four hundred dollars on the dot we're now up almost at six hundred do the quick math that's fifty percent since December you back things to January we were trading about four twenty four nonetheless Tesla above a hundred billion market cap pretty remarkable checking in on other stocks with action today Netflix with their earnings last night down about two percent and IBM big blue in the positive by three percent stay tuned folks we got Dave White Steve Rhodes Tom O'Brien all this afternoon we'll be right back