1. Introduction to Computational and Systems Biology
Вставка
- Опубліковано 19 січ 2015
- MIT 7.91J Foundations of Computational and Systems Biology, Spring 2014
View the complete course: ocw.mit.edu/7-91JS14
Instructor: Christopher Burge, David Gifford, Ernest Fraenkel
In this lecture, Professors Burge, Gifford, and Fraenkel give an historical overview of the field of computational and systems biology, as well as outline the material they plan to cover throughout the semester.
License: Creative Commons BY-NC-SA
More information at ocw.mit.edu/terms
More courses at ocw.mit.edu
Just gonna throw this out there.
You can use two bits to represent A,T, C, G, and if you reuse one value for a variable we'll call K, you can XOR A to T and C to G using K. For example:
Let A = 0 (00b), T = 1 (01b), G = 2 (10b), and C =3 (11b). (The values in '()' are binary representations, not a multiplication operation.)
Let ^ symbolize XOR (as is the case in python).
You will see that A ^ T = 01, and that G ^ C = 01b;
So we let K = 01b
Now,
A ^ K = T
T ^ K = A
G ^ K = C
C ^ K = G
And we have a way to simulate the replication of DNA in a memory efficient way. A single 32 value (a dword in Assembly, sometimes an unsigned int in C), can represent 16 bases, and the complementary strand can be easily calculated in parallel with a singe XOR operation using the hexadecimal value 0x55555555 (01010101....b, 0x5 in hex is 0101b in binary, or two K's next to each other to produce a nibble, a half a byte).
I encourage you to work this out on paper to see for your self. With 64 bit registers and MMX(128 bit) registers, many more values can be packed into each register and operated on at once using various techniques.
underrated comment
Though this will definitely speed the process up, but what if it isn’t about speeding it up!? What if we miss tiny pieces of the puzzle! The pieces which we were actually looking for! Scanning through the present data at a higher rate is efficient, but not necessarily a smart move.
@@SachKol that makes no sense. Packing memory more efficiently doesn´t miss any pieces. It´s the same work, just done faster.
@@technik27 I’ve moved past Computational Biology, seems too far fetched right now.. but maybe I’ll come back to it someday
bro, never in a million years will i be smart enough to think like this. i am going to be useless in this field.
Thanks computational biology and biomedicine , like all field in math and physics . Great lectures and educational contibution.
hi . can someone provide the link to the stats primer?? thanks!
Useful part starts at 46:00
History of computational and systems biology starts 6:15
Similar MIT courses 29:00
wow MIT students have such a prominent advantage for being taught by some of the top scientists in the world, like the Nobel Prize winner Ron Weiss, the top geneticist George Church, etc.
You say that, but occassionally the Nobel prize doesn't help you teach any better. I've seen some really dry MIT Courseware lectures on bioinformatics that sent me to sleep. And then there are Eric Lander lectures, which are just... XD
hello from 3 years in the future . so meh ? they give lectures sure but these classes are like 50-100 kids so really that is over blown tbf. the TAs answer most of the question. they have the advantage of 1 being a recognized name 2 being very very well funded. whats kinda funny though is that go check how much these high brand schools like actually pay these teachers. its not so much....... ul get funded and feel great about urself but end of the day these schools dont pay that much more if u take into account they are in high cost of living areas
Ron do not hold any Nobel prizes
And yet you can watch all the lectures online for free! So this is not an unfair kind of advantage.
Is the Primer on Statistics mentioned during the lecture available for non MIT students?
@@kennynicoll6277 Thank you very much!
thanks
Thank you!
When it comes to the syllabus, is it possible to find an online version. I'm currently studying science at Monash University (Australia) and due to my double major of chemistry and biochemistry/molecular genetics I am unable to do the unit of computational biology (due to prerequisites and time restraints).
I'm keen to learn more if available
knowledge is power. Its nice that you can learn computational biology even though its not a part of the course. How will you use this knowledge? Without a degree in it, will its worth be any less?
See the course on MIT OpenCourseWare for the complete course materials (ocw.mit.edu/7-91JS14). There are readings, lecture slides, projects, assignments available (and the syllabus too). Sorry we did not see your comment earlier.
i am very surprised that we dont talk about the immense influence of the human nervous system it's nature it's localisation it's function we could see easily the analogy with the computer the brain would be the recipient of thousand of logiciels that control each organ of the body by transmission of electrical commands thru the nerves this a new modern paradigm that deserve very serious consideration time for a quantum breakthrough !!!!!it would get us out of status quo research !!! imagine the consequences !!!!
+MIT OpenCourseWare The link is dead! Help with the correct one! PLZ
+Hossein Izadi Rad Sorry, we had a problem with our redirects! The link is working now.
39:00 Don’t share code… I felt some nostalgia hearing this sentence in the era of ChatGPT 😢
Hi, are you trying to learn computational biology? What's the goal?
With so many different courses being taught by the same lectures, where can you access the additional content? Will I come across the A.I. lectures naturally in this series, or do I need to look for it elsewhere?
if ur looking for ml they have 2 different courses covering ml in genomics and deep learning specifically. i dont know if they are any good but they are easy to find on the MIT OCW website. I plan on checking them.
@@thryce82 I cannot find the courses pertaining to ML and Deep Learning applied to genomics on the OCW website.
Is it possible that you could link them?
what are the prereqs for this? I am masters in computer science, but I have no idea about biology, hell I don't even remember what a protein is. How much biology is needed and what should I learn before learning this. Thanks
There are different prerequisites for the various versions of the course. There is a TABLE of prerequisites in the Syllabus, see the course on MIT OpenCourseWare at: ocw.mit.edu/7-91JS14. o.O
Prof. sounds like Jesse Eisenberg.
Great coverage but better illustrations and more conceptual material would serve this course better.
Is the recitation with additional content recorded and available?
Sorry, there are no recitation videos but there are recitation slides. See the course on MIT OpenCourseWare for the materials at ocw.mit.edu/7-91JS14.
Hi, I am BSc in computer science. I am good at C++.Should I study Computational and Systems Biology?
what a terrible speaker