Chapter 9 of the book of Joshua. When you when you look at Joshua and you start seeing how that Joshua has entered into the promised land, you will see that if you use the the model of looking for types, for patterns in scripture, you're going to find that there's an interesting thing that's going on. Let me read verses one and two and I'll develop what I just began by saying, and it came to pass when all the kings who were on this side of the Jordan in the hills and in the low land and in all the coasts of the great sea towards Lebanon, the Hittite, the Amorite, the Canaanite, the Parasite, the Hivite, and the Jebusite, you know the rest, heard of it, that they gathered together to fight with Joshua and Israel with one accord. So Joshua and Israel have entered into the promised land. They've already taken Jericho, they've already taken AI. They're now about to find themselves in a situation with people called the Gibeonites. Now when you look in typologies, it's interesting that there are some actual typologies or patterns that you find in scripture and they're actually mentioned in such a way. For example, when you look in Galatians in the New Testament, and I'll develop this as an introduction, when you look at Galatians in chapter 4 in the New Testament, you see that there are two individuals who are mentioned there. One's name is Isaac, the other is Ishmael, and when Paul is speaking there in Galatians chapter 4 concerning Isaac and Ishmael, he speaks of one being the Son of promise and the other being the Son of the flesh. And what they turn out to be are types, a type of promise and a type of the flesh. And so you see these kinds of things in scripture where there are certain things that are spoken of, but they also represent something beyond just what you see on face value. You'll see that the Passover lamb that is found in the book of Exodus and is the lamb that is normally associated with Passover, you see that that's really a type of Christ because Paul makes that clear in 1 Corinthians chapter 5 verse 7. Or you'll see that the Lord Jesus Christ is speaking concerning manna and he speaks how that the children of Israel ate manna and survived, but we're told in John's Gospel chapter 6 verse 58 that the manna from heaven is really a type of Christ. You see that Paul in 1 Corinthians chapter 10 is speaking concerning the children of Israel as they are in the wilderness. And he's reminding the Corinthians concerning Jewish history and how that there was a rock that was there that was to be spoken to instead of being struck twice. And then Paul makes it very clear there in 1 Corinthians chapter 10 that the rock he said is Christ. And so what you have is you have what are called types. In Romans chapter 5 verse 14, Adam is spoken of in Romans 5 14 as a type of Christ. So you can see that in your study of Scripture that there are times when certain things may have a double meaning. There may be another meaning associated with it. Jericho could be a type. AI could be a type and gibbonites can be types. And there are some very well known teachers of the Word of God who would make the case that indeed they are. So when the children of Israel enter into the Promised Land and go to battle against Jericho, that is being presented as being a type of the world. When they go against AI, there are those who speak concerning AI as being a type of the flesh. Now Jericho could be a type of the world because it had all those goods and and it had such a promise of life there. AI, well the children of Israel didn't even take the time to consider what kind of strategies they should have. They were just going to enter in and they were going to take AI and they only needed a few thousand soldiers to do it. So you can actually develop these things. And so one of the one of the commentators I was using speaks concerning the gibbonites and says, and these undoubtedly if you were to look at them as a type would be a type of the devil. Now we have three enemies that scripture speaks concerning the world, the flesh and the devil. And so here we have a type, we'll say of the devil because you're going to see this in a spiritual way in just a moment how that this can have an obvious appearance of that. Now as we begin and I'll show you that in a moment, as we begin we need to remember that the Israelites have begun the conquest of Canaan. They have experienced great victories and they first entered in to the center of the land. They took the city called Jericho. They defeated Jericho and then they were defeated by AI at first but after they dealt with their sin they conquered that city. Now the Bible makes it clear that both of the cities were destroyed and according to chapter 8 verse 26 here in Joshua, Joshua demolished the city of AI. And so the news of the children of Israel traveling throughout the land and beginning to take these cities as this news has reached the ears of some of the inhabitants there and what they've done as it says here in verse one is they formed an alliance. Their mutual fear of Israel initially caused them to agree to unite in opposition against them and so that's what you see. The Hittite, Amorite, Canaanite, Parasite, Hivite and Jebusite they hear of it and according to verse two they gather together to fight with Joshua and Israel with one accord and so they're uniting in opposition at least initially they're going to do that and they're going to attempt to or they want to keep Israel from taking the land. Now that reminds me of Psalm two. In Psalm two verses one through three it says why do the nations rage and the people plot a vain thing. The kings of the earth set themselves and the rulers take counsel together against the Lord and against as anointed saying let us break their bonds and pieces and cast away their cords from us and so they're uniting but they have really no chance. God is giving the land to the nation of Israel. Now as this is taking place verse three it says when the inhabitants of Gibeon heard what Joshua had done to Jericho and AI they were craftily and went and pretended to be ambassadors and they took old sacks on their donkeys old wineskins torn and mended old and patched sandals on their feet and old garments on themselves and all the bread of their provision was dry and moldy so they strategize they have a they have a plan and what they're going to do is they're going to attempt to deceive and they're going to be successful at doing this the the the Jews. Now though the kings had united to oppose Israel it appears that the Gibeonites here have chosen another path. Now when you look at a map there are around seven miles outside of AI there are a short distance about five miles to the southwest of Jerusalem and this particular city that's being represented here this is a city of Gibeon this this city is actually a very powerful city. If you look into chapter ten for just a moment it says it in verse two Gibeon was a great city like one of the royal cities and because it was greater than AI and all its men were mighty and so you're not looking at a pushover city you're looking at a at a powerful city but this these people of the city are afraid because they've heard what is taking place they're certain they're going to be destroyed and because they're certain they're going to be destroyed because they know that Israel has going in and taking these cities and all they come up with a plan so they make it appear that they've traveled a great distance from a very far country everything from their saddlebags on the donkeys to the moldy bread is designed to deceive the Jews and so in they go verse six they went to Joshua to the camp at Gilgal said to him and to the men of Israel we've come from a far country now therefore make a covenant with us but the men of Israel said to the high vites perhaps you dwell among us so how can we make a covenant with you how do we know that you're from a far country how do we know this you see at first the the people of Israel the men of Israel hesitate they're aware that these people may be deceiving them remember with me that Israel had been commanded not to make any covenants with the inhabitants of the land God had specifically said to them you are to make no agreements with them you're not to do that in the Old Testament book of Numbers chapter 33 verses 51 through 56 it says speak to the children of Israel say to them when you've crossed the Jordan into the land of Canaan then you shall drive out all the inhabitants of the land from before you destroy all their engraved stones destroy all their molded images and demolish all their high places you shall dispossess the inhabitants of the land and dwell in it for I have given you the land to possess you shall divide the land by lot as an inheritance among your families to the larger you shall give a larger inheritance and to the smaller you shall give a smaller inheritance therefore everyone's inheritance shall be whatever falls to him by a lot you shall inherit according to the tribes of your fathers but if you do not drive out the inhabitants of the land from before you then it shall be that those whom you let remain shall be irritants in your eyes and thorns in your sides they shall harass you in the land where you dwell moreover it shall be that I will do to you as I thought to do to them so they had received marching orders make no covenant with these people have nothing to do with them you're to destroy them why because these people were extremely evil and so at first Israel is hesitant they say we don't know where you're from maybe you dwell from around here how can we make a covenant with you and they're keeping in mind what God's word had said to them well in verse eight they said to Joshua we are your servants Joshua said to them who are you where do you come from we are your servants now that's not them saying we voluntarily will become your slave labor that's a polite thing you know it's it's a it's a way to express just a politeness you know there is a time where you would you would say your name and you'd say at your service and it's just a phrase that you use just to say that you're harmless that you don't intend any harm to that person at all so they're they're going about making it seem as if they're they're friendly towards them and courteous towards them but they're not volunteering to become their slaves whatsoever verse nine says so they said to him when Joshua says who are you where you from they said from a very far country your servants have come because of the name of the Lord your God for we have heard of his fame and all that he did in Egypt and all that he did to the two kings of the Amorites who are beyond the Jordan to see on King of Heshban and King of Bashan who is at Ashtarot so notice how they go about deceiving Joshua they say to him we came from a very distant land so that's given the impression that that we're not part of this area that that you are conquering but we're distant from here but it also is a way to to provoke in in Joshua a sense of honor for his God because they're basically saying we're from a far distance but we've heard a view and we've heard of how powerful your God is and so it's a form of flattery and they're saying we've heard that that he delivered Israel out of Egypt and we have heard how that he has given you victory over two very famous kings but I want you to notice something notice that they don't say and we've heard how that you crossed the Jordan and they're not saying to him and we heard of how you have taken Jericho because those were recent events and and they're given the the impression that they're from a distance away and therefore they wouldn't have heard of all of this recent news and all so they're very deceptive the way the enemy is they're very deceptive and they're bringing in the strategy to cause them to to feel that they are harmless well verse 11 therefore our elders and all the inhabitants of our country spoke to us saying take provisions with you for the journey and go to meet them say to them we are your servants now therefore make a covenant with us this bread of ours we took hot for our provision from our houses on the day we departed to come to you but now look it is dry and moldy and these wineskins which we filled we're new and see they're torn these these are garments and our sandals have become old because of the very long journey and so they draw the attention to all and this is where we're going to start looking at some things a little deeper they draw attention to the outside evidences they're drawing their attention to that what you can see moldy bread tattered wineskins worn out garments and worn out shoes are all outer evidences of a great distance that they've traveled and the time it would have taken for them to go that distance and so they're setting them up right now in verse 14 the men of Israel took some of their provisions but they did not ask counsel of the Lord so Joshua made peace with them made a covenant with them to let them live and the rulers of the congregation swore to them let's look at this and try and become practical about this lesson that we're learning here they made a decision based on outer appearance they failed to seek God's direction over the years I've had people approach me who have said to me this has happened more than once pastor I have an opportunity to get a good job in another city I'm going to move to another state and I was just wondering if you could pray for me because we're planning on taking the job but just wondering if you have any advice I've heard that more than once and so the very first thing I have asked and I will always ask this the very first question I have always asked is this where are you going to go to church what church are you going to go to and the response normally is and it's normally almost the same almost by word for word to be honest with you it's normally oh there are a lot of churches in the city and I'll say well great that's good to hear which one are you going to go to oh we're going to decide when we get there really you're going to decide what church you're going to go to once you've made your move then what's the prayer what do you want me to pray for that you make a good choice because the bottom line is just because you have an opportunity to get a good job I'm not saying it's not a good thing and it's not of the Lord at all I'm not saying that at all but just because you have an opportunity to move to a better place and by the way there are a lot of places that are better than this doesn't mean you're supposed to all of you who've been in this church know that before this church began I was an assistant pastor in another Calvary Chapel and when I resigned my position from being the assistant pastor I came home and I told my wife Marie that I am no longer going to be assisting in this particular church and I said the Lord has allowed me to be set free and so I have a chance I could possibly be delivering bread as a bread delivery man in San Luis Obispo because I have a friend of mine who was as a manager over a bread distributorship there and I told Marie I could go and deliver bread you know I've been delivering the bread of life I can deliver some Parisian bread I mean bread's bread right I'd like to go to San Luis Obispo because I liked it I've been going to San Luis Obispo since 1968 I go to San Luis Obispo on vacation every year sometimes twice I'll I'll go for weekends you know I like San Luis Obispo friend of mine is a pastor of Calvary San Luis Obispo his name is Brian Brian calls me up just before he leaves to plant the church he used to work for word for today and he calls me up and says David we've never met but I edit the tapes for the radio program he said and he says I work on the radio program and I've listened to you for a long time now you have mentioned San Luis Obispo and so many of your studies I want you to know that I'm going to go and plant a church there and I said great lay a great foundation Brian because I'm going to come and steal that church from you because I want to go and live in San Luis Obispo I mean this is going on for years so I come home and I tell Marie you know I'm no longer going to be here in the church I we have an opportunity we can put the house up for for sale and we can move to San Luis Obispo it's a great place to you know it's by the beach it's just it's real quaint you know and and Marie just smiles at me and she says you know that God hasn't called you there you know that I said he didn't call me to be married to you either so that's it stop it stop speaking truth see what appears to be your heart's desire what appears on the outside to work doesn't always really measure up to what you think it is you have to pray you have to seek the Lord you cannot make judgment based on just outer appearances I cannot tell you and I and I and forgive me perhaps I have some visitors today who are listening or maybe somebody will hear this on the radio in the future I am not saying that I'm the greatest pastor in the world though I am what I'm saying what I'm saying is and I'm not saying that this church is the best church in the world and and all of that that could be misunderstood and I'm trying to be careful just to say that's not what I'm saying there are great churches no doubt wonderful churches great teaching super worship God is there that's not what I'm saying what I am saying is you have to pray and seek the Lord before you root yourself and go somewhere else because there have been too many people that I have spoken to over the years who have written or called me or come to visit who say I made a mistake I should have sought the house of the Lord a place to serve and place to to go to church because on the outside it looked like it was great but when I got there there's no place to fellowship there's no church you know it's kind of like the Wizard of Oz there's no place like home you know there's just it's just different and and I and I am drawing I'm dried up now I get those reports still to this day I still do and so you have you have to pray you have to seek the Lord you have to ask God what do you have what what is it that you see that I don't see what is it that that I I'm looking on the outside and in this particular case I'm looking at the saddlebags I'm looking at the clothing I'm looking at the food I'm looking at the sandals and as every appearance that they've come from a distant land and have been on the road for some time it all has the appearance but they're making a big mistake because as it says in verse 14 they did not ask counsel of the Lord they didn't seek the Lord in this they made a decision based on outer appearance they failed to seek God's direction and this failure to pray gave place for them to be completely deceived now Joshua did not intend to disobey God he was deceived his mistake was he did not seek the counsel of the Lord he didn't seek God's direction Joshua looked at the outer appearance but he did not seek God's direction he failed to be what the New Testament would exhort us to he failed to be what is called vigilant in prayer vigilant in prayer in the book of Colossians chapter four verse two Paul says it like this continue earnestly in prayer being vigilant in it with thanksgiving continue earnestly in prayer being vigilant in it with thanksgiving continue remain steadfast and strong in prayer apply steady effort be vigilant be awake and do not grow weary so when he speaks of this it means to to remain watchful and be alert and be aware in the event that there's some trouble you need to be watchful and you need to be alert and when you see something you need to go in the Lord beyond the surface and the way to do that is through prayer Joshua knew God's word Joshua knew he was not to make a covenant with these people he knew God's word but he didn't seek the Lord in prayer and that was his big mistake he didn't seek the Lord's direction all he could see again is the outside but God sees beyond the outside in Jeremiah 23 24 we read can anyone hide himself in secret places so I shall not see him says the Lord do I not fill heaven and earth says the Lord can you play cosmic hide and seek with God and him say you know I give up I can't find you is there anything that's hidden from his sight here's something for you if you think you can hide from God your God's too small your God's too small if you think you can hide from God your God's too small because God can see all there's nothing hidden from his sight he sees it all and so for me the wisest thing that I can do is is pray God it's this seems to be right it seems to be so right but you see there have been many times when I have moved because it seems right and I made some big mistakes and so I don't want to do that again I don't want to I don't want to make a decision without seeking you first I need the peace that comes from you I need to know I need confirmation and I don't want to move without that sense that you're directing me in this I just don't want to do that Hebrews 4 13 says there's no creature hidden from his sight but all things are naked and open to the eyes of him to whom we must give account so God sees all and because he sees all it's always wise to seek his direction first in prayer again Joshua knew the word he was not to make a treaty with these people so it was not a failure of knowing God's word on the subject it was a failure to pray for direction there's a writer who's real well known for his prayer life in the things he writes concerning prayers name is em bounds em bounds and em bounds wrote he cannot be stated too frequently that the life of a Christian is a life of warfare an intense conflict a lifelong contest it's a battle moreover waged against invisible foes who are ever alert and ever seeking to entrap deceive and ruin the souls of men the life to which holy scripture calls men is no picnic it is no past time no pleasure jaunt it entails effort wrestling struggling it demands the putting forth of the full energy of the spirit in order to frustrate the foe and to come off at the last more than conqueror it is no prim rose path no rose scented dalliance from start to finish it is a war from the hour in which he first draws sword to that in which he doffs his harness the christian warrior is compelled to endure hardness like a good soldier and so the christian life is a life of warfare satan desires to destroy there are so many people who seem to think that satan is kind of like not that much of a problem and he doesn't really have that much of a problem with you if you walk out today know this god loves you and satan hates you know that he wants to destroy you and one of the things he loves to do is make you mad at god when it's him all along who's been bringing the pain to your life and then you get mad at god how could a god do this to me how could god we blame god for so many things we blame god for things that god should never be blamed for and yet we do it's all your fault if you really loved me you wouldn't have let this happen in my life you wouldn't have taken this from me or hurt me in this way if you really loved me and the enemy just smiles within over that because he's causing you to turn on the one who loves you the most in this universe and that's what he wants you're in a war and never forget it never forget it you are in a war 24 7 he never takes a break he never takes a vacation he never takes r and r of any sort he is after you constantly and there are times when you feel like you've gone under a wave and you're about to drown and you pop your head back up and take a deep breath and you say i finally can breathe and here comes another set and you go down again and you think i can't take this anymore and all along you begin to say this is god if god loved me if god cared about me if i've discovered something through those long processes the lord has a way of using him for my good he refines my faith and strengthens me and makes me more courageous and more bold it also has a way of developing within me a stronger faith than i've ever had before and the losses that i've experienced like you we've all gone through losses i've actually come out of those losses stronger trusting god more because my god has proved himself to be faithful every time and the enemy cannot win there's no way he can win he's already lost he's already he's already the loser the greatest loser in the universe is is satan because god has already proven himself victorious but what he wants to do is he wants to cause you to think that that you're losing you haven't lost you're more than victorious in jesus christ hold fast to him hold fast to him don't let go and seek the lord in prayer ask god god show me your glory show me your strength show me your power reveal to me that which is necessary at this moment for me to be able not only to make it through but to make it through victorious in you and watch what the lord will do he refines you and strengthens you the enemy wants you to look only on the outer appearance only on the outside and he doesn't want you to see his deceitfulness and so you seek the lord and you pray and you ask god for direction and that is what we need to do seeking god in prayer is of utmost importance because we want to live lives that please him and when we pray we're simply admitting our need for his help and we're just admitting that we need his direction and when we pray and then seek him we're also adopting the the heart of humility because we're abandoning our pride and we're revealing our dependence on him trust in the lord with all your heart lean not on their own understanding in all thy ways acknowledge him he will direct your path that's a promise from god trust in him why am i to trust in the lord with all my heart well because you're my tells me that well if you trust in your heart your heart is deceitful it is wicked it's desperately wicked who could know it so i don't want to trust just my own heart i am not to lean on to my own understanding i'm to acknowledge him and i do so through prayer and his word that's what god has called us to do well joshua failed to do this and what happens verse 15 tells us joshua made peace with them made a covenant with them to let them live and the rulers of the congregation swore to them he didn't sin willfully but he did not value the privilege of actually asking god for direction either there's this old song and and you'll recognize the lyrics in just a moment i'll read them to you don't worry i will not sing them but we used to sing this song when i first got saved and uh we actually had two songs we combined and and this was one of those songs but it's what a friend we have in jesus and and it goes what a friend we have in jesus all our sins and griefs to bear what a privilege to carry everything to god in prayer but it goes on to say oh what peace we often forfeit oh what needless pain we bear all because we do not carry everything to god in prayer and that's true sometimes we carry things we need not carry and sometimes we suffer things we need not suffer because we didn't seek god so by not seeking god joshua is deceived into making this covenant ecclesiasties five two says do not be rash with your mouth let not your heart utter anything hastily before god god is in heaven and you on earth therefore let your words be few but they made this covenant in verse 16 it happened at the end of three days after they had made a covenant with them that they heard that they were their neighbors who dwelt near them then the children of israel journeyed and came to their cities on the third day now their cities were gibbian cheffa rah mont claire pomona birath and kiryat yareem but the children of israel did not attack them because the rulers of the congregation had sworn to them by the lord god of israel and all the congregation murmured against the rulers then all the rulers said to all the congregation we have sworn to them by the lord god of israel now therefore we may not touch them this we will do to them we will let them live lest wrath be upon us because of the oath which we swore to them and the rulers said to them let them live but let them be woodcutters and water carriers for all the congregation as the rulers had promised them so they had made a val before god and when you make a val before god you don't break it you know we have our new year's resolutions and people make the resolutions those are not vows to god those are simply resolutions they make the resolution every year anybody here ever make resolutions i don't you know do you anybody here make really i'm interested anybody make reviews yeah you're very few of you do you break them don't you because we do well i'm going to lose 20 pounds then i'll gain 25 you know i mean that i'm not going to do this i'm not going to do that i'm going to stop this i'm going to stop that i'm you know we we make resolutions well resolutions one thing promises and oaths to god's another another thing in the old testament it makes it very clear that if you make a promise to god you're to keep it in numbers 30 verse 2 if a man makes a vow to the lord or swears an oath to bind himself by some agreement he shall not break his word he shall do according to all that proceeds out of his mouth and so when you made an oath you were to keep that oath so they made an agreement and they were to keep their oath their word was made to god and their word was what bound them there was a time in the history of the united states by the way that all you needed to do is give your your word and and stick your hand out and shake somebody's hand and that's all you really needed that you didn't need to have a lot of contracts you didn't need 50 pages of contracts you just took your hand out and you said i'm going to make that i'm going to make good on that debt and you made good on the debt there was a lot of integrity a lot of people had integrity some people would default yes that's true of course human nature being what it is but overwhelmingly your name meant something your integrity meant something you were trustworthy and that mattered even in my day when i was growing up my dad was the kind of man that if he had ten dollars and he owed money or he could feed the family my dad was kind of at first make his payment and anything that was left over we would get that was just the way it was there was no complaining in my house about that my dad's name meant something to him his word was his bond and if you wanted to insult my dad refuse him credit because my dad would pay his bills on time and we learned that that some meals are fine three days in a row we learned those things we learned that my mom could make mashed potatoes one day and then something she called potato pancakes the next and that was fine we learned that you could get some tomato soup you could actually get tomato sauce put it in water get a potato cut it up get some frankfurters cut those things up boil them and that's dinner we learned that that was our soup we learned all of that because you want to know something my dad taught us pay your bills on time be a man of your word have integrity that was poured into my life and though there was a period in my life that i can confess to you that i really didn't value that for the last 42 years as a believer i have valued it tremendously because my name means a lot to me integrity means a lot to me that's how i run this church we make sure that we pay our bills on time we take care of those things because that gives honor to god you see that's how that works right so your name ought to mean something your your your word ought to mean something and so when they made their their oath they said we're going to let you live there's no way that they're going to back off and secondly because that oath was made as a promise and it's something that they had vowed they would not break it well it says in verse 21 the rulers said well let them live but they're going to be wood cutters and water carriers no those were the lowest tasks so they made them do the most menial work in society in verse 22 joshua called to them and he spoke to them saying why have you deceived us saying we are very far from you when you dwell near us now therefore you're cursed none of you shall be freed from being slaves wood cutters and water carriers for the house of my god they they had used deception to secure an oath but israel was still bound to honor that they had been careless when they made such an oath and therefore they had to respect their word and so joshua makes it clear we will respect our word but you're going to be our slaves basically in verse 24 so they answered joshua and said because it was certainly told your servants that the lord your god commanded his servant moses to give you all the land and to destroy all the inhabitants of the land from before you therefore we were very much afraid for our lives because of you and have done this thing and now here we are in your hands do with us that seems good and right to do to us so he did to them and he delivered them out of the hand of the children of israel so that they did not kill them that day joshua made them woodcutters and water carriers for the congregation for the altar of the lord and the place where he would choose even to this day well they believe that the god of israel was giving the land to the israelites so they basically lied to live the result a life of slavery but for them it was better than dying do not make decisions lightly one of the things that my staff who works most closely with me those who work most closely with me on staff will tell you about the way i do things and i'll share this with you in conclusion is i do not make decisions quickly i wait anytime somebody tries to hurry me to make a decision the decision will be made it'll be no because if you pressure me to make a decision now that's not the lord i'm not going to do it it's like when i've gone into a car lot i've looked at a car and my friendly salesman says to me well i can't guarantee this price you know more than an hour so i say well i hope somebody comes in within 59 minutes to buy it because i'm not going to buy it just because you're trying to pressure me to make a decision i do the opposite when somebody tries to pressure me i dig my heels in and i say i'm not moving i'm not moving because this pressure is not the spirit this is the flesh so when if you try to pressure me to decide something on your behalf right now that will not happen i'm not going to allow that to take place because if it's important enough to decide it's important enough to pray about we're going to pray before we do anything and when i do whatever it is i'm supposed to do it will be in full peace with the lord and if i make a decision i will repent if it's a bad one because i seek the lord that's just a habit i have i encourage you to i encourage you to the habit too take time to pray seek the lord before you make any decisions don't go without her appearance because often appearances are deceiving that's what you learned here with joshua they looked like they came from a great distance but in reality it was just a great deceit that's how the enemy works he works on the appearance he doesn't work on the substance he wants you to follow what appears to be the right thing or god by his holy spirit will give you direction if you just wait on him learn to wait on the lord learn not to make snap decisions and i guarantee you if you learn that lesson you'll have less pain in your life over time because you'll be making the proper decision because you waited on the lord to direct you so wise thing to do let me encourage you in that


Welcome to this Introduction to Python and Programming course. My name is Alexander Hess, and I will be your instructor. So over the last couple of semesters, I've been teaching courses similar to this one at the university level, in particular to students in Bachelor and Master programs at a business school. So in these courses, I usually don't have any prerequisites. So I don't assume you know anything about programming and Python in particular. So what is the objective of this course? The objective, besides picking up a new programming language, is that I want to prepare you for further studies in the field of data science. So you may wonder, why data science? Well, I think that one of the most common applications of coding just happens to be the field of data science is you study at a business school. How is that? So in my case, for example, I am pursuing a PhD in logistics. So in my day-to-day job, what I do is I work with realized data, usually big data sets. And I try to solve typical logistical problems. So for example, I try to minimize some routes that you want to have in order to ship some product and so on. And these are typical applications. So in the field, we just analyze data. We run all kinds of statistics. Then we build optimization models. We build lots of simulations, like Monte Carlo simulations and other things. And in order to do that, you just need to know how to code. And Python happens to be one of the languages that are very good in these topics. And even in other disciplines at business schools, coding skills are getting more and more important in recent years. So that is why the goal, the actual end goal of this course is to prepare you for further studies in the field of data science. So what that means is I'm not focusing on things that you could also do with Python. For example, web development. Web development, that means building a web page or building a backend for some cool fancy mobile phone app. This could also be done in Python quite well even. And many big companies do that in Python. But however, we are not going to focus on that. So that is what, so when I have to choose what I put into the course and what I don't put into this course, that is what I have in mind. Or does it help you become a better data scientist somehow? If so, then most likely I will put the material in this course. Okay, so what you're currently seeing is a file in the format of a so-called Jupyter Notebook. So currently this is a web browser and I'm in full screen mode. If I leave the full screen mode, you see that I'm in a web browser. And the format of the file that I'm currently viewing is a so-called Jupyter Notebook, formerly known as iPython Notebook. That's the old name for that. So why am I using this format in this course mainly? Well, one of the other options I would have is to make your program, for example, in a terminal window. When you watch Hollywood movies and when there is a computer hacker in a Hollywood movie, usually what you see is a person sitting in front of, let's say, 10 big screens. And on all of them, there are these black boxes where a person can type some stuff in, some commands, and then the computer does something and then usually they solve some cool quizzes and so on and some other problems. And that is a good way to code. And I do that on my day-to-day basis a lot, a lot. However, that is not very beginner-friendly. So that is one of the reasons why I choose the Jupyter Notebook format. And in a future video, you will also see the other advantages, especially for a beginner in using Jupyter Notebooks. So how do Jupyter Notebooks work? Well, these files you can think of, they're kind of like Google Docs in the cloud. However, they are just running as we see on my local machine. And in these documents, they are made up of so-called cells. And here you see an example of such a cell. This is a code cell that contains actual Python code, in this case, one plus two. So if I execute this, then the computer tells me that one plus two is three, okay? So congratulations, Python knows arithmetic. But that is only a simple example. Another example of Python code would be a typical Hello World program that you usually learn in any programming language if you take a course. So what this code does here, it calls a built-in function that Python knows called print and it gives it some text, which is Hello World. And if I execute this, what Python does is, it simply prints out Hello World, okay? So that's also trivial, but it's another example of a code cell, okay? And in the materials, what you will see is the materials that are accompanying this course, they are written in a book, so to say, that is written in Jupyter Notebooks, okay? So each chapter is laid out in several notebook files. And so you can open them and you can read through them just like in a book. And in between the text, you will see code examples and you can execute the code, you can play with the code. And yeah, that is the format I use and also the exercises that are part of this course are also laid out in Jupyter Notebooks, okay? So this is a very good format and we will also see some other advantages soon. So let me briefly go over a couple of examples of organizations of companies that use Python in the real world, just to motivate you a little bit more of why it's so cool to learn Python. So here we see a couple of big tech companies, but also companies like NASA. We see an investment bank like JPMorgan and so on. So what do these various companies do with Python? So Google, what they actually do is they have an internal rule that says, Python, where we can, see where we must. So see is another programming language that is a lot faster if than write than Python. However, it has some other disadvantages. One example is writing code and maintaining code written in C is a lot harder than code written in Python. And in the business world where you have to not only write a program once, but you have to maintain it. You have to always make changes over time in a very short timeframe. It pays off to use a language that is good at that. And many languages are not, okay, but Python is. So that is why Google uses this strategy. They say, okay, if you really need to, if you really need speed in a computer, then we may have to go through other programming languages. But if we can, we take Python. Okay, that is one of their official models internally. And for example, the scrapers, so the servers that basically go to the internet and scrape all the websites and collect the data and put them on Google servers to index them. That is actually written in Python code. So a big company like Google does that. Other companies like Spotify, Facebook, and also Netflix, they mainly use Python to run data analytics and to run their machine learning algorithms. So at the end of a song in Spotify or at the end of the movie on Netflix, you know that you are recommended other songs or movies to listen to or to watch. And many of these so-called recommender systems are written in Python. So that is a typical data science application, also called a machine learning application.  Okay, another example is Dropbox. So Dropbox is one of the companies that not only uses Python on the servers, but also on their client software. So if you are on a Windows or on a Mac machine, download Dropbox and install it, you're actually running a Python code on your machine. So Dropbox has written a Python code that gets deployed on machines and then their servers are also running on Python. So they are using lots of Python. And the inventor of Python, Guido van Rossum, he actually worked a long time ago for Google and then Dropbox, they actually, so to say stole him from Google in a way. And until he retired, one and a half years ago, he worked at Dropbox. And so Dropbox is very much connected to the Python community, JPMorgan. So all the people out there who want to go into quantitative finance or just finance, if you go and join their onboarding program, as an analyst, for example, you will have to do some introduction course in Python, usually. Then here we have NASA. So why did I put NASA here? Well, usually these days, especially in the field of data science, people want to work with big amounts of data. And so when we want to answer the question, like who has the most data in the world? Of course, companies like Google and Facebook and Netflix, they are among them. However, NASA is also among them. And NASA, when they collect data from telescopes, they're actually collecting more data than can per second than can be stored on a hard drive. So they are really working with big, big amounts of data. And they are also losing a lot of Python data science applications to run analysis with data they collect. Okay, and then also here we have Instagram. Instagram, they actually have, they are running in their web backend, they are running Python heavily. So whenever you communicate via an app or via a web browser with Instagram, there's also a lot of Python involved in the background for making the web requests work. Okay, so there are different fields of applications, but you have already heard from the examples that companies use a lot of Python for data science applications. So I think that is a good motivation for why you should continue with this course and study Python really, really hard and to become good at it. Okay, now to end this presentation here, I want to give you three brief tips on how to study and how to learn programming. So the first one is the most important one is what I call the ABC rule, which is the always be coding rule. So it's just that easy, just try to do some coding each day. So if you take this course and in one of the formats where there is at the end of the day an exam at one of the universities I'm teaching that, then I don't suggest you wait until two days before the exam and start to study, okay? This is not gonna work. Coding and Python also as well, but you should understand it more like a math exam, right? You have to study throughout the semester, you have to do exercises on a regular basis to get used to that. You have to review a lot, you won't understand a whole lot of things in the first time around, even when you try hard. Sometimes you just have to play with some stuff a bit in order to really understand how something works. And that can only be learned if you work on it on a regular basis and either just, if you want to, let's say, learn Python in the next six to eight weeks, then maybe take one hour every day as compared to maybe five hours every Saturday or so that's doing something, doing a little bit every day is a whole lot better than anything else, okay? Another tip is, I'm going to refer here to Paul Graham, who is one of the co-founders of Y Combinator, the Silicon Valley-based company that invests in startups and tries to help startups become the next unicorn. Paul Graham, he wrote an article that is also linked in the book that is called The Maker's Schedule. And in this article, he compares two kinds of people. So on the one side, you have so-called manager type of people. On the other kind, you have maker kind of people. And the big difference is that the manager has like a schedule where they work. So usually as a manager, you have maybe a call at nine o'clock in the morning, then 10, you have a meeting and at 11, you have the next call and so on. You have deadlines, you have to answer lots of emails at home, so they come in and you're required to respond within two to three hours and so on. And that is a typical manager. So it's people that always have to get some stimulus from the outside world and have to communicate. On the other side, there are makers. And makers in Paul Graham's article, the first example he gives, for example, artists, but also engineers and programmers, of course. So what is the difference? Well, typically, if you talk to artists, they can't just start now to paint a painting and then in an hour from now they are done or in two hours from now they are done. So usually what they do is they start to work on a painting and then they don't like what they do, so they throw it away and they take another painting and they try to come up with a similar painting but then do some things differently and at some point they like it. And then maybe they continue to work on it and at some point they are done. And the big difference is they require some what I would call a flow state. So they require some intuition and some creativity to come up. And sometimes you need just time for that. So we all know that when we study for an exam and tomorrow we need to really know something, then it may be good to study one day, sleep over it, study, to review some stuff, sleep over it again. And then over time, by sleeping over it, then you slowly over time understand some concepts and remember stuff. And yeah, so this is just the way we have to view programming. You will have to, you will listen to my videos, you will read the book, you will understand lots of stuff, I hope. But then when you are at the problem set, then probably you won't come up with a solution right away. So what then you should do is, you should do what the artist does. You should try to come up with some first program and see if it works and if it doesn't. And then probably you will throw it away and you will come up with a second version with a different approach and maybe that will work, but maybe it will be the third one. So what I'm saying is that the program is, even for someone that is experienced, it is a highly iterative process. You do something and then some part of it is good, some part of it is not good and then you continue to work.  So and the reason is because it is very hard to break down a software project or learning to code on a time schedule basis. It is more like a creative process here and you have to plan for that. So you have to plan that you don't start to study too late if you have to make a deadline or study for an exam, but also you have to understand that maybe you work on a problem and you make mistake after mistake and then you sleep over it and the next day you wake up and all of a sudden you know the solution to the problem and that is very common even for real life projects, okay? So just keep that in mind, that is the maker schedule and it's an interesting article, so go ahead and read it. And then last, the third tip that I give you is what I call faith iteration. So depending on who you ask, what are good tips on how to learn to code, usually people will give you one of two answers. So one answer could be take some prototype project and just try to finish it. So for example, if you want to go into web development, then a good prototype idea would be just try to come up with a website and just build it, okay? So, and that is it. But then on the other hand, if you follow this approach, you learn how to finish a project, but you don't learn a lot of the background information and that you can only learn when you take like a course like mine, but also other courses if you read books and so on. And the important idea is that these two phases, the phase where you just study, study, study and the phase where you just build, build, build, none of them is better than the other, they just, they rather compliment each other. So that is also, so what I suggest is always study at some points but then also take one or two days where you build something if you want to come up with some data science tasks then maybe just take a simple data set that you can get maybe from cackle.com or from some other source and just try to make some simple analysis and just try to figure out how could you do this analysis and that would be your prototype, okay? So just bear that in mind. And if you'd only use books and only watch videos, you're also not gonna get very far, okay? You need the prototyping phase as well, okay? So just prepare for that. These are three tips and the ABC will always be coding do it on a regular basis, I think is the most important one, okay? And in the beginning, when you really learn to code, there will be a lot of frustration involved but after time, things will get a whole lot easier. Okay, so that is the first part here in the presentation. So I will see you in the next video.


I'm trying to block this door. Are they gonna rush this in? I hear him. I'm gonna try getting out of the other way if I don't. We're not gonna have a chance. I'm dropping down. I'm dropping down. I baited him. Other guy's up top, somewhere. I hit him. I took off his shield.


Now it's my second time and I enjoy it very much to talk with such a bright bright group of people from around the world Very smart people from around the world For me the biggest interest here right now is the green transition of industries Especially because the automotive industry is right now transitioning very quickly into green energy and the green Green engines coming for the for the cars and for the transportation and also green solutions So it is not only the energy part, which is very interesting in discussion here But also the biggest influence of IT and IT solutions on energy efficiency and also on the consumer behavior So we have the artificial intelligence Sector which was discussing great things, but also we had green certificates and and the trade with green certificates we had a great discussion on on the carbon capturing Solutions, so I must say and top level discussions on every area, which is interesting me Every company expects great global governance Meaning that if there is a trend which is absolutely needed and getting the climate Supported in not heating up anymore is a concern for all of us here so it is a Climate here right now on the conference showing that everybody is concerned with getting not only green energies Green solutions clean climate, but also distribution of wealth, which is you know the wealth part You have here the global self as well represented. So how you can do it so to make it equitable If you want to walk Fast you walk alone if you want to go far you walk with people So you work in the group and I think working in a group will bring us much further and we have to make a huge change So I expect to be collaboration Which will bring us further and which will bring us better solution because there is no single market right now Like only one market in Europe right now Asia and the United States are driving change So we have to be global in the automotive business


warning. This video will contain spoilers after chapter 1037. You've been warned! Hello I'm Renaka Mataji, this is Joygirl, and today I want to discuss the elephant in the room. Or elephant at sea. You guys know what I'm talking about, let's talk about Zanesha. Now this is a speculation that I've held for quite a while now and I have brought it up before in the past but it didn't get the chance to fully flesh it out. And so now I thought that this would be a good opportunity to do so obviously because of the fact that Zanesha has become a hot topic recently and obviously that's a result of chapter 1037 because we saw in the final panels we saw Zanesha or at least her shadowy silhouette coming to Wano joining the raid. But speaking of shadow and speaking of raid, this video is sponsored by Raid Shadow Legends. Raid Shadow Legends is a free to play game that you can download yourself using my links below and I'm still having so much fun trying to fight the new clan boss Hydra. The ultimate beast with six heads each one having unique mechanics to terrorize your champions. I mean how terrifying does he look. The graphics and the designs of all their characters and settings is something that I really enjoy about this game. It really allows you to immerse yourself in the land of Tulliria because it also just so happens that this month alongside releasing a bunch of new champions Raid's also introduced a brand new faction wall script for one of my favorite factions the Shadowkin and I can't wait for the crypt to open up so that I can dive right into it. There are also tons of new year events and tournaments including a special fusion event where you can get one of Raid's newest legendary champions. So now's the time for you to start playing Raid and if you use my links in the description box below or scan my QR code you'll get a free starter pack worth around 30 dollars to kickstart your game. We're talking a free champion, Virgus, 200k silver, one energy refuel, one XP boost and one ancient shard so that you can summon awesome champions as soon as you get in game. All of this treasure will be waiting for you here and only for the next 30 days for new players so make sure that you don't miss out and that's it. Click the link, join the game and I'll see you in Raid Shadow Legends. Alright so now let's go back to a different raid. Now Zunisha showing up at Wano has meant that she's become the source of so much speculations and discussions and whilst that has largely centered around the mystery of the devil fruit the special devil fruit that the Gorose were talking about the idea that I actually want to share in this video centers around another mystery in the one piece world. Now I'm sure most of you guys are familiar with and remember Ohara's theory video that blew up the fanbase last year and if you guys aren't one of the literally millions of people who watch that video Ohara made a video with the Japanese YouTuber Yudoran and that video largely centered around the possibility of Ennis Lobby being the missing right eye of Jaya. Now they go into some really fun details into the Japanese language and the puns that could be made between the chapter numbers and the chapter titles so if you haven't watched that then I do highly recommend you do but I have to say that when I actually first watched that video it really lined up quite nicely with an idea that I've always had about the missing eye of Jaya except it wasn't Ennis Lobby because when I had always looked at that skull map of Jaya and pondered about the possibility of there also being a right eye given that Shandora was Jaya's left eye I always thought that that missing piece could be which is obviously being carried by Zunisha as the Mokomu Kingdom so soon after Ohara's video came out we actually did a stream with him we did a let's talk wanna collab and so for those of you guys who watch that stream you guys might remember that I did actually bring up this this speculation but I didn't get to flesh it out in full detail and so I thought that now that Zunisha has become such a hot topic and the source of so much intrigue I thought this would be a perfect opportunity to share my thoughts so hear me out I don't think that Zunisha is originally from the New World or even if she is I think there has to be a huge link between her and Sky Island and one of the reasons why I say that is because it was once revealed that Zunisha's diet consists of giant seaweed and Sky Island apples now the giant seaweed makes sense we see Zunisha reach down into the water you know feed herself and also give water to fertilize zoe but the Sky Island apples that is I think oddly specific and obviously given the fact that we are talking about the missing piece of Jaya which has obvious connections to Sky Island because of the knockup stream that shut up Jaya's left eye I think a clear connection can be then made to Zunisha as well and the thing is is that the more I actually looked into the connection between Zunisha and Sky Island or Shandora or Jaya the more I looked the more possible clues I could find something else that seems to really connect zoe or at least the minks to Sky Island is the heavy symbolism of the moon now obviously the minks transform into their Sulong forms with the full moon whereas the Shandorians along with the other Sky Island races we know are races that originated from the moon through a Nails cover story now I know that the moon could also work well with some other islands and some other races other elements in one piece as well with Wano for example there is obviously a heavy moon symbol in the Wano arc and actually that would really post some fun ideas because we also have the mountain god Bors in Wano and then looking at Zunisha we could maybe theorize on the mega fauna that you know used to possibly roam the one piece world but anyways if we're looking at clues that link Zunisha and the Mokomo Kingdom to Skypia or to the Sky Islands directly and specifically we've actually also got some humans who look quite similar to minks and by this I'm talking about Masira and Shouju who we met in Jaya and they were the ones that helped Luffy get to Sky Island now they are known to be humans but I've always thought that they have quite a ply animalistic characteristics and almost as if they could be minks themselves and so with all of these clues that seem to connect Zunisha and Zou to Jaya and Shandora I think it's possible that Zou is the missing right eye of Jaya for one we know that Shandora was built around 1100 years ago Robin revealed this as she was reading the ponder glyphs back in chapter 261 and then it's only natural to assume that if Shandora was Jaya's missing left eye and such an eye existed then there would also be a right eye so then if Jaya was a complete skull and had a right eye then that island which made up that right eye that peace would also have to be around 1100 years old and so interestingly one of the only islands that we know to have that length of history happens to be Zou in chapter 802 Law says that the civilization at Zou has existed for around a thousand years and I think this is an important point because I imagine that there are only a very few civilizations that has existed for such a long time has existed for over 800 years and the reason why I say that is because all of the other countries all of the other islands must only have a history of around 800 years that is when the new kingdoms were formed as a result of the 20 kingdoms who existed before then going up to form the world government going to marriage while and that's when the new kingdoms had to form instead so that rough timeline of a thousand years or a thousand 100 years matches quite nicely between Zou and between Shandora which I think could be quite suggestive and another big potential clue or a big reason why I actually think this is that when you look at the map of Jaya when you look at that skull not only is there that missing left eye where Shandora was but when you look at that right eye it doesn't look the same as the left it's not just a hole it doesn't look like the one on the left which has obviously been catapulted upwards or even as Ohara mentioned in his video about any sloppy being pulled downwards because what it looks like from the map is that it actually got torn out from the side it looks like it's been torn out from the right it seems like if there was a right eye and it was taken away it was different to what happened with Shandora and the knockup stream because it looks like it's been ripped away from the side and so then if that's the case I think there are a few ways we could think about how that could happen one of them could be oars we know that there was the existence of an ancient giant race and oars was actually literally known as the continent puller so an ancient giant like oars maybe oars himself could have pulled away the eye but the other option is of course Zunisha given the fact that Zunisha is a huge ginormous elephant ginormous creature but also an ancient creature and currently has zoe on her back the way that I could picture it is if Zunisha went underwater mounted the island mounted that piece of the eye on her back and then walked away and ripped off ripped off the island with her and at first I have to admit that seems quite fanciful for me the idea of Zunisha going underwater thought might have been a bit wild especially given how large she is but then an interesting fact that I found out is that elephants are natural born swimmers I never would have thought that elephants swim so that was really cool for me to find out but then I think that also adds credence to the fact that Zunisha could have gone underwater to mount the island before ripping it off we know that Oda likes to draw on real life events and real world facts of course unless it comes to his uh paleontology but apart from that the fact that elephants can swim they can go underwater I don't know I think adds to the speculation a little bit so then the remaining mystery and the very intriguing question is why Zunisha is carrying zoe where is Zunisha going what was her punishment what is she being sentenced for what crime did she commit because Miyagi did heavily suggest that Zunisha isn't just walking around aimlessly and she is actually walking towards a destination and this is an atonement for some sort of crime and now obviously with chapter 1037 we've seen that Zunisha has come to Wano but I'm less inclined to believe that Wano has always been her original destination I personally think it's less likely that Wano is the place that she's been searching for all of these years and it's more likely that she's come maybe because of something that Momo said or maybe because of the voice of all things by Momo or Luffy maybe Luffy calling out to Zunisha when he fell off Onigashima earlier in the raid when he fell off the rooftop during his fight with Kaito so then in that case if Wano hasn't always been her original destination and it's merely a new stop or stop along the way then I think it's possible that her true destination is Jaya maybe to return the minks to their homeland because Miyagi also did say that the minks wouldn't be able to stay on Zunisha on Zunisha's back forever and that one day that they would return to their homeland so is that place of origin Jaya and is that where Zunisha has been going because in that case we would go back to what I originally said that it doesn't seem like Zunisha has always been in the new world and I could picture a similar scenario to Lubun who can't go past the reverse mountain where Zunisha has just not been able to go through the red line but this is sort of the idea that I've had about Zunisha about the links between minks and Chandra about how this all fits in with the missing right eye of Jaya and the biggest speculations about what happened before the void century during the void century and I'm glad that I finally got the chance to share this with you guys now that Zunisha has risen as a hot topic but I'd be interested in reading what you guys have to say on the topic so please do leave a comment below don't forget to like and share the video please do subscribe for more one piece discussions you can always join our joy fleet discord server or even become a patreon member and I do want to thank all my patreons for help supporting the channel this is joy girl and I'll see you again soon


A Grand Rapids angler landed an unusual trophy when he reeled in a shark jawbone while fishing on the Mississippi River. Joe Piskall caught the jawbone near Grand Rapids over the weekend. He and his son Joey brought it to a DNR office where a fisheries biologist identified it as being from a sand tiger shark. That's a saltwater species that can survive in fresh water. Its origins remain a mystery. Joey Piskall says the jawbone will be cleaned up and hung on the wall. If you've enjoyed this segment of Lakeland News, please consider making a tax-deductible contribution to Lakeland Public Television.


So welcome back everyone welcome to the third and last part of today's lecture Today or have we talked a lot about the databases different databases that are out there? We've talked a little bit about how databases are structured and why they are useful and why they can be useful in our and I want to spend like the last 50 minutes or somewhere around that that we have to Show you how you can get your data in R, right? So we want to talk about biomark and of course if you want to have data in R And this data is available online and then of course you can manually search create your Excel file But this is kind of manual slave labor because you have to just copy paste stuff from from the website into your Excel file and kind of do it yourself and I've did this many many times right sometimes you run into a database where the database itself Does not provide a different way of getting your data Yes, so the data is in their database and the website is presenting you the data But it presents it to you in a way that you cannot easily bulk download it And so the problem here is that it's very error-prone You can download bulk data via FTP, right? And that is usually the Way to go when you are doing bioinformatics is just go to things like ensemble go to the FTP site and say well Give me the GFF file So the gene description file and then had this file will contain all the genes on the genome Of course, this has less chance of creating errors But then the problem becomes is that all of these databases they store their data in a slightly different Format in a slightly different different structure and because they do that You end up with different data formats on your hard drive. So you downloaded the file from ensemble You've downloaded some files from tremble And now you want to start merging this data in in each other and you really can because you have to Load in the data in different ways because the format is different have one will have more columns Sometimes they're they're it's not really obvious what the what the primary key is or what the what the foreign key constraints are and so one of the best ways that I have found to get Biological or biomolecular data into R is to use bio mart and bio mart is one of these tools which I Use all the time So have bio mart can be used to retrieve your data directly into R And that has as an advantage that if the database gets updated or if genes get And new genes get discovered and added to the genome or new proteins get discovered and that when you rerun your analysis Automatically this analysis is updated and that's one of these things that an FTP server doesn't do you download the file at 20th of January 2021 and when you redo your analysis in in March or in April Had then the data on your hard drive hasn't changed So you have to either go to the database again and again download this whole big file with data And that's one of these things where bio mart really really shines it really gives you a very Nice way of keeping your analysis up to date with the data, which is currently in databases So bio mart allows you to query databases from our So bio mart describes itself as a community-driven project to provide unified access to distributed research data to facilitate the scientific Discovery process and it contains most if not all Biologically relevant databases so all big biological databases have a way to be queried via via bio mart Biomart besides being available for are it's also available for things like pearl for python You can query it using soap and rest and you can even query it directly from an XML file So it's a really really good way of of of getting your data in a structured format and this format You can more or less decide yourself as so you never have to reformat things just based on the fact that the database changed Head like you you have with FTP files or when you make the files yourself So there are some core concepts when you're dealing with bio mart So a mart is an information provider So a mart is kind of like a supermarket and the supermarket provides a certain type of information Well, it's not so much a supermarket. It's more like a specialty store, right? So a specialty store Cells for example shovels and another store sells clothing and then you have a third store and that sells books So the mart is the information provider. So for example ensemble is a mart, right? Because ensemble is an information provider an Information provider like a mart Contains many many different data sets or can contain some of them contain only one data set Stuff like ensemble contains many different data sets And so a data set in ensemble is usually structured around an organism. And so you have for example the data set Mouse genes you have cow genes you have human genes, right? So those are different data sets Another the other three terms that we use here are more or less the way that you can query the data So we can ask for certain attributes Yes, so you connect to a mart and a data set and then using the attributes you can get or you can you can tell The information provider. I want to have this columns with this type of information And I'm requesting that Then you have filters filters are things which allow you to filter the data that you retrieve for example a filter car could be the idea of the gene or the name of the gene or The location on the genome has so that is a filter that you can apply and you can apply Different filters and you can combine filters together to kind of filter down your data And then you have things which are called values and those are the things that you are querying for so that just a little bit of terminology before we start diving into kind of how to now use bio mart So for this example, and I'm not going to do this live I was originally planning on doing this live, but the last week ensemble and bio mart are having some serious connection issues So had then it would it could mean that we're sitting here five to ten minutes waiting for data to come back from bio mart So just to prevent that I made slides for you guys And so that we can just go through the slides and and we don't have to wait for queries to finish or If we're unlucky the whole system is down, which is it just happens, right? It's a community project And so it it has some funding, but it's not something like Amazon, which is a ninety nine point nine nine nine percent of time So let's say that we want to investigate mice right could be plants could be Humans but for this example, I took mouse and we want to look on chromosome three Between 15 to 45 megabases right though. That's the interesting region that we just decided that we are interested in And so for example, we want to know what are the important genes at this location and what We want to get all of the genes in this region. We want to get their location We want to get the number of axons that they contain and for example things like the number of functional snips Inside of these genes that we are interested in and so these are very common questions in bioinformatics when you are dealing with Have for example, you did a QTL mapping and you identify that this region of the mouse chromosome is controlling the length of the tail or The size of the ears of the mouse and you now want to go and see well What gene might be responsible for that and are there any variants in this gene region? Which might be causing this phenotype to be different between different mice that we have All right, so in This case we're starting to do are and of course when we create a new script as always you want to make a good header Right, so the header in the file. I wrote it down here. So I'm going to analyze mouse chromosome 3 in this region Hey, it is copyrighted by me. It was first written then and was last modified So this is kind of the standard information that I put in all my scripts, right? And after we've created a good header, we load the biomark library Of course, we have to install it first and but after we've installed it We can just load it and then we have to set a working directory because we have to work at a certain path or at a Certain part of our hard drive because we just don't want to save everything in see user documents And so we set our working directory to where we want to store our data So where we want to write files and where we want to read files although we're not going to read files And because we're going to get our data from biomark into our directly All right, so that's now we need to Connect to a mark right and since we're interested in mouse and we're interested in genes and genomes head then then we Can just connect ensemble. So the first query that we do in our in in our is say well use mart ensemble And then what this will do just like the database provider in our SQL light It will give us back a connection object. So this connection object is a variable Which contains the ability to do queries on and so we can use the list data set function To list all of the data sets which are available on the ensemble Information provider has so the the ensemble mark contains different data sets and had these data sets We want to just list so we can use the list data sets and when we do that we get back something that looks like this, right? So it's a it's a massive list of all the different data sets that ensemble provides and you can see that most of them are Name of the species that you are interested in then an underscore then a gene and then an underscore ensemble So these are the names of the data sets in there and then there's a little bit of a description because hey Who knows what an a Mexicanus is? Well, it's actually a cave fish. I Didn't know that but if you if you're interested in your species then generally, you know the scientific name But if you don't and then you can just look at this this this second column and the second column will contain the information on what kind of what kind of species you are looking at the third column Did you just say gay fish?  I said cave fish as in a fish that lives in a cave I'm sorry. I'm sorry that it no, we're not we're not talking about What's he called again Kanye Kanye West no, we're not talking about Kanye West. We're not saying gay fish Although I'm just said gay fish So If Sorry Now I'm from my up to pole. Yes. So the first is the name of the data set The second one is the more or less description Do you like fish sticks?  I can see how long I stream this I really like the thing but so The the first column is the name of the data set the second column is just a human readable description Which doesn't use the official term and then the third column is the one that that is interesting And this is something that you have to more or less Remember and the thing that you have to remember is of course which version of the database are we using right? So you can see here for example that the gay fish database the cave fish database is p marinas Underscore 7.0, right? So this is if we write a publication and we want to mention on which version of the genome we did this Then we have to specify This this in our publication, right? So how we use bio mar two or three of our genes and we are using the cave fish gene database version 7.0 and of course for every different species you have different versions and they get updated independently of each other All right, so that's the first thing right so have we go through this whole list, which is a long list and we we actually Don't have mouse. Oh, yeah here all the way in the bottom must must close gene ensemble I know it's very small But head that so head contains the version of the mouse genome database that we're using And so let's connect to this database. So again, we we call the use mart function and this time we the first the first parameter is the data provider that we want to collect to and then the second The second term or the second parameter of this function call is now the data set That we want to connect to right and we again just overwrite our mart object And this this will now allow us to query The attributes and the filters which are available for this data set because of course different data sets have different Attributes right every every one of these data sets is kind of a big Excel table with information But some things are available for mouse, which might not be available for cow And some things might be available for fish which might not be available for mouse And so we have to know which attributes we can query and which filters we can use to ask The database right so and as a tip normally there are like thousands of attributes So I generally focus on the first like 20 or 30 or I use the rep command To search for something very specific, but just saying list attributes mart We'll just run down like a massive amount of data on your screen And then you have to scroll up and start looking and so it's generally the things that you want are in the first like 50 to 100 Attributes because those are the most used attributes So if we list the first 10 attributes from the mart right then we can see that we can retrieve things like The ensemble gene ID we can retrieve strings like the gene description The chromosome name the start position the end position Is this gene on the positive strand or the negative strand? On which band is this and this is relatively old and I don't think we talked about this But if if it in the old days when before sequencing become became very very Well cheap, it's not cheap, but it's cheaper than it was right, but but like 15 to 20 years ago locations of genes would be by chromosomal band, so It would say 5 p 7 q 3 and this would describe where on the genome it was and this is this is based on More or less looking through a electron microscope at the chromosomes And then when you see the chromosomes in the electron microscope You see these little Bandings and these bandings are due to higher and lower GC content But they used to originally use the bands to identify positions on of the genome and something like omem They they still mention which band a certain association was or is on And then we can list the filters so the filters are things like chromosome names So we can filter down by chromosome and we can filter down by start and end position We can also filter by the bands of course and we can use things like markers and we can filter based on strand But the thing that of course we want because we wanted to look at mouse genes Chromosome 3 from a certain position to a certain position Number 9 is the filter that we want right because the filter that we want is the chromosomal region At which allows us to specify a chromosomal region saying 1 chromosome 1 double-point from a hundred base pairs to ten thousand base pairs on the negative strand or we can say from chromosome 1 From a hundred thousand base pairs to two hundred thousand base pairs on the positive strand Right so had the attributes are the things that you retrieve the filters are the things that you are going to provide the database And so the filter that we need is obvious the obvious filter that we want to use here's chromosomal region because we're interested in mouse Have we found a QTL so we found an association and now we want to kind of drill down Which genes are there and and which other things can we do with it? So let's define an initial value for our filter So I'm just going to say that okay, so I have to make a decision right Do I want to look at the positive strand or do I want to make look at the negative strand? But in this case I just want to look at the positive strand right and normally you would look at both strands And you can actually drop the the fourth parameter here So you can just say three double point fifteen million double point forty five million and then you close your string But that the last double point one It allows you to say I want only positive or only negative strand But you can just leave it out and then you get all of the genes But for this example, I just said well, let's limit ourselves to genes on the positive strand and I Actually had a discussion with a PhD student recently who said the next time that I'm going to look for a PhD position I'm going to Make sure that the gene that they are working on is on the positive strand because Strandedness in DNA. It just drives you crazy. If your gene is on a negative strand You will mess up the direction because it's just it's much easier when your gene is on the positive strand So in this case even though the gene the causal gene might be on a negative strand We're just limiting ourselves to forward strand And of course we want to try to retrieve all the genes that are there So we we try to retrieve gene IDs And so I define my region and then I've defined my attributes So I just make a little variable and the attributes that I want to retrieve are the ensemble gene ID, right? So just just give me the IDs of the gene in this region Right and now we can execute the query and this is kind of the core of biomark So biomark provides this get PM function, which is get from biomark and so we execute the query using this function So what we say is we say get biomark the attributes that I want to retrieve are my attributes The filter that I'm going to use is chromosomal region and the value that I'm going to provide the database is the my region And then I have to specify in which mark I want to search So I have to specify mart equals mart because my variable that I define the connection variable is called mart, right? Define that before And so the mart is mart just means that use this information provider and this data set So after I execute this query I can of course just ask for the number of rows of the gene IDs because that's the variable that I store it in So I get back a matrix and this matrix has 211 rows, which means that there are 211 genes in the positive direction on the DNA in our Region that we were interested in so in the region chromosome 3 from 15 megabases all the way up to 35 Megabases and of course you could have done this in a different way You could have gone to ensemble you could have loaded all of the mouse genes and then load those into R and do the filtering yourself Have it then of course you're spending a lot of time for something that biomark just provides for you so So of course we can get our attributes, but we can extend our attributes We can add more attributes to get more information because getting the ID is not enough Have we we also want to get some other information for example We might want to get the gene symbol have because normally you don't mention the n smooth G and then the ID You just mentioned the the mouse genome in information system symbol and so just like in humans mouse genes have Names which are more or less They are decided on by a committee and they're linked to humans had to to have a common vocabulary So when we talk about a certain gene everyone knows which genes you mean Had that I'm getting the description of the gene as well I'm getting the chromosome name so because I want to know where the gene is located So I'm getting the chromosome name the start position of the gene and the end position of the gene Yes, so I can just extend my attributes with making a little vector with all the things that I want to retrieve Again, I can use the get biomark function and here I show you the first 10 elements And so what you see is that more or less the first gene located in this region I don't know if the list is sorted by start position probably not probably just Gives it back in a random order, but had the first gene that is there It's called GM 24704 and it is a predicted gene. So it's not a real gene It's just the computer said that there was a gene or there this region looks like a gene So head doesn't have a it's not a proper gene so to speak and it's located on chromosome 3 from here to here You can also see that it gives back micro RNAs and stuff, right? So Why that's I didn't want any micro RNAs or predicted genes I was actually interested in real genes, right real genes which code for proteins have because I Have this association and I really want to find a gene And I don't want to deal with like things like micro RNAs and just predictions, right? I want to make sure that it's real. So, of course, I can now do two things, right? I can Add the biotype as a column. Yes, so I'm just going to say my attributes and then I'm going to say comma Biotype and then it retrieves the biotype because the biotype is either Micro RNA link RNA predicted gene or protein coding gene, right? So a protein coding gene would be the thing that we are looking for So you can add the biotype and do the filtering yourself in R But you don't have to and you can just make your filter more complex and you can filter for the genes biotype And so instead of just retrieving all the genes which includes micro RNA and predicted genes And we can just make our filter a little bit bigger like we did with the attributes and to Tell the database that we are only interested in protein coding genes So here this is a little bit different So we have to define our filter saying that well We are going to now provide you with two pieces of information that we want to filter on The first piece of information that we want to filter on is the chromosomal region and the second piece of information that we want to filter on is the biotype so the type of gene Of course now I have to define the values that I want to search for and here You have to be careful because this now needs to be a list because you can provide multiple regions, right? I don't have to limit myself to one region and I don't have to limit myself to one biotype I could specify three biotypes or two I could say give me all the protein coding genes and micro RNAs but because This can be a vector and this can be a vector if I want to now Define my values then I have to use the list function and because the list function can store in the first element the Vector which contains all of the regions that I'm querying and in the second element of the list So in the second part of the list I can say multiple things like protein coding micro RNA and then these I call my values and then again I just do the query so I'm saying give me the attributes the filter that I want is my filter the value is my values, right? That is the variables that he defined and again query from the same biomark All right, so then the question can be answered. So how many protein coding genes did we now find in this region? Well, we just look at the number of rows of of what we retrieved And it tells me that there are 58 genes on the forward strand on the mouse chromosome 3 from this position to that position And then we can start with with the next part, right? And the next part what we wanted to know well for each gene We want to know how many axons it has and we want to know how many snips are located in the axon So how many snips are there which have a possibility to change the protein? So to change the amino acid All right, so let's retrieve the gene data or let's retrieve the axons first Because we need to know the axon locations before we can query snips and we have the gene start and end position Of course, but of course a gene has introns and axons and we're not generally not interested in in snips Which are located in introns and we're only interested in axons Which are has so parts of the of the protein are parts of the DNA which are coding for the protein So 58 protein coding genes and of course we want to use the computer And so we need to go through the different genes Yes, so we can use the ensemble gene ID now as the filter and then we can query per gene information Right, so we we are going to write a for loop and in each loop. We're going to request all the axons which belong to that gene and How do I do that? Well, I'm just going to say well I now want to retrieve gene specific attributes. I'm calling this gene at root So what do I want to retrieve? Well, I want to retrieve the ensemble gene ID. I want to retrieve the axon ID I want to retrieve the axon the axon start and the axon end position Yeah, of course I don't have to ask for the the axon chromosome because I already know that I'm only working with chromosome 3 But you could add the chromosome to it if you are querying multiple regions at the same time So what do we do? Well, we say just for gene in the gene IDs that we got back, right? So I'm just using the data that I got back from biomarket. So what I'm going to do Well, I'm going to now provide biomarked with the ensemble gene ID So I'm telling it that you will get an ensemble gene ID from me. Which ID am I providing? Well, that's that's this gene value, right? Because we're going through the list one by one And the attributes that I want to retrieve are the gene attributes Yeah, so when I when I run this little piece of code and now I put in a cut here to just So the cut here says well show the gene name and then show how many axons we retrieved So for example for the first gene, so 39335 Have we retrieved 13 axons the next gene has 16 axons and the next gene has eight Right. So this is this is very easy very quick and have Just a very basic for loop And and and we just retrieve the data directly and if I save my code and run it in like two weeks, um, then numbers might change right because Data about genomes is always progressing Yes, so someone might find that this gene actually has not 13 axons, but 16 And so then this number will automatically update. Um, and I don't have to do anything for that all right, so, um For the final question, how many snips are there? Um, so the the snips are actually in another mart So they are not in the gene mart, which is logical. They are in the db snip part Yes, so they are they are they are a part of ensemble, but they are not Um, um, they are not in the same data set. So there's a different data set And they're actually in a different mart. So they're actually in a different data provider. So ensemble As a data provider itself provides you gene and axon and these kinds of information But if you want to connect to snips, um, then the mart that you want to use is called ensemble mart snip Um, and then of course, we want to look at the mouse snips So that is the musculos snip and we just call this snip mart instead of the mart So we don't want to override the old one. So So when we do this how we can say snip mart is used mart ensemble snip mart Take the snips from mouse and then of course we can list the attributes again And here we see that we can get the ref snip id. So the rs id We can get the source we can get the description the name the start the end The strand at which it located the alleles says so is it a ct snip or is the ta snip or a gc snip Um, and then we can also get things like r is this snip validated Has so what information is in the database that supports that this snip is real Like how many people have reported this snip if it's only found by by one group from Uh afghanistan then of course, you're not really going to trust that snip although it might be real but you don't know but if this snip has been reported by 15 different groups from from harvard to oxford to to other like well-known universities like The prestigious humbled university had then of course had then the validated gives you more More certainty than that this is real And of course we we have to list our filters How can we how can we tell the database what we want to retrieve right and here again? We see that we can use the chromosomal region and in this case We would want to use the chromosomal region again because we have for each axon The chromosome the start position and the end position So there's no filter actually here for ensemble gene id because snips are not coupled to genes They are they are located on the genome So we need to use the axon start and end position And so we can query all the snips using the chromosomal region again And then we can filter again based on things like the consequence type. So the consequence type could be Non synonymous right as in changing the amino acid structure But we could also filter based on for example the sift score So the sift score is a prediction of how impactful this The impact will be and and this is left as an exercise for you guys Because i've been been talking already for a long time like two hours and 40 minutes And you have to do something during the exercises as well So the exercises will be using biomark to retrieve Part of the of the snip database and filter down All right Tier white white tier is there a tier? Oh, that's interesting Yeah You see the mood box. It actually went wrong. Why is there sometimes weird? I found a bug. Yeah, you're hacking my mood box. Don't hack my mood box. Don't don't do that Interesting interesting I can I can fix that later on There's no reward. No, there's no reward for finding bugs. Um, well eternal gratitude. That's a reward in itself, right? All right, so today I told you about why we need to use databases.  What features do they have? Just as out as you need to use capital letters And and don't shout poop in my my chat Don't shout poop that like i'm not going to ban you or or put you on a timeout, but um So It has to be a single word you have to do like this All right, so I told you about databases organization features types of databases this some important databases some examples And I told you about bio martini ensembles that belong to that So that's more or less it for today. Um, so are there any questions and actually welcome to the stream, uh, testers ours Welcome to the stream, um, and um Questions I will actually stop the recording now and then we can just use the last like 20 minutes