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RobEdwards
Australia
Registrace 20. 10. 2012
ASM 2021 Phage and IBD
Dr. Rob Edwards from Flinders University discusses the expansion of phage that occurs during irritable bowel disease. We don't know why (yet) this happens.
zhlédnutí: 2 168
Video
ABACBS Presentation 2020
zhlédnutí 1,8KPřed 3 lety
Dr. Rob Edwards from Flinders University talks about his phage bioinformatics approaches at the 2020 Australian Bioinformatics and Computational Biology Virtual Conference
Why does paired end sequencing help assembly?
zhlédnutí 39KPřed 5 lety
Dr. Rob Edwards from San Diego State University wonders why paired-end sequencing helps with DNA sequence assembly.
illumina paired end sequencing
zhlédnutí 104KPřed 5 lety
Dr. Rob Edwards from San Diego State University describes how Illumina paired-end sequencing works.
Sanger sequencing
zhlédnutí 10KPřed 5 lety
Dr. Rob Edwards from San Diego State University describes Sanger sequencing - the original and the best!
Pacific Biosciences Sequencing
zhlédnutí 40KPřed 5 lety
Dr. Rob Edwards from San Diego State University describes Pacific Biosciences SMRT single-molecule long read sequencing.
Oxford Nanopore ONT Sequencing
zhlédnutí 37KPřed 5 lety
Dr. Rob Edwards from San Diego State University describes Oxford Nanopore MinION sequencing
454 pyrosequencing
zhlédnutí 26KPřed 5 lety
Dr. Rob Edwards from San Diego State University philosophizes on 454 DNA sequencing.
What does it mean to sequence a genome?
zhlédnutí 8KPřed 5 lety
Dr. Rob Edwards from San Diego State University wonders what it means to sequence a genome! For an overview of genome sequencing, see the course manual: linsalrob.github.io/ComputationalGenomicsManual/GenomeSequencingOverview/
Introduction to Illumina Sequencing
zhlédnutí 38KPřed 5 lety
Dr. Rob Edwards from San Diego State University introduces Illumina DNA sequencing. For an overview of genome sequencing, see the course manual: linsalrob.github.io/ComputationalGenomicsManual/GenomeSequencingOverview/
Ion Torrent Sequencing
zhlédnutí 11KPřed 5 lety
Dr. Rob Edwards from San Diego State University outlines Ion Torrent Sequencing. For an overview of genome sequencing, see the course manual: linsalrob.github.io/ComputationalGenomicsManual/GenomeSequencingOverview/
Genome Peek
zhlédnutí 935Před 5 lety
Dr. Rob Edwards from San Diego State University introduces Genome Peek, a quick way to look at contamination in genomes and to see the composition of metagenomes. Check out the paper at PeerJ: peerj.com/articles/1025/ and the website at edwards.sdsu.edu/GenomePeek/
Introduction to k-mers
zhlédnutí 22KPřed 5 lety
Dr. Rob Edwards from San Diego State University gives an introduction to nucleotide and amino acid k-mers
Introduction on counting k-mers
zhlédnutí 15KPřed 5 lety
Dr. Rob Edwards from San Diego State University provides an introduction on counting k-mers in DNA and protein sequences
Counting k-mers with Bloom filters
zhlédnutí 3,1KPřed 5 lety
Dr. Rob Edwards from San Diego State University describes how we can use the Bloom filter to efficiently weed out k-mers that appear only once.
Can also be used with RNA?
Why are you adding the scores and not multiplyng them? (At 5:00)
Is it used for the same thing than the Needleman-Wunsch algorithm?
How do you control what molecules run through the pore? You may have some contamination.
Hello. How do you avoid growing other things? Or how do you avoid being analyzing other molecules, which will be contaminating our analysis?
uu sigma
It's been amazing, thank you for sharing knowledge to the world professor
i understood rehashing but i wanna know how does the glass board work? is he writing inverted(that couldn't be right?) or is this some editing magic or any concept of physics i dont know???? please if someone knows tell me!!
Am I tripping or it's just the video editing😵💫
I think I found out 3 problems in this lecture, maybe I'm wrong but here they are 1. at 0:20 Dr.Rob mentions we need to set root to black after whenever we do manipulation, but he didn't do this in code i think we need to add root.black = true; after each color flip sequence in correctColor method to make sure root is always black, thus it solves other problems caused by root not being always black eg. node.parent.parent.right.black = true; node.parent.parent.black = false; node.parent.black = true; root.black = true; 2. in checkColor method, we check if node is root and we do correctTree if needed but what's a problem is node can become root after we do correctTree by either leftRightRotate or rightLeftRotate so then when we call checkColor on node.parent it can cause NullPointerException so I think we need to check for that too if ( node.parent != null) return checkColor(node.parent) 3. it's a minor thing, I don't think if statement at 11:20 isn't required bypassed if aunt is null || there is aunt and is black so aunt must be not null && red
i wrote new versions of code public void checkColor(Node<K,V> node) { if (node == root) ---return; if (!node.black && !node.parent.black) ---correctTree(node); if (node.parent != null) ---checkColor(node.parent); }
public void corretTree(Node<K,V> node) { if (node.parent.isLeftChild) // aunt is right child ---if (node.parent.parent.right == null || node.parent.parent.right.black) // either aunt is null or aunt is black ------rotate(node); ------return; // aunt is red ---colorFlip(node); ---return; // aunt is left child if (node.parent.parent.left == null || node.parent.parent.left.black) ---rotate(node); ---return; // aunt is red colorFlip(node); }
public void colorFlip(Node<K,V> node) { // from our entering conditions during checkColor and correctTree, // grandparent and parent and aunt all can't be null node.parent.parent.black = false; node.parent.parent.left.black = true; node.parent.parent.right.black = true; root.black = true; // very crucial to make root back to black if needed }
I don't think checking if (node.parent.right != null) necessary, we hand rightRotate(node.parent.parent) and after that, the node once our grandparent becomes node.parent.right so it can't be null?
as soon as i heard that my private key must be kept a SECRET, i stopped watching any further, becuz then it is just . . . ANOTHER form of "a password", right ? Security through SECRECY . . . just does Not work 😅🤣
Not really. You don't need to memorise the SSH key, you only need to know where you saved it. You don't generate it either.
why 31 ?
As ppl pointed out, node.parent is still point to node, not the tmp we need to make node.parent to point tmp but without parent pointer in Node class, it's hard (need to find node.parent starting from root) let's say we use parent pointer too in the Node class, then the leftRotate method can be like this, hopefully public Node<E> leftRotate(Node<E> node) Node<E> tmp = node.right; if tmp == null // 어쩌다 오른쪽 자식이 없는데 회전을 시도하게되는 경우를 다뤄줍니다 ---return node; node.right = tmp.left; if node.right != null // tmp에게서 null이 아닌 노드를 물려받음, 그 노드의 부모를 변경해줘야 함 ---node.right.parent = node; tmp.left = node; tmp.parent = node.parent; // tmp의 부모를 node의 부모로 변경합니다. null이어도 괜찮습니다 if node.parent != null // node.parent가 null이면 tmp가 root가 되므로 스킵해야합니다 ---if node.parent.left == node // node가 부모의 왼쪽 자식인지 확인, 주소 비교로 가능 ------node.parent.left = tmp; // node.parent가 기존의 node 대신 tmp를 가리킴 ---else ------node.parent.right = tmp; else // node.parent 가 null 이므로 root 입니다, root를 업데이트 해줍니다 ---root = tmp; node.parent = tmp; // 이제 node.parent를 tmp로 업데이트 해줘도 순서상 문제가 없습니다 return tmp; comment i wrote is in korean, sorry too lazy to translate hopefully this is correct and helpful to others watching this amazing course
but why?
Loved the part of blinking lights. Me gusto mucho xD
No need for Putty in Windows, you can "Add / Remove Features" from Settings / Control Panel and add OpenSSH (11MB), then you can access all ssh commands from terminal.
Thank you for another incredible video!😊❤
Thank you, perl is so good, that help me so much! 😊
Thanks for this video. It is really great.
Nice Video!
Still don't know why it's helpful. Thanks anyway
Thank you! I am ADHDer trying to understand all this for my masters in data science and your videos most helpful. Subscribed
2:48 isnt GGTTA the overlap of the sequence?
Great explanation
Very clear so far 👍🏻
How are a bunch of students of a somewhat difficult engineering major freaking out about a mirrored video in the comments
Thanks you sir😊
thank youuuuuuuuuuuuuuuuuu
Nice
My professor: *copies and pastes mathmatical proofs onto powerpoint slide* Dr. Edwards: *actually thinks about how to explain the subject-matter to others*
7:00 150bp from both end will have 100 bp overlap on 200bp . Like total length 12 bp has 6/6 no overlap ,but 12 shorten to 8bp will have 4 overlap of 6/6 both end read
I’m a little bit lost in my analysis: - I am expecting a 70bp amplicon at the end. - When I look at the size of my reads 1 and 2 before reassembling, I have 12 to 131 bp for R1, and 21 to 148 bp for R2. - How, with these highly distributed read lengths, am I supposed to choose the size for reassembling?
What's that you're writing on? Really great to learn
Im in love with you
arigato
Ok but, why? Why the size like a prime number? How does it guarantee less collisions? How it works compare with even size
Easy way to remember omega means slower algo is imagine the symbol is a long worm that has to slowly coil upwards to move- where as O is like sonic speeding in a ball
Čau dědo, miluju tvojí torbu <3
Its called quick sort but its not the quickest
you made this incredibly simple! thank you!!
Your hard work continues to pay off. Thank you for your generosity!
I am not exaggerating when I say that the THUMBNAIL of this video explained this concept more accurately than a 50-minute lecture from my university professor.
thanks
Thank u for ur great explanation, got it from the very first time
That means encryption done with public key can only be decrypted using equivalent private key.Right?
Thank you! Very well explained and easy to understand! 💛
Very informative lecture. Thanks
THIS IS WRONG
thats impressive you are writing with left hand towards left to make us see numbers on the glass from our side. Thats pretty cool & true skill !
I think it's inverted