Hello everybody, welcome back to another episode of Anabaptist Perspectives. I'm here with Daniel, we're in Shippensburg, Pennsylvania, and yeah, introduce yourself and tell us a little of your background in Christianity and admissions work. I think my background is going to be a lot different than what you're used to. I grew up in a family with an alcoholic father and a mother who was always working, and she was, I mean, she was kind of a workaholic, but it was because my father was an alcoholic. Anyway, we had a very dysfunctional family and Sen really ravaged our family and Satan had his way.  We went into houses and robbed them, we went into houses being built and demolished them after staying the night there illegally. When I was 13 we started throwing rocks in the road at the Highway 85, the fastest, one of the busiest highways in Atlanta, and then it graduated the big sticks and then logs until people crashed, and it was days of doing it until we got caught, then I got a felony, and they they asked me like, like I had no concept of right and wrong. I had a girlfriend one time around the same age, and she went to a party and I didn't go to the party and she kissed the guy.  I started to see something was wrong with me, you know, it took a long time, and I couldn't read. My six-year-old daughter right now reads better than I did when I was 16. Anyway at 13 my football coach invited us to the whole football team to something called the Starlight Crusade, and it's they had like free pizza and games and big Christian artists and like speakers. I mean at the time I didn't know who they were, but they had a speaker that basically described me and then they talked about hell and how you don't have a relationship with God, and I was like, I need to change. I can't change. I don't know how to change. I'm gonna go give my life to this, to Jesus. Went down there, didn't know what I was doing, prayed a prayer, they took me to the side, they counseled me, and basically said, hey now you're saved, it doesn't, you can't lose it no matter what you do, so don't worry about that. This is when you're, how old? 13. 13, okay. But thankfully like they they then baptized me, and I didn't know much, I couldn't read, my parents didn't go to church, they told me to get a Bible, go to church, and we did go to church some, but it was very seldom. We went to a Methodist church when I was really young for a while until they brought a homosexual in and had them speak to the young children and to make them not afraid of them or something, and it made my mom you know want to leave, which I think was healthy to leave. Went to some Presbyterian churches and Baptist churches and just on and off like Christ or Christmas Easter a few times a year.  Well I didn't really get that concept either because then I became a bully of bullies, I went around like when I saw bullies bullying others I'd believe him, so it didn't really, I wasn't exactly Christlike, but there were some concepts that I really thank God for keeping me pure sexually and from drugs. So when I turned 16 I got my license, the first thing I want to do is go to church, find a church, because we didn't go to church, and I went to this church called Central Christian Church which was very different from all other churches I had experienced. I actually believed in obedience. My pastor always said so many times, if you hear me say something that doesn't line up with the Bible, don't believe me. And then like whenever I ask him questions, for example about baptism, he would say, we'll go read every verse about baptism and come back and you tell me what it means. And so like it was very different. Like I came back and I said everything that said, and then he was like yeah, well that's baptism. And where all other churches throw away all these verses that are very important about that subject and most subjects. So there was somewhat of a healthy thing, but they were still God and country. I'm not sure they completely saw the Sermon on the Mount for today. And so there's a lot of things that helped with finding into baptism and that, but then I went to public supermarkets where I worked for a while and I just told everybody about God all the time. Every customer, every person. And I was probably one of those really annoying people, but lots of people came to Christ from it and like three of the employees went to Johnson after they came to Christ. Johnson Bible College before me because they were older than me. And I went around school with my Bible. It was the first book I learned to read. They realized they then gave me CDs. I think it was Ricky Fernandez gave me all the CDs of the New and Old Testament and he said play these and read with it. And so every night I'd go home and just go through the whole Bible. And I just assumed everybody in church knew the Bible really well. So I'm like playing catch up for a whole summer. I'm reading, reading and listening, reading and listening. And then I learned to read in the summer. I went to high school. I was on the technical track and it's people who aren't going to be able to go to college. And so you just basically learned like skills like home act, welding, whatever, whatever kind of and I chose computer stuff like computer sciences.  I mean, I just had learned how to read. That's why I was held back in middle school and elementary school. They put me in honors classes. So that skipped a level. And but then I decided to go back because I didn't want the hard work. Anyway, back to that's kind of the slant of Christianity. Then we went to how we got to missions. The way we got to missions, I went to Johnson Bible College planning to be a preacher because God called me to the ministry. There's two different times in my life that was clear call when I was at Johnson and I was on the preaching program. And it was the first year and every Wednesday we had missionaries speak. And my pastor from Central Christian Church, he had a sermon on Noah about making yourself available. And after he did that sermon, I always asked, God, is this what you want me to do? Is this where you want me to go whenever a missionary preached? And so I ended up asking that a lot. And I was working at Quiznos at the time as a manager and going to school full time. And so I was doing my homework really late at night. And then I was doing it in chapel, which I wasn't supposed to be. I really wasn't listening to the guy. He was from China. And after he got done speaking, I said, is this what you want me to do? Is this where I'm going to go? And like, he made chills all through my body. And I was like, God, I'm not going to make a decision off of emotions. I want to just know. And is this what you want me to do? Is this where I'm going to go? And it kept increasing and increasing. Tears started coming on my eyes, which is where it really strained for me, especially at that time. And I was like, okay, I'll go. And the second I said I'll go, I knew I was supposed to go. I knew nothing about China. Absolutely nothing. Then I found a professor who lived in China. I had a missionary there for 10 years. And I asked him if he could teach me Chinese. And I got him to convince the school to make it the language I learned for the Bachelor of Arts. Anyway, that's how we got to the mission field. So that brings us up a little closer to today. So you've had that call. You went to China. So then where along in this process did you encounter the Anabaptists? I don't think there's an Anabaptists in China. I mean, there's not many of them. So you've lived there for a while, I'm guessing? Yeah, 10 years. So when we were there, there's a lot of story I'm going to skip. I started working with this guy as a Baptist guy. And my view of the Bible and his view were so different. And God kept telling me to keep working with him. I'm not this Pentecostal kind of guy that gets all these messages. But every time I wanted to leave, God was like, no, you're going to stay. So we started a church.  If you believe that baptism has any part of your salvation, or if you believe this and that, just so many things. And then you should be able to eat blood and not worry about it. And just some weird things. And so, but he was so confident about his position, so confident that it made me realize is my confidence and what I believe, right? I started to second guess everything that I was taught. And I was like, okay, what is right? Because he's saying all this is right. And he's so confident. And I'm so confident. I'm not arguing with him because I want to be united and start a church. And then we started a seminary school and started raising these pastors up. And when I was telling him what he was telling him was very different. A few years later, we decided to start our second church plant. But I was so afraid to teach at that point, because I didn't want to teach wrong and be judged for it. So I just, we got a group of people together, a few kind of believers and mostly non believers. And we just started reading the Bible. And they were so interested in the Bible, like I wouldn't even, I would barely say teach anything. And we would just read and read. I know it sounds crazy, but they're great though. Like their take on the Bible was, yeah, that's just wonderful though. I mean, I'm guessing that was very refreshing. Yeah. You almost like disentangling it from some of these, I don't know, squabbles, disagreements, etc. One of the nights, there's maybe eight or nine Chinese with me. And we read, we started a habit of reading a whole book through and one sitting. So it was Thursday nights and we read Luke all the way through. And when we got done, it was like close to one o'clock and we started at six. And I was, I was kind of worn out and I thought everybody else was, but they were so passionate about it. They're like, let's read Matthew now. And I'm like, I don't know about that. And then whenever we read the book of Philippians, they were pointing out stuff that like I had never, I had neglected. Like there's a phrase that's in the Chinese, it's, it's a little different than the English. It's an all, no matter what, and all things don't complain or argue. And they took it so serious at the beginning of the church was like anybody who's complaining and arguing at least at first, it changed a little later, but it was so refreshing. It was like, there's no disunity when there's no complaining and arguing. There's stuff that I've read my whole life, but I didn't take it as serious. Like they were saying, this is God's word. They haven't been raised around it. They haven't seen it and they don't want to put it down and they want to do everything it says. And so their faith really challenged my faith. And plus I was looking at the Bible in a new way, like what if I'm wrong about all this stuff? And then there was this guy, David Paulson, who just died recently, an English guy who has a book called Kingdoms in Conflict and once saved always saved question mark. And, but he has all these sermons online that are translated into Chinese and they were like, would tell the basics of a book. And so we'd started watching those before we read the book. He got fired just about from every church he ever worked at because whenever he found the truth, he would live it and he would teach it. But his story really affected me and I hated it that they didn't adopt the head covering, but then in his commentary on Corinthians, first Corinthians that came out in 2016, he had a realization because in there it says we should be, at least in prayer and when we go to church. Anyway, he was a man who sought the truth and he really influenced us. And then one day the church ladies came up, well two of them and said, should we be wearing head coverings after we read first Corinthians? And I was like, well in school I was taught it was about, you know, something about prostitution and I just went through all these theories that were in school and I just thought of them as fact. So I just kind of said no. And then I got home and like the very next day my wife comes to me and said, should I be wearing a head covering? And she wasn't even a part of the study. She was at home with the kids. And I was like, this is weird, like, let me read it. And I read it. And I read it again because I had just told the Chinese ladies, oh, it's just the hair, the hair is the covering, or it's, you know, these different things. And then I'm like, this doesn't make any sense. What I told them makes no sense when you read it all the way through. And I was like, you know what, you need to pray about it.  And I knew that it would kind of possibly make weird relationships between all the other Christians we work with. So the next day she came out and I don't remember what it was on her head, but she had something on her head. And I was like, okay, we're doing this. Wow. And then way later, I asked her like, why are you wearing a head covering? And I hope I can get this right. But she was like, I was reading it. And I realized I really want to honor my husband. And I was like, man, that's like really cool. I didn't know exactly what moved her to do that. And I was like, okay, I'm for it. And then we started to tell people about head coverings, but I was the only one that we knew that wore head coverings. And so it was like, are we some cult? We're like reading the Bible as what it means, what it says, and we're doing the things that it says to do. And then so we started researching. And I don't know if it's the first thing I saw, but it was one of them, the just war debate with Dean Taylor. And then when he said, what if the Bible actually means what it says or whatever the quote is, they did, did such a good job. Like I had, I felt like non resistance 100% was the way to go after I watched it. I rewound it and saw all the books that David had wrote. So I bought all his books, started watching followers the way and Kingdom Fellowship. And it was so refreshing. I was like, okay, these are people that have come to the same conclusion, but I didn't know it was like 500 year history. I was just like, okay, there's people that exist that believe this way, eventually get chased off from China, from the police and our pastors we trained for the second church plant and the first church plant were arrested and beat. And they just got arrested again recently, a few days ago. And they were looking for me two of the times. And then all the missionaries in the city, not all of them, many of the missionaries in the city asked us to leave because if they get us, they'll probably link us to all of them. And so we left that city not planning on going back at the time. We didn't really know. Well, so okay, so what's the timeline at this point that you got, I guess, quote, kicked out of China? When did that have? A year ago. Oh, wow. So this is a pretty recent journey for you still. Yeah. Like all these things. So like, they even finding those teachings, David Burso, Dean Taylor, all of that was. And yours. Oh, and ours. Okay. Oh, that's neat. Yeah, yours helped me realize it wasn't just this little cult somewhere. It's like, okay, this is all over the place. That's wild.  So you're basically sitting in China finding these things and you're like, I don't know, googling stuff and you find our videos, which is kind of wild because we watch the analytics and we get hits from all over the world and we have some from China. So that could have been you. Anyway, that's kind of wild. And how long ago was that process? It was a long process in China, a few years in China. There's a lot more of the story that's very interesting, but I don't know what to get into. So, but like, this is still a, I mean, this is a fairly new, I mean, kind of a new process for you in some ways. Yeah. Our faith has been, for the most part, Anabaptist faith. We understand the two kingdoms along like from David Paulson. Yeah, but probably more in depth than at the last three years and then especially the last year. So, you know, in this story, so you're up to the point where you've had to leave China. So obviously here we are in the States. You've joined an Anabaptist fellowship here in America, at least for now until maybe you go back or whatever your plans may be. Tell us about that process. Was that a hard adjustment to, I don't know, I guess a new culture, a new, yeah, with all the dynamics going on there, like, wonk us through. What was that like? Well, one of the first experiences, I went to a coffee shop and Chinese dress a lot more modest than Americans. And I kind of forgot about that. And then I got to this coffee shop and I'm reading one of David Brasov's books. I think it was the Heretics book and I was, I think it was the second time I was reading it. Like, I realized I couldn't look up. Like, I had learned to train my eyes before I went to China. But then when I went to China, I didn't really need to like bounce my eyes all the time when I was out in public and not look. And so I got home and it's like, this is weird. I can't go to Starbucks and read a book because, like, like there's so much modest dressing. Anyway, we went to churches in the area and we went to one Bible study. There's like a probably three or four Bible studies of one church. But one was about Galatians 5. And this was, I think, a Calvinist church. We didn't choose. It was just like family wanted us to go to church with them. And they were talking about Galatians 5 and about circumcision. And he's like, well, what's the circumcision of today that will cut you off from Christ? And he said, let me start baptism. If you get baptized and you think it'll make you closer to Christ, you're cut off from Christ. And then the next guy said something else. And the next guy said, it's like if I look at less pornography, to please God, I'll be cut off from Christ. And the next guy mentioned the same thing. And eventually I was like, can we read all the way through where it lists? And I said, can we stop for a minute? And we read Galatians 5.16 through 22 and it lists all these sins. And it says, if you live this sort of life, you'll not inherit the kingdom of God. And I was like, I'm so confused. And I was kind of angry. And then we had another Bible study where we were talking about the Sermon on the Mount. After they said one thing, they would make an exception. And they'd make so many exceptions that it was like, well, turn another cheek really doesn't mean anything. And then they talked about not letting your left hand know what your right hand's doing. And then right after, everybody talked about all their giving everywhere. And I was like, I'm so confused about all this. And then so we started to look for Mennonite churches where like, we have to find these churches. My wife would look them up. And she found one in Tennessee. So we went to it. And really, I'm from Tennessee. So I'm curious, which part? Somewhere near Knoxville. So it's no kidding. Okay, that's really close to where we live. So we went in, there was only one we could find online. We went in and the lady has all the ladies have jewelry. This one lady has really short hair. And we sit down in a Bible study, not very many people. And then right after, and my wife's the only one with head covering and modest dress and no jewelry, she stood up and said, I'm the elder here. I looked at her and I was like, is this a Mennonite church? And the next one we found was online, a brethren in Christ church. And their whole first sermon we listened to before we were going to go see him was all about homosexuality. And then at first I thought, well, they're just saying like, you know, don't be afraid to witness and to help people from that kingdom and to hear just like any other sin that we need to Jesus will give us the power to crush Satan and sin. But then by the end of it, I realized they were condoning it and welcoming it like to stay in that sin. And so so we started getting really depressed. It was like, is there anything really out here? Where is this? And then we called called around and Matthew and the followers away, they kind of didn't want to talk on the phone, but I didn't feel like typing out our whole story. And then finally we call he called and we started talking and he's like, and we had already planned on coming to Kingdom Fellowship. We came up Kingdom Fellowship and we were very nervous. And my wife had nothing that looked like anybody's dress that we saw from the films on Kingdom Fellowship weekend.  So we were like, how do we do this? Do we try to sew these clothes? And we're willing to submit. We were reading scripture and polycarp and saying like, submit to your elders like you submit to Christ. And I'm thinking like, we can't submit to any of the elders of any of the churches we've been to, like it just won't work. We won't be able to do that. We want to live for Christ. So we have to find somewhere. So we're willing to submit in every way. Marvin Dolly, he, I guess y'all might know him. Well, people around here know him, but I called Kingdom Fellowship and he was the one that answered. And I was like, what do we do? Like, I don't even own a pair of khakis and my wife doesn't look like the normal dress up there in a Baptist dress.  And he's like, just comments actually all kinds of people up here. And we got there. And the first thing he said was, you need to meet Patrick. Because I was nervous. He saw I was like, so nervous. Oh, that's wonderful. Yeah, we've interviewed Patrick. But no, we should link that because Patrick's story is just phenomenal. But anyway, yeah, and I saw this tattooed guy and jeans and untucked shirt. And I was like, okay, if they're handling Patrick up here, they can not the Patrick's bad. He's a great, great guy. Absolutely. But it was just like, okay, someone that looks like that, they're okay with that, they'll be okay with us. So it calmed our nerves. And then Patrick was really awesome with us. And then the next day, he was sending us around to everybody wanting us to tell our story. And he was very nervous. But then I met some people from our church, which is close by, we were planning and going the followers away to try to maybe join over there because we didn't know that there are so many other things. And the price out in Boston, like we don't have a we were living in a camper, you know, and traveling around in a camper. And we're like, how can we make it work up there? So we met some people from a church nearby, and they let me speak one Sunday. And then I don't know if they thought we were serious, like we're coming back. But we went home, basically told everybody we're moving, and then we moved up this way. And for us, it wasn't hard at all to accept the Brotherhood Agreement and stuff like that, because we know what we're submitting to, you know, it's like, okay, I had read the King Jesus Claims as church and like all through that. It was a really hard read, but I read it really slow and meticulously. And I realized like the individual, me being so individualistic, I don't know the word, and not of a holistic thought, like I saw myself as an individual kind of embassy, not like a loner. I didn't want to be that, and I wanted to be a part of something. Our old thought processes were all broke down. I was like, let's find somewhere and just do whatever they say. We met one brother. He was a great guy. But my wife said, hey, we're going to Hagerstown to see Kent Hallbaker. Is there anything fun to do down there while we're down there? And this guy, our brother of ours, I guess, doesn't believe in fun. And he was like, fun.  But then later people had turned to church that it's okay to have fun. But it was like some of that process of, you know, kind of learning to navigate all of these new things, I guess. I mean, I see potential faults and all of it in the fundamental, but I also see that there's a history here of people following Christ and his kingdom. There's people that are born anabaptist, but until they adopt the hermeneutic, until they actually believe it for themselves and obey it, and really follow Christ and not just culture. And I think a lot, most of the churches nowadays hopefully are finding that, like they're not just driving certain color cars or whatever for just because their church says to, but because they see the reason for it. They actually see the principles of Christ in it, and they do it for that reason. I'm kind of a grafted in anabaptist by the way we take scripture very literal. And we do bless those who persecute us. When someone hits us on the right cheek, we turn, give them the other cheek to hit. Any kind of persecution we show love. Anyway, it's just, it's a blessing to be an anabaptist, and I'm not ashamed of it. This next Christian transitions, like, right into that, then, you know, these changes, the new process, some of the different challenges and things coming to the anabaptist. How do you approach it when you're discussing now what you believe anabaptism with your friends, family, etc. that maybe don't believe that way? You know, how do you bridge that gap? In 2 John 1st 9, it says, whoever transgresses and does not abide in the doctrine of Christ does not have God. So doctrine's teaching, who doesn't abide in the teaching of Christ does not have God. He who abides in the teaching of Christ has both the Father and the Son. If anyone comes to you and does not bring this doctrine, these teachings, do not receive him into your house nor greet him.  So there's lots of verses like this one where it emphasizes the teachings of Christ, and there's lots of churches that I've come from, and lots of them that do emphasize Christ's teachings all through the Gospels, but lots of them throw all of his teachings until after his death and resurrection out. So all the parables, all the all the Sermon on the Mount, Sermon on the Plains. And so I just go back and say, as Kingdom Christians, we actually believe all the teachings of Jesus, and it wasn't some law that was made raised higher to show us that we can't do it, but if we die with Christ and have the Holy, raise with him and have the Holy Spirit, we can do it. And the yoke is actually light. And the Christ yoke is light because we're yoked with other brothers. It's not this individual thing. And I don't want to leave out Finney and the followers the way. I know I mentioned them earlier, but one of the biggest things for us moving up here was when he talked about, he found the people group. In a lot of these churches, they have like almost zero percent of people looking at pornography and like in the high 90 percent of people retaining the faith, not all the Anabaptist churches, but a lot of them. And when I heard that and compared to the statistics of a lot of evangelical and Protestant churches and most every other church, I was like, I want all my kids to be in the faith and there's no way we can't, we shouldn't move up somewhere and find one of these churches. We wanted a brother like a brother who actually would believe the same thing. Not like people who said, well, you shouldn't do this, but if you do, it's okay all the time. Like it doesn't really matter. You're saved anyway. But salvation is a process that says we're saved. We're being saved and we will be saved throughout the whole Bible. And we're being salvaged and saved and being made as image bearers for Christ and for the Kingdom so that we can be good representation, good ambassadors and brides and children of Christ for the King. When I talk to them, I basically mention those things is that we are trying to follow all of Christ's teachings and not minimizing any of them. It's actually not as hard as I thought it was going to be relating to people. My parents, I said my dad was an alcoholic and my mom was a workaholic. They have grown so much. My dad has been sober for 20 plus years. And he's in the ministry to help recover alcoholics. Although my mom was for a long time of her life working a lot, she was a big reason I came to Christ in the first place. And I held on to that purity value that she gave me. And both of them right now are amazing parents. And I pray that both of them come up here and adopt the Kingdom Christianity. And we're talking about it all the time with them, but they have come a long way. My brother as well, he is no longer on drugs, one of them. And he's reading his Bible and he's talking about moving up here for sure. I mean, he's pretty sure he's going to move up here because he sees how people are at. It's not just by word. Christianity is not just by thought or by word. It's by thought, word and action. And this is one place where our faith actually gets put into practice and not just by thought and word. I did mention them as in the past. I didn't clarify that this was not how it is now. So I just want to make that clear. Well, thanks so much for taking the time to share your story. That's, wow. Yeah, that's a powerful step.


Drones destroy 12% of Russia's oil refining capacity in two days. During the last two days, 12% of Russian oil refining facilities were damaged by Ukrainian UAVs. This was reported by Bloomberg. According to the publication, the three facilities attacked by Ukrainian drones in two days account for about 12% of Russia's oil refining facilities. Air strike on March the 13th caused a fire at one of the country's largest oil refineries, the Ryazan Refinery of Rosneft. The refinery had to shut down two primary oil refining units. The Ryazan Refinery, about 200 kilometers southeast of Moscow, has a capacity of 17.1 million tons a year or about 340,000 barrels a day. It is a major supplier of motor fuels to the Russian regions around the capital. The small Novoshak-Tinsk Refinery in the southern Rostov region was also shut down due to a drone attack. The latest wave of attacks, which began on March the 12th, damaged a unit of L.U.K. oil's Norsi Refinery in Nizhny Novgorod and an oil depot in Orel region. Ukraine has repeatedly struck Russian oil infrastructure since January in a campaign to hurt the country's economy. The latest attacks come ahead of Russia's presidential election this weekend. The targets this week are major refineries, particularly the Rosneft Facility in Ryazan, which has a refining capacity of 340 barrels per day, according to Andi Lipov, president of Lipov Oil Associates. The campaign of Ukrainian attacks this year has hit refineries, representing 25% of Russia's total refining capacity of 6.8 million barrels per day, according to Lipov. About 50% of Russia's refining capacity is within range of a Ukrainian drone attack, he said. The attacks will curtail Russian diesel exports and turn the country into a gasoline importer, he said. We're seeing oil prices rise, really being led by products on the back of these attacks, which have been going on with some regularity since January, Lipov said. The market is pricing in higher and higher probabilities of supply disruptions, especially when you damage refineries. The factory is about to explode! It's a bit smelly, and I don't understand what's going on there. Man, he's not going to fly away from Ukraine, he's going to leave us alone. Oh, another one! We've reached the Ryazan factory, it's about to explode, and the right side is on fire in front of the cars. Here we are standing on the f**king bridge, and the Ryazan factory is about to explode. Here it is. Look! It's going to explode! It's probably going to explode somewhere around here, right? Yes, yes, yes, yes. Look!


Roeddwn i'r ysglaenio vaen nhoc o'r ysglaenio gyda'r Llyfrgell Llyfrgell Rydynnef ac E'r Llyfrgell Llyfrgell Rydynnef a'r Eidl Llyfrgell Ryfyn i gyfle i ysglaenio'r Ysglaenio Plyfrgell Ryfyn, o ddim yn rhan yn y sglaenio gyflym yn y llyfrgell. Felly, rwy'n gyd yn gweithio i ni'n meddwl o'r ystyried o Manchester. Felly, rwy'n gweithio i gyd yn gweithio'r problemau ar yn ymwneud, ac yn ymhyggurau'r ddatatau yma, sy'n gweithio o Manchester. Rwy'n gweithio i ni'n meddwl o'r ysgolodau sy'n gweithio am yr oedd yn gyffredinol yng Nghymru 16. May. Felly, mae'n rhoi'n gweithio i ni i'r prys. Felly, dwi'n gweithio i'r ffactorion o'r 2010 o Manchester. We've got four faculties, engineering physical sciences, medical and human sciences, as well as humanities and life sciences, of which there are 20 schools and hundreds of specialist research groups. We've got 5,000 plus research staff and 3,500 plus postgraduate students, all of which are doing research, working with data and it's the wider problem of what we've got to handle. In total, £279.4 million of external research funding was brought in in 2010, which means we have a big responsibility to these guys that are funding us to manage the data. Research data management in Manchester. Prior to any of our projects, we have had an institutional scholarly repository called e-scholar for journals and publishing papers, et cetera, and thesis. In 2009, we were funded by JISC for a project called Madden, which is Manchester Data Management. The reason why we went forward with this was basically, as Mark referred to, issues in the UK where things like Climate Gate, Freedom of Information Act, and it raised the awareness of institutions of, you know, the problems in managing research data. Also, funders change it, well, the policy updates that Mark referred to as well. EPSRC in particular that Mark referred to have issued that universities should have a path for developing a framework for research data management later next year. And then something in place by 2015. So they're actually saying you as an institution should have some sort of framework for research data management. So that's another reason. OK, wasted resources. You've got scientists that are actually creating data at instruments, doing their research, keeping it to themselves. Well, really, these instruments that they're using are very expensive, yeah? So we want to save on money that way. But also it's public money, yeah? And that's wasting public money, yeah? And also, you know, as Mark pointed out as well, I've got to mention Mark a lot in this as one of our funders. We've got responsibility to the public, OK? And also there's the risk of data loss. So Madden, our initial project, which was actually working on creating a data management system for just a few users. We didn't try to tackle the whole university at this stage. We worked with the life sciences and medical and human sciences, a couple of groups at each. And we did a user requirements analysis only to find out what we already can and you to a point. And that was our data management throughout these groups was ad hoc, inconsistent, you know. It was dependent on the user group how they actually handled their data. Multiple copies of data all around the place on laptops and USB sticks on external hard drives at home. Wherever you think about it, you know, it was difficult to track down which was the right version. You know, after a certain period of time, it goes very cloudy. You've got, you know, if it's not managed properly. And that's mentioned USB discs, external hard drives laptops, even large service somewhere. You know, it was a problem of where the actual data was actually being stored and transferred. So fragmented and decentralized storage, which was a nightmare.  You know, it's not something that you can rely on. You know, as it was referred to, my background is scientific visualisation.  You know, you just, you need something that has proper service background with regards to backup, etc. And also, because of all this kind of approach by the actual groups to keep things to themselves, it was a limited means of disseminating. Not everybody, and if people were trying to, when I started my PhD, a little story, I went looking for a really large data set to visualise. Something that would be free on the open market that I'd be able to take and work with. And it was so difficult. I mean, this is ten years ago, but it was so difficult to actually get somebody to share data with you, yeah? Why should I have to go out and recreate data if I'm just trying to do an experiment such as, you know, how do I parallelise big data? Anyway, so that's a bit of a sidetrack there. So, limited means of disseminating. And, of course, there was no archiving policies to support long-term curation, or the retention needs of our funders. Normally, one of the approaches is just to store the data under a desk on the PC or on hard drives. So, that is not complying with the funders. So, Madden brought about a simple software solution that allowed the researchers to handle their projects, their research data. It linked up with our research office systems, so that in the data management planning exercise, we cut down the duplication of input of data, such as, you know, who my collaborators are, where my data is going to be stored. You know, who can I share this data with? Ethics issues, you know, has it been signed off, et cetera. So, anything that you could think of data management planning was involved. And it also gave us a platform for compliance. But this, as I said, this was only for life sciences and the medical and human sciences. And this project was funded from 2009 to 2011, at which point, at the end of 2011, we were lucky to be funded again by JISC on a project called MISC, which is Madden Inter-Sustainable Service, and is looking at creating a research data management infrastructure service for the University of Manchester. In setting up this project, we got 250K from JISC to support the project team. You will notice that the 750K from the main university, most of that, apart from 245,000, which was for storage, was, and remember, this is a transition project. It's not the service. The service will require a hell of a lot more money for storage and, you know, staff input, et cetera. But the rest of the money that was put towards this project was for staff time. In building up what, working towards a service and research data management infrastructure, we had to involve a lot of people from across the university. IT services people, in particular storage and infrastructure services, the library, the research librarians, are going to be helping teaching about research data management. The research support services are the research offices. We've got a percentage of time, about 27 research business managers, to work with the researchers to do their data management planning, et cetera. So that's just a small example. And of course, there's a steering group and, as well, a technical architecture group which are all about delivering the service. OK, so one of the main outputs of MIS will be, is the policy. And as I said, it was ratified on the 16th of May. And when we started looking at doing this policy, which was really a bit before the project took off, we started looking around and thinking, where do we start on writing a policy? We've got the RCUK common principles which Mark put up. And that is something that, you know, we thought was really important and would be a starting point. But as well as that, we've got all the other individual funders policies external to the RCUK councils. We've got European councils. We've got charities, et cetera. We've also got our own University of Manchester policies. And one thing that you don't want to do in writing the policies to have your policies contradicting each other. So an awareness of what is actually happening in your institution is very important on what policies. And we've got thousands at Manchester. That got part of the money that we did buy in time of a person or somebody that was a policy maker. The Digital Creation Centre again in the UK is a fantastic point of contact. It has a list of policies that have already been ratified. In particular, Edinburgh's policy was very useful and a point for us to start from. They were, I think, the first in the UK. Yeah. Well, Kevin, that was the first in the UK, weren't they, too? Oh, OK. That's why I was very wary of saying that to actually publish a policy. It was a good example for a lot of us universities who are actually involved in the GISC Research Data Management. One thing I should advise is that if you are going to have a policy, have an academic champion that's really good at going out and buying in support for your policy. We started very early on before the project about, say, about September in moving towards a policy last year. The policy has been ratified in May. We didn't expect it to go through that fast. So now we've got another issue on our project in that we've got to have an interim service that we are going ahead with. And when you are writing the policy as well, you want something that's simple and clear for the people to read. You don't want something that's like a political agenda. You want to make it easy to understand because it's so easy to misinterpret things that are legally written in legal terms. OK, so sneak preview. So in writing the policy, what was necessary was clear ownership and responsibilities. Now, Mark, as I mentioned before, talked about the NERC policy and the UPSRC policy and who the owner should fall upon for being responsible. What Manchester has taken is a shared approach. So the university will support its researchers. By the way, the policy is 12 points behind it. It's a lot of procedures and guidance that has to be written and is currently being written before we actually make people do things from September. So we want to make it sound as if it's not a stick. It's a nice, easy place to work in. Easy to put it out for the researchers. OK, so the first point is we adopted the RCUK common principles. We've also said that we will take into account any other research data management requirements. So we're thinking about policies from funding bodies as they come about. This policy is not a fixed thing, by the way. It is something that will be reviewed continuously in the movement and the growth of the funding, the funders policies as well. OK, what we do also say, talk about, is intellectual property rights. So there was a question in the previous talk about who owns the intellectual property rights. At Manchester, our IPR policy says for staff the university owns the IPR. PhD students who are paying are a different kettle of fish. This is where we actually had our first stumbling point and where you have to involve your university lawyers and make sure what you're actually going to put in is the correct wording. This is where I talk about legal wording being not the way to go, but we need to simply put out that, again, if you're a PhD student, less agreed otherwise, you work with the Research Data Management Service at the University. As well as that, PhD students are funded by Research Councils. As been said before in the talks, it's public money. So they haven't owned this anyway to share their data and to manage their data accordingly. Also one thing to be very aware of is multi-partner collaboration. We talked before about data being stored in many different places and ownership of data being a bit muddy. For us, we said that it was the responsibility of the PI in using the data management plan to actually state any of these details about the research data, who owns it or if they don't own it, what you allow to do with it, licensing, sharing, etc. So going on to data management planning, we've said that every research project should have a data management plan, which must be maintained throughout the project lifecycle. We see it as a live document. Now the thing is with data management planning can be hundreds of questions for a researcher to fill in. So what we're doing as part of the research data management service is integrating the data management planning with working practices. By working with the research office and the research office systems, we're taking data that's filled in when a researcher fills in a research application and filling out the data management plan. Again, when they fill in an ethics form, ethics comes with the ethics system into the data management plan. It's the building up of work processes to make the research's life easier, because what you don't want, and one of the feedback messages from our consultation of the policy was, oh gosh, this sounds very bureaucratic. Do we have to do this? Yes, we have to make it easier for the PI. Again, we've put the responsibility of the PI, of doing the data management plan and the PI. Where can data be stored? OK, so we're going to create this service at Manchester, which has some central storage. However, we are very aware that research funded by councils such as NERC have their own repositories. So what we actually say, well, OK, if you've got access to another repository that you have to use because your funder says so or you're using because of your community, as long as, in our procedures and guidelines, it's a recommended and approved repository, that's fine, just as long as you state where the actual data is in the data management plan. And, as Mark said, it would be very expensive to hold everything. It's very expensive for universities, especially when funding charities like the Wellcome Trusted, you have to keep data for 20 years, from the last time it was actually touched. How can we afford that? I mean, one of the concerns of the university is overheads. So if we are thinking of costing in the retention of data for a 20-year period, our competitiveness goes out the window. Right, so going back onto the policy, the next point seven is about metadata. All relevant data, by the way, notice we've got specific terms because, again, what would be good would be a checklist which we could give to our scientists, which Mark's NERC is looking at. That tells them what they have to store because another question that came out of our consultation was what data do I have to store, everything? Or, you know, can you give us some guidelines? That's going to be in our procedures and guidelines anyway. So it's going to be very interesting to hear more about the actual checklist that Mark was referring to. So, yes, we require the researchers to create metadata that describes the data so that, you know, in reuse, people can understand, you know, what this data is, how it could be reused, you know, what variables were applied to the data and producing it, et cetera. And also, we see several levels of metadata. It's not just about how the data is created or acquired, but how can it be discovered easier and to make reuse relevant. Okay, so retention periods, that doesn't need much saying. We've stipulated that, you know, the data has to be kept according to the funder's guide and the University of Manchester guidelines. We have our own guidelines as well, which is amazing how many people don't actually know that researchers don't actually know what their university requires or them to do, but they know what the funder requires them to do. Openness and Publishing, again, you'll notice that a lot of the keywords we're using are the RCUK given keywords. So, to make data openly available to other researchers, but also by protecting our own research is by saying, of course, you're going to want to have the impact on your research, so there'll be a limited period of privileged access to ensure that we get the research done that we want to. But also, if data is made openly available to ensure that compliance with ethical approvals, rights of the data subjects, anonymisation of data, the Data Protection Act in the UK, and also all the IPR issues, et cetera, are maintained. And also, we protect our researchers in the medical human sciences, those that cannot make their research data available. But we also protect ourselves as well as an institution saying, well, maybe you might want to share with some specified users who, you know, may be needed to verify the integrity of the research, and in doing so, you must think of the confidentiality. And also that we realise that published research may only require some of this information. So we're kind of like trying to say, tread carefully. And of course, we haven't got a stick anymore. We did have a stick at point 12, but that was complained about, which said, you know, this could be a case of research misconduct if you don't follow this policy. But we've got this softly, softly gentle reminder and saying that, remember we've got a university code of good research practice here. And, you know, it's an overarching framework for this policy. And hint, hint, that means if you don't really abide by this policy, it is research misconduct. If they read that into it, I suppose. So, as I said, it was ratified on the 16th of May. The ratification path was, it was quiet, quieter than I thought it would be. It went out to several university groups, first of all, the university research group and research support group who were the main guys who kind of like decide upon whether it's a good thing to do and made most of the comments. Then it went out to a consultation consultation in March of this year. One thing in that that I should point out to people in actually setting it out to consultation at such a wide university, there's going to be communication path breakdown and you must have some sort of backup plan on how, if it does break down, you know, you've still got to keep your path going, your policy going through the system because otherwise, if we hadn't got to the planning resource committee on the Senate Board of Governors, it would be next year because over the summer it goes really quiet at UK universities and we wouldn't be able to get all these guys together to improve our policy. So, you have to have backup plan for the communication. Consultation period, as I mentioned, brought up the bureaucracy of it all. So, making us aware of, you know, what other, what researchers were actually doing and how difficult this could make it for them and it's all good, good advice that came through and we're working with specific users now to ensure that fed back into the consultation period. And that was the main gist of the policy. Yeah, it's still a work, it's still a work in practice because we've got to write the procedures and guidance so it's not public yet but it should be by September. Yeah. Okay, thank you. Thank you.


And my family is going to have that better life. Cation, that's what they're gonna do. Mark my words. Peace for the past year. I want you to step over here for a second. Let me talk to you. All right. Not yet. Really need to start looking, though. Got a wife and boy back home to support. Why don't you come by here on Monday? I'm looking to hire a few men, as per me, got a partial advance. Well, be true with you. My dad didn't really want me going underground. But I figured when I've been through, I can pretty much handle anything. I'll see you Monday. All right. Today, dear. Oh, it was good. Went fishing. Went fishing. Catching a thing. Where are you going, boy? How are you, dad? Good, good. Listen, have you thought about it? Stevie, I promised your grandfather you'd finish school. You'd be the first bargo to wear a suit and tie to work. Look, dad, it's just for the summer, okay? Just talk to the super corpsman. But I promise I'll finish school. You know I'm getting married this fall. I just need your help. That's all. Boy, I'm going to get you hired. It's only for the summer. And you will finish school. All right. Thanks a lot, dad. Becky, you know mine safety has improved since my daddy worked in the mines. I know that, but I worry none the less. They make all the miners take training before they go underground. There's still danger in the mines. And I just hope no one gets careless. That's what I'm going to say, bud. It's all right. How about you? All right. All right. And they ain't a sore hole. Yeah. We ain't nervous or anything. Just a little bit. That ain't nothing to worry about. We'll be all right underground. I hope so.


So if you're not here for the cancer data and it's analysis practical workshop, you're in the wrong room So now it's time to leave Otherwise, I will get started So as Michelle indicated all our material is going to be or is currently or will be on the biofrancs dot ca website and What we do for all the material there and we have this in front of all our presentation is a creative commons license which basically provides Says that you can take this material you can share with your colleagues You can use it and your own teaching material if you need to you can It's a it's got a share like and which means that if you share it then you have to say where you got it from who which which lecture and so forth and There's sort of a viral component into it as well and that if you use our slides in a talk for for yourselves That means you have to share your slides too. So that's that's a little catch But it sort of encourages people to share their slides in addition to that. I'm overly I'm overzealous. I think sometimes but I like to share and I like to encourage sharing and I like people to Tweet blog whatever they like to do there. They're also all available to do it So we had to slide on I I mentioned on biofrancs dot ca. I also put them on slide share as as From there as well so more than a year So today, I'm going to talk to you about databases and so the databases in which we find Cancer genomic information There are many of these out there and so we're not going to cover all of them We're going to actually only cover a very small fraction of them and as Jun Jun mentioned we're also part of the international cancer genome consortium ICGC Which is one of the many acronyms you'll hear about today and so So we're gonna have heavy focus on ICGC resources ICGC Includes the TCGA and other acronym the cancer genome Atlas as an NIH funded project and so we sometimes talk about ICGC and TCGA and And it's sometimes unclear which is what and what it means and so forth and I'm gonna hope to clarify that with you today So you have my contact information here and the schedule is that we'll talk I'm gonna give you a bit introduction about I'm gonna do a little plug and advertisement for the biofrax dots Canadian biofrax workshop series a few databases about how to get permission to access some of this data and the issues relating to accessing human data and the privacy and ethics issues related to that and Shortly a quarter for a small for a few slides only I'll talk also about cosmic which is a very important database used in cancer research. It's actually Comes out of the Sanger Institute here and is a also integrated with the ICGC data portal so biofrax.ca is a Website hosted at the OSCR which is the home page for the canine biofrax workshop series It's also the hope we also post biofrax jobs. We also post profiles of Canadian bioinformaticians and Links directory and so forth. There's quite a few resources But the bulk of the most important thing about this website is the fact that it hosts The workshops and you can apply to the workshops and so forth one of the flagship workshops that we have Is the biofrax of cancer genomics and And it's these are this is a five-day workshop. We we provide we have once a year and it's The details of this workshop are here next year. We're planning to host this workshop to end a few other ones it's a bit cut off but is we've got We will probably have up to 12 workshops next year, so we have a cast of genomics I just mentioned we have a high throughput biology on which is basically Next-gen sequencing workshop. We have introduction to our And exploratory analysis of data with our we have RNA seek workshop. We have Pathways we have statistics Analysis of metagenomics and the three bottom ones are new workshops We're going to introduce next year, which is biofrax of big data. So learning how to use cloud computing to Work with the various with the various data types, but mostly next-gen sequencing data Epigenomic data analysis and quantitative genomics. So these are all like two three-day workshops except for the cancer one Which I told you was five days and they're offered mostly in The summer but we probably expand a bit outside of that time period and all workshops have to have not only this workshop We'll have this material online, but all workshops have their material online So for each of these workshops that took place last year You can go online and get the PowerPoint or the PDF files or there's a movie file So like Michelle mentioned we record the voice over the PowerPoint. And so you have the lecturers Voices in a movie format that you can download to your iPod and listen to or watch while you're getting home on the train So the course if you have any questions you want to email us about this course the course underscore info at biofrax.ca the website is there and There's a mailing list that you'll get announcements about new workshops It's very low volume mailing list Where you get a few announcements about the new workshops scheduled and the material being online and so forth So this is sort of my opportunity to sort of share with you that Part of the reason why we make the material online available is that open access open data open source are really essential for science and so this is our our sort of showing you and demonstrating and applying this to our what we do and it Being open about what we do about the science we do is that it's not only a Think we should do it's a responsibility and obligation and something that comes with the privilege of getting publicly funded To do this work and so obviously the workshop series are Are subsidized by our institution and so it's a we we get sponsors We get we collect fees for the workshops and so forth But we it's not for it's not for it's not run as a for-profit organization It's really run to break even so that we can pay for all the expenses of the things that we have to pay for So I'm gonna start off This database of cancer data lecture and with Showing you a few slides from this book the emperor of all maladies and how many people have read this book We'll have the class great. I think it's a great book. I really enjoyed reading it some great quotes in it Cancer therapy is like beating a dog with a stick with to get rid of its fleas. So that's not very good and obviously to Understand cancer and to understand what is not functioning properly is is key to the work we do and so we think that understanding that the Cancer at the genomic level understanding the mutations and the pathways that are involved in cancer We'll be able to have better understanding of what best therapies we can apply and obviously there's a whole Series of pathways and Biological functions that need to be understood to be able to intervene in ways that can make Make us and do advances and can't cancer therapeutics the Another quote from bird roguestine from the book is that the revolution cancer researchers Can be summed up in a single sentence cancer is in essence a genetic disease we sort of Tweaked it a little bit at OICR and we sort of cancer is a disease of the genome and I think Everybody here probably agrees and understands and understands this but of course it The Challenge a big challenge in treating cancer becomes that every tumor is different and every cancer patient is different even with the so-called same Same pathology and so even if you see two patients with whoops That wasn't supposed to happen Even if you see two patients with pancreatic cancer for example, you will see very you'll see different mutation profile you'll see different Phenotypes and so forth so trying to understand what's common between these patients what's common between patients of tumor of cancer of the same type and And what's unique about them is is also Critical and so one of the things that is important to be able to do at the beginning is to Know what already known about Various tumor types that you're interested in and so this is why we have databases is to actually store and Have information retrievable so that we can understand what's already known and First thing you do when you want to look up for a database of interest and so you go to Wikipedia and you look up Cancer databases or cancer genome databases and this is one of the second or third page that comes up and if you look at that page you will see a number of Databases that are available and we're only going to talk about three of them here today The ones that have the red circle next to them, which you don't see on there, but it's on the hand up is so the TCTA ICTC and Cosmic as I mentioned before and I Have here some some publications that you can look up So if you just replace the the integer there the number the PubMed ID On the URL at the bottom with that ID then you'll get these papers From TCGA the cancer genome atlas ICTC, which is the International Cancer Genome Consortium or Cosmic the database of somatic mutation and There's also a paper about data access, which I'll spend some time talking about as well so the other thing I should mention and Is that everything I'm presenting to you today will probably be changed next year or six months from now Or what have you for example TCGA? We know we're actually working with the Colleagues in in the in the US to actually change the whole TCGA data portal and how TCGA data is going to be Available so what I'm presenting to you if you came and took our cancer genomics course next year You'll get the new version and that's probably true of every year and all of these for many of these resources That said today the TCGA Will always exist in one form or another with a different user interface to understand it and view it the data Will remain the same because the TCGA? Project itself is basically almost finished and that they've generated the data now They have to their the data will be available in a number of different portals and different views But the data there's not going to be much more new data It's funded by the NIH in the National Cancer Institute within the NIH and It's also Initially was funded also by the NHGRI the National Human Genome Research Institute And so those are two different institutes within the NIH and national Institute of Health And so NIH is built of about 13 or 15 different institutes and the NCI is is the is is the largest one of all this is the best-funded one So there was a pilot project for the TCGA and and then a full project which is just finishing now and I mentioned the ICGC so when the ICGC in the International Cancer Genome Consortium started TCGA joined force and was part of the ICGC so ICGC and TCGA or TCGA is part of the ICGC That said the TCGA data is available. There's information on on there. They have a wiki to maintain and the way the TCGA project was developed over time is to Divide the various tasks not so that each center would have to do Qc or quality control on their samples or or sequencing and so forth so they they've just They've identified several centers that would do these specialized tasks and and therefore would have Centralized concentrated efforts for different tasks across the country across the US So the TCGA data includes Sequence reads so the raw data that's present at the cancer genome hub There's sort of analyzed data variation calls and so forth available on the cancer genome portal and Integrated also as I mentioned with the ICGC and later today you'll you'll be looking at some of this data in our labs so the the flow of information Goes from these various Qc places collecting of of tumors and so the the big challenge with the TCGA and the ICGC is always to get high quality samples and to get Patients that have this this specific tumor type you're interested in and to have them early enough in their diagnosis so that they have not been treated yet and early enough Or or high quality enough also of samples And so one of the first things that the TCGA pilot discovered is that there are many tumors that were Biopsied I were actually of quite low quality and that meant that any downstream analysis extraction of DNA RNA and Proteins and so forth was sort of moot if the if the tumor itself that you started with was of low quality and so they They caught themselves doing these these Sort of not the best quality of sample but because it's centralized they were able to change your SOP their standard operating protocols and Update and improve the workflows to to to make things better the other thing that we learned that the TCGA did and then we are doing also at the ICGC is To have a data coordinating center and this is actually NIH has learned that from its many years of funding many initiatives of many genome projects from from the last 20 years basically and And to have a centralized place that hosts the data Standardizes the way the data is presented and so forth and so that's been key For TCGA and it's been key for ICGC as well So the The data portal itself provides a platform to search download and analyze TCG data sets and They have two data access tiers and we you'll find that this comes around in other data portals as well So you have what we refer to the Open data and the control data so open data is things that can be freely shared without you Don't even have to identify yourself you can just download it Manipulate it and do whatever you want with it and the controlled access data is for all the data that is deemed Where you could re-identify should you have the right? Expertise The patient and so if you have a few snips for example a blood sample from a patient You could re-identify them within this database because you're looking at raw data from their genome And so any data where any data type that's considered re-identifiable So here we know we do not have access to names and addresses and home addresses Things like that, but we do have access to their genomic information and the genomic information itself is Good enough to identify Re-identify the person should you have some other DNA to match it with and so this is where So if we have access to genomic information to raw genomic information not mutation data, but Genome variants so inherited variants then that is deemed Identifiable and that is being controlled access And that's an important thing to keep in mind as we work with this data So the data browser which actually Is not a data browser I use very much because I use the ICGC one mostly and And you'll see that the ICGC has some of the TCGA information and then we'll sort of Explain that as as we go along that said if you have access to controlled access and from TCGA Sorry Michelle Oops, I have 15 minutes left 10 minutes left 1145 okay, I'm gonna speed up Okay, the ICGC so ICGC.org that's our home page It's an international project. So the idea of the ICGC is to collect 25,000 tumors from 50 different tumor types So it's 500 tumor per tumor types as 25,000 tumors, which is 50,000 genomes And it's a 10-year project and right now we're in year seven of this project So you think we're about three quarters of the way done, but we've accumulated about half the data only so the next quarter We'll down we'll finish the other half But that's sort of true for most projects and if actually we see this course accumulation of data You have a good idea of how Fast and it was slow at the beginning and as we go along it gets faster so On the home page in the top bar you have information about the various various panels that are available at the ICGC website and Each project you can sort of browse and you can click and you'll see for example the pancreatic cancer Which is one of the projects we do at the OICR is Takes you to the project that describes the project and so forth And so this is more who's involved what is the goal of the project which funding agencies and so forth But that's not that interesting if you're looking for the data. So if you're looking for the data the place to go is the data coordinating center the DCC site and that's available as shown to you here on the home page and For example, this is will take you to the DCC ICGC.org and so the next lecture is going to be all about this So I'm not going to go too much details about this, but well, you'll be spending sometimes This is the page where you'll be starting from what I'm going to do is I'm going to try to explain to you how the data that is ends up in this place where it came from and So this is a rather complicated slide, but it basically points out the two sources of Data that the main sources of data that compromise comprised of for the ICGC So ICG as I mentioned TCGA is part of ICGC So there's the TCGA part and the non TCGA ICGC part, which is the other half and that's all the other country So it's Asia Europe South America Yeah, and one African one sort of Middle Eastern country and so At the OICR We bring all of this together. So we get all the open data from the TCGA and All the open data from ICGC. We put that on a data portal and then all the controlled access data IE for example germline variants We cannot get those from the TCGA because those have to be behind Are held behind the TCGA so at the ICGC So the TCGA has a DB gap to control for controlled access and at the ICGC We have DACO which is data access compliance office. And so because we don't have DACO users which are ICGC Users that are allowed to look at controlled access data Do not have access to DB gaps You have to get two permissions from two different groups to be able to access everything And so once you get both of them And then oops, sorry once you get access to both of them then you can access the whole thing So as I mentioned TCGA is part of ICGC But there are difference there are differences between the two they have different tumor types. They have different Geographic rules They have many so different countries have different rules many countries versus one Jurisdiction so TCGA is only one country and ICGC is many countries And we have actually different definite. This is where it gets a bit complicated We have different definitions what we call controlled data and in different access rules as well so ICGC has these are the on the on the left hand side all the Open access data and on the right hand side the controlled access data And so you'll notice that at the bottom here. I think you see it. Yes that all Somatic variants from exome or a whole genome are controlled open So a somatic variant mutation whether it come wherever it comes from is controlled. It is considered open open data On the TCGA only variants that come from exome data are considered open Somatic mutations that come from whole genome data are considered controlled access And the reason there is that they don't the the US and the NIH and so forth do not consider And I don't know why they think that but they don't think that the Whole genome mutation calling softwares are perfect I don't know why but they don't think they're perfect. And so they think that what happens in the whole Genome effort. There's some variants germline variants that sort of filter through my accident And there are probably are some the way to identify those will probably take us 10 years and it won't matter anymore in 10 years But that's a separate the discussion not from here But it's important to consider that if so when we show you on the icgc data portal variants from TCGA tumor we're only showing you variants that have come from exome sequencing not from whole genome sequencing Otherwise if it's from a let's say Australian tumor It's got both the mutation there will be either from exome or whole genome and right now the Majority of the data is from exome. There's about let's say 10 15 percent That is from whole genome, but I think in the future the more and more will come from whole genome And so the difference between the two will become more apparent So there are some a lot of similarities though So all the icgc and TCGA users agreed to keep all computer systems You know things secure and and to protect controlled access data and to monitor the the usage of it and so forth And they've all agreed also to destroy it once they finish their work and they only use the secure transfer protocols and encrypt controlled access data and so forth and But if you look at this is one example of one file that we keep on our on the icgc data portal Which is a simple so what we've done is we've archived all the mutations From all tumors and we put them in this VCF format, which is the standard format for mutations so this file is Got all the mutations all the semantic mutations that we have at the icgc. So that means it has all the whole genome extracted mutations from non TCGA samples and TCGA samples is for and for TCGA samples. It doesn't include mutations that have come from Whole genomes because we don't see those because they're not open in data. Okay So This is the icgc portal overview So one of the examples I'm going to quickly go over is how to get access to this controlled access data and so You basically identify yourself you fill out a form detailing the project contact people the technology you'll be To assure that it's keeping the data secure and and the fact that you've read all the data agreements and then you All this gets put into a PDF you sign the PDF You get it signed by an authority at your institution that's able to fire you should you Not agree to or should you break any of the rules aligned in this document? and then you send it off to the DACO office, which is a number of legal experts that will bioethicist types that will review your application and then grant you Access to so this is the DACO form. This is identifying yourself And this is starting the process you fill out a form. It's a bit like an income tax forms And it's pretty long lots of panels and so forth and What you do is I mentioned all the various categories and recently as of last week We actually added a cloud storage issue so because we all know now that doing a lot of this work in cloud Is it different requires different permissions? So if you're going to use clouds you have to opt in to to agree to a number set an additional set of rules That you will be Abiding by if you don't want to use cloud computing for to look at analyze your data Then you can opt out and then you don't you you don't have to worry about those but there are Number of groups obviously in Europe with the safe harbor rules have been changed or have been Challenge recently and so forth. So we had to to to abide to Adapt to those changes. So we these are all the documents You said and you have to sign off on having read two different two new documents We've added recently is the the best practices on using being secure in the cloud and the global Alliance Framework for responsive responsible usage of genomic data and and as well So if you sign off you do the form and you validate it without having signed off then everything's read and something's wrong But if you check off all the things properly Then the validation gives you a green light and it allows you to print a PDF Sorry allows you to print this PDF that you can then sign and and get off to the Daco office And now on the website, you'll have the the list of all the Daco approved projects and And basically This gives you you now have the Daco approval You have to do a similar process You have to go through if you want to get access to TCGA data and it's there totally independent of each other And you have to do that one and there's also a cloud component in that one as well So quickly in the end, I'm just going to talk to you a little bit about the cosmic Database which is out of the Sanger Institute here in Hinkston and so the catalogue of somatic mutations and cancer and So basically the way Cosmic works is it gets its data from places like the ICGC and From PubMed so from reading the literature and it looks for all the papers that talk about some somatic mutation So you can think of cosmic and cosmic is predates ICGC and TCGA so they've been collecting mutations somatic mutations for a long time But you can anticipate that papers that Collected such data before whole genome sequencing or exomes were being done We're doing targeted sequencing or even they would look at one gene And so they say look at K-RAS and 10,000 different individuals and look at where the mutation was And that's the kind of information that goes into cosmic So today if you look into cosmic and look show me all the mutations on K-RAS You will come from those time types of papers that looked at specifically, you know 5,000 patients and They looked at that one gene and didn't look at any other gene and also will or they looked at a gene panel So they look at 10 genes or 20 genes and it's also includes data from ICGC slash TCGA but TCGA it's only getting the data from From exome sequencing not from whole genome sequencing. So right now in ICGC. There's about 12,000 Genomes represented and about 2,000 of those are from whole genome and about 10,000 from exomes so it gives you an idea of the ratio and what you'd be missing from from the TCGA side So cosmic as I mentioned some mutations only from various sources and There are lots of different ways it's a very rich website and lots of different ways of looking at the data there And also mentioned it's also integrated into ICGC portal so from the ICGC portal you'll see a cosmic link So you can go from a gene of interest in the ICGC portal to the cosmic equivalent So there's FAQs frequently asked questions available on their portal and lots of different ways of looking at your various genes of interest and So just a few screenshots to show you all that and so I'm finishing off now. So Nope any seat. We've only missed the best lecture And so in closing so remember that these sites have Lots of documentation The things are changing very quickly like I mentioned things I mentioned about TCGA today will be different next year We know they're going to be different because we're actually building the next one And so we are the changes are coming quickly There Don't be afraid to explore don't be afraid to go click on things and find out what's there and If you're interested in what you've what you're hearing about today There's we do a five-day workshop. So today we're doing a four-hour workshop We spread this into five days so you can imagine that we can do a lot more in five days And this is a different slide than the one you have your in slide deck because I found some other people They've been involved with the workshop and there's actually some more that I'm missing But the CBW is it's like I said has been running for 16 years and These are only people really from the last seven or eight years and it's really an exciting and Very great group of people to work with so thank you very much And if there are any questions, I'm gonna be here for the rest of day as well Okay, any questions or we move on to the next


Secure user memory, the purpose, code data and execution isolation of a secure user firmware, principle, a user flash vision executed at boot time, whatever the boot mode configuration. On the executed, the secure user part is closed and cannot be accessed anymore by any mean until the next boot. It's configured thanks option bytes, so it's a static protection, and it's supported on G0G4 family, H7, L5, and under L5, this mechanism is also called HDP. The secure memory on the G0G4 family. So it's an area located at the beginning of the flash and executed after the reset. The configuration is done thanks one option byte, sex size. There is a second one if you've got a dual bank and could be only modified in ADP level zero. So if you combine sex size with ADP level one, if you want to remove the secure memory, you have to do a regression from ADP level one to ADP level zero, which implies a flash maceras. The granularity is a flash memory page size, and this secure memory can be locked at application execution time. Then the secure memory is no more visible. You just have to write in the flash register, but I will just detail after that we can also use a services from the RSS or the system book loader. Debugger can be disabled when executed some sensitive data. So it could be really useful in ADP level one when you want to do some secret usage like authentication or decryption. So as I previously said, the secure memory could be locked thanks to services in the system book loader. The reason is that as soon as the secure port bits or is a bit in the flash control register is set to one, the secure memory becomes invisible to the whole system. So if you do it in the secure memory, then you will be in fault because even you the core can't access to continue the program. And if you are doing it after in the non-secure part, imagine a hacker managed to connect just before this, he could just stop and manage to see the contents. It's why we've got such kind of services. So if I so map the resets, then the option byte loading, this is done by hardware, then we've got code execution in the secure memory, then we will call a system boot loader services to set the secure port bit, then the secure memory becomes invisible and we jump to the application code execution. In the application code execution, we can't see what is in the secure memory. It's completely invisible. I'll just show you the flash control register, secure port bit version, and then the debugging link which is enabled. Then you can decide to disable it to do something quite secure or quite secret, I would say. Then don't forget to re-enable it to be able to connect on your target. Then the debugger become available. Now for the GZero, we've got an additional features. If you combine the boot lock with the ADP level 1, then by default the debugger will be disabled. I write a quotient because if you don't have the re-enable of the debugging link inside your code, you are an ADP level 1, but you can't connect at all on the port. Even the boot loader is not allowed. So take care. There is no way to recover from this situation. So here we've got the classical system, but imagine we've got the boot lock plus the ADP1. Then the debugging link is I would say disabled by default. Then you need to re-enable it, then the debugger become enabled.  Let's talk now about the secure memory on the STM32H7. This configuration could only be done in the secure access mode. That means when you activate the security option byte, bit, sorry, to one. The secure memory error is executed after the reset whatever the boot mode. There is one secure memory area per bank and it has the granularity of 256 bytes. The secure memory is locked thanks to services in the RSS. The secure user memory can never be accessed by the debugger or by the codex M4, in the case you are in a dual core. So the same schematics are done with G0. On the reset, we've got option byte. Here we've got the RSS boot. You can have the detail of this boot inside the reference manual. Then we've got the code execution in the secure memory. Then you need to code the RSS exit secure services. Then we jump to the application code execution and the secure memory has completely disappeared. From the debugging link point of view, the debugger is disabled during all the secure memory execution. Then you will become enabled. So here you imagine the risk. If you've got a configuration when you configure all the option bytes but have nothing in the secure memory area, then you will never jump to the application code and your debugger is also disabled. So caution also here. So in the secure access mode, to configure the secure user memory area, you need also to call a root security system services. So that means you need the execution of some firmware to be able to configure the secure memory. This is quite different from the GZero. I will have just an animation after to make you better understand this. So as I previously said, the secure user memory configuration could be removed on ADP level regression or flash bank eras. But if you eras the secure memory era and keep the option byte configured, then the debugger is disabled because you will start it on the secure memory era without any code here. So we get stuck in this vision and there is no possibility to recover. So really take care with this. Now the animation to show you how you can activate the secure memory area on the H7. First we need to have the secure access mode. So the security bit and the option byte set. Then we need to program the secure firmware in the future secure memory area because it should be here when we will start after. Then we will prepare the parameters for the sec area start. So the value we want to put in the option byte but it's not our code that will will configure those option bytes. We will just path those parameters to the services of the RSS which name is reset and initialize secure error. On that stone there is a reset and you get this configuration now. That means you are booting on the RSS which select which user memory, secure user memory should be launched, then it will jump to the user memory and remember about the access. Debugging access is only possible outside the secure user memory. Same thing for the Cortex M4, the second core when you are in dual core. Of course the core M7 could access to anything. Let's move now to the secure memory on the L5. So here it's closely linked to the trust zone configuration but I want to have a couple of words here. So the secure hide protection also called HDP. On close this part cannot be accessed anymore by any means until the next boot. It's located at the start of the flash watermark based secure error. To sum up what is a flash watermark based secure error I would say on the L5 we've got a Cortex M33 with trust zone and when this trust zone is activated you've got two words inside your chip the secure one and the non-secure one. Here that means the HDP will be inside the secure word and at the beginning of the flash. It's configured thanks to option byte so an hdp activation and then the hdp end which is the end address because the beginning is the beginning of the secure part. Across all the family I think it was clear it was on the L5 or the version h7 g0 and g4 on specific device. So you have to check for each one the reference where it's possible on it. I think that's all for the secure memory now we can go on with on zone.