Difference between revisions of "BCH394P BCH364C 2022"

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(Lectures & Handouts)
(Lectures & Handouts)
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'''Mar 15,17, 2022 - SPRING BREAK'''
 
'''Mar 15,17, 2022 - SPRING BREAK'''
* Don't forget to finish HW3 and turn in the proposal for your course project by "March 22th".
+
* Don't forget to finish HW3 and turn in the proposal for your course project by "March 21st".
  
  
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'''Mar 8, 2022 - Live demo: nanopore sequencing'''
 
'''Mar 8, 2022 - Live demo: nanopore sequencing'''
 +
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 21'''. In past years, we've run into problems with Rosalind timing out before Meme completes although it usually runs eventually, so be warned you may have to try it a couple of times.
 +
* '''Due March 21 by email to the TA+Instructor''' - One to two (full) paragraphs describing your plans for a final project, along with the names of your collaborators. Please limit to no more than 3 per group, please.  It's also fine to do this independently, if you prefer. (Do you have a particular skill/interest/exciting dataset you need help analyzing? There is now a channel on the class slack where you can ask around for partners.) This assignment (planning out your project) will account for 5 points out of your 25 total points for your course project. Here are a few examples of final projects from previous years: [https://sites.google.com/view/bch394pproject/homepage?authuser=1 0] [http://sites.google.com/site/ch391fall08finaloconnellwang/?pageDeleted=%2Fa-monte-carlo-simulation-of-protein-polymerization-in-budding-yeast 1] [http://sites.google.com/site/polyomamirnatargeting/ 2] [http://sites.google.com/site/pathtarandmore/ 3] [http://sites.google.com/site/zlutexas/Home/project-for-ch391l 4] [https://sites.google.com/site/structureandevolutionofaprd4/home 5] [https://sites.google.com/site/modelingpyrosequencingerror/ 6]  [https://sites.google.com/site/bioinformaticsch391lproject/ 7] [https://sites.google.com/site/emilo83/home 8] [https://sites.google.com/site/ch391lchipseq/ 9] [https://sites.google.com/site/arabmybgrant/ 10] [https://sites.google.com/site/biogridviewer/home 11] [https://sites.google.com/a/utexas.edu/immunoglobulin-team/home 12] [https://metabolicnetworkpathways.wordpress.com/ 13] [https://sites.google.com/a/utexas.edu/quantum-tunneling-on-enzymatic-kinetics/home 14] [https://sites.google.com/view/bch394ssy/home 15]<br>
  
  
 
'''Mar 3, 2022 - NGS analysis best practices'''
 
'''Mar 3, 2022 - NGS analysis best practices'''
 +
'''Problem Set 2, due before midnight Mar. 3, 2022''':<br>
 
* Guest speaker: Anna Battenhouse, CBRF
 
* Guest speaker: Anna Battenhouse, CBRF
  
  
 
'''Mar 1, 2022 - Genomes II'''<br>
 
'''Mar 1, 2022 - Genomes II'''<br>
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 24'''. In past years, we've run into problems with Rosalind timing out before Meme completes although it usually runs eventually, so be warned you may have to try it a couple of times.
 
* '''Due March 25 by email to the TA+Instructor''' - One to two (full) paragraphs describing your plans for a final project, along with the names of your collaborators. Please limit to no more than 3 per group, please.  It's also fine to do this independently, if you prefer. (Do you have a particular skill/interest/exciting dataset you need help analyzing? There is now a channel on the class slack where you can ask around for partners.) This assignment (planning out your project) will account for 5 points out of your 25 total points for your course project. Here are a few examples of final projects from previous years: [https://sites.google.com/view/bch394pproject/homepage?authuser=1 0] [http://sites.google.com/site/ch391fall08finaloconnellwang/?pageDeleted=%2Fa-monte-carlo-simulation-of-protein-polymerization-in-budding-yeast 1] [http://sites.google.com/site/polyomamirnatargeting/ 2] [http://sites.google.com/site/pathtarandmore/ 3] [http://sites.google.com/site/zlutexas/Home/project-for-ch391l 4] [https://sites.google.com/site/structureandevolutionofaprd4/home 5] [https://sites.google.com/site/modelingpyrosequencingerror/ 6]  [https://sites.google.com/site/bioinformaticsch391lproject/ 7] [https://sites.google.com/site/emilo83/home 8] [https://sites.google.com/site/ch391lchipseq/ 9] [https://sites.google.com/site/arabmybgrant/ 10] [https://sites.google.com/site/biogridviewer/home 11] [https://sites.google.com/a/utexas.edu/immunoglobulin-team/home 12] [https://metabolicnetworkpathways.wordpress.com/ 13] [https://sites.google.com/a/utexas.edu/quantum-tunneling-on-enzymatic-kinetics/home 14] [https://sites.google.com/view/bch394ssy/home 15]<br>
 
 
* We're finishing up the slides from last time. Note that we give short shrift to read mapping/alignment algorithms, of which there are now [https://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment a very long list]. Here's an interesting discussion by Lior Pachter of the [https://liorpachter.wordpress.com/2015/11/01/what-is-a-read-mapping/ major developments in that field.]
 
* We're finishing up the slides from last time. Note that we give short shrift to read mapping/alignment algorithms, of which there are now [https://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment a very long list]. Here's an interesting discussion by Lior Pachter of the [https://liorpachter.wordpress.com/2015/11/01/what-is-a-read-mapping/ major developments in that field.]
 
* Here is [http://blog.thegrandlocus.com/2016/07/a-tutorial-on-burrows-wheeler-indexing-methods an excellent explanation of how the BWT relates to a suffix tree and enables fast read mapping to a genome]
 
* Here is [http://blog.thegrandlocus.com/2016/07/a-tutorial-on-burrows-wheeler-indexing-methods an excellent explanation of how the BWT relates to a suffix tree and enables fast read mapping to a genome]
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'''Feb 24, 2022 - Genome Assembly'''
 
'''Feb 24, 2022 - Genome Assembly'''
* A gentle reminder that Problem Set 2 is '''due by 11:59PM tonight'''<br>
+
* A gentle reminder that Problem Set 2 is '''due by 11:59PM Mar 3'''<br>
 
* If you would like a few examples of proteins annotated with their transmembrane and soluble regions (according to UniProt) to help troubleshoot your homework, here are some [http://www.marcottelab.org/images/5/5a/Annotated_peptides.txt example yeast protein sequences].
 
* If you would like a few examples of proteins annotated with their transmembrane and soluble regions (according to UniProt) to help troubleshoot your homework, here are some [http://www.marcottelab.org/images/5/5a/Annotated_peptides.txt example yeast protein sequences].
 
* From last time, some definitions of [https://en.wikipedia.org/wiki/Sensitivity_and_specificity sensitivity/specificity] & [https://en.wikipedia.org/wiki/Precision_and_recall precision/recall]. Note that the gene finding community settled early on to a different definition of specificity that corresponds to the precision or PPV in other fields. Other fields define specificity as the true negative rate.
 
* From last time, some definitions of [https://en.wikipedia.org/wiki/Sensitivity_and_specificity sensitivity/specificity] & [https://en.wikipedia.org/wiki/Precision_and_recall precision/recall]. Note that the gene finding community settled early on to a different definition of specificity that corresponds to the precision or PPV in other fields. Other fields define specificity as the true negative rate.
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'''Feb 17, 2022 - Gene finding'''
 
'''Feb 17, 2022 - Gene finding'''
* Science news of the day from one year ago: Kudos to the McLellan lab for solving the coronavirus spike protein 3D structure in 12 days (!), with a paper in [https://www.biorxiv.org/content/10.1101/2020.02.11.944462v1 bioRxiv] and [https://science.sciencemag.org/content/367/6483/1260.abstract Science] in record-breaking time, and cited nearly 4,000 times already in a single year (but what a year!)
+
* Science news of the day from two years ago: Kudos to the McLellan lab for solving the coronavirus spike protein 3D structure in 12 days (!), with a paper in [https://www.biorxiv.org/content/10.1101/2020.02.11.944462v1 bioRxiv] and [https://science.sciencemag.org/content/367/6483/1260.abstract Science] in record-breaking time, and cited over 6,000 times since then (but what a couple of years!)
* [https://research.utexas.edu/cbrs/classes/short-courses/spring-2022/ Short classes at UT] start this week in genome sequencing, proteomics, and bioinformatics
+
 
* We'll finish HMM slides from last time, then start [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C-GeneFinding-Spring2022.pdf today's slides on gene finding]
 
* We'll finish HMM slides from last time, then start [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C-GeneFinding-Spring2022.pdf today's slides on gene finding]
 
* For a few more examples of HMMs in action, here's a [http://www.marcottelab.org/users/BCH394P_364C_2022/MinionHumanGenome.pdf paper on sequencing the human genome by nanopore], which used HMMs in 3-4 different ways for polishing, contig inspection, repeat analysis and 5-methylcytosine detection.
 
* For a few more examples of HMMs in action, here's a [http://www.marcottelab.org/users/BCH394P_364C_2022/MinionHumanGenome.pdf paper on sequencing the human genome by nanopore], which used HMMs in 3-4 different ways for polishing, contig inspection, repeat analysis and 5-methylcytosine detection.
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'''Feb 15, 2022 - HMMs II'''
 
'''Feb 15, 2022 - HMMs II'''
* We're finishing up the slides from last time. I've also [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C_Spring2022_syllabus_updatedforstormdays.pdf updated the syllabus] to account for missing 3 lectures.  Mainly, we'll go all the way to the last scheduled class day (previously, we stopped 1 day early), but we were otherwise able to accommodate most of the missing material in a way that doesn't add any additional load on you all.
 
 
'''Problem Set 2, due before midnight Mar. 3, 2022''':<br>
 
'''Problem Set 2, due before midnight Mar. 3, 2022''':<br>
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C_ProblemSet2_Spring2022.pdf '''Problem Set 2'''].   
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C_ProblemSet2_Spring2022.pdf '''Problem Set 2'''].   
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'''Feb 10, 2022 - Hidden Markov Models'''
 
'''Feb 10, 2022 - Hidden Markov Models'''
 
* Happy Class-Before-Valentine's Day!
 
* Happy Class-Before-Valentine's Day!
* Don't forget: Rosalind Homework #2 (worth 10% of your final course grade) is due '''by 11:59PM February 17'''.
+
* Don't forget: Rosalind Homework #2 (worth 10% of your final course grade) is due '''by 11:59PM February 16'''.
 
* More stats for comp biologists worth checking out:  [https://www.huber.embl.de/msmb/ Modern Statistic for Modern Biology], by Susan Holmes and Wolfgang Huber. It's currently available online and [https://www.amazon.com/Modern-Statistics-Biology-Susan-Holmes/dp/1108705294/ available on dead tree]. (FYI, all code is in R.)
 
* More stats for comp biologists worth checking out:  [https://www.huber.embl.de/msmb/ Modern Statistic for Modern Biology], by Susan Holmes and Wolfgang Huber. It's currently available online and [https://www.amazon.com/Modern-Statistics-Biology-Susan-Holmes/dp/1108705294/ available on dead tree]. (FYI, all code is in R.)
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C-HMMs-Spring2022.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C-HMMs-Spring2022.pdf Today's slides]<br>
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'''Feb 8, 2022 - Biological databases'''
 
'''Feb 8, 2022 - Biological databases'''
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 17'''.
+
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 16'''.
 
* Just a note that we'll be seeing ever more statistics as go on. Here's a [http://www.marcottelab.org/users/BCH394P_364C_2022/StatisticsPrimer.pdf good primer] from [http://www.bio.utexas.edu/research/meyers/LaurenM/index.html Prof. Lauren Ancel Myers] (who leads the [https://covid-19.tacc.utexas.edu/ UT Austin COVID-19 Modeling Consortium]) to refresh/explain basic concepts.
 
* Just a note that we'll be seeing ever more statistics as go on. Here's a [http://www.marcottelab.org/users/BCH394P_364C_2022/StatisticsPrimer.pdf good primer] from [http://www.bio.utexas.edu/research/meyers/LaurenM/index.html Prof. Lauren Ancel Myers] (who leads the [https://covid-19.tacc.utexas.edu/ UT Austin COVID-19 Modeling Consortium]) to refresh/explain basic concepts.
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C-BiologicalDatabases-Spring2022.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C-BiologicalDatabases-Spring2022.pdf Today's slides]<br>
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'''Feb 1, 2022 - Sequence Alignment II'''
 
'''Feb 1, 2022 - Sequence Alignment II'''
 
* We're finishing up the slides from last time.  
 
* We're finishing up the slides from last time.  
* Science news of the day: We're just past exactly a year from publication of the SARS-CoV-2 genome papers [https://doi.org/10.1038/s41586-020-2008-3 1] [https://doi.org/10.1038/s41586-020-2012-7 2]. The release of the genome sequences immediately launched the COVID vaccine design process. [https://www.usatoday.com/in-depth/news/investigations/2021/01/26/moderna-covid-vaccine-science-fast/6555783002/ Here's a great write-up of the story of the vaccine development process], including the McLellan lab's key S2P double proline mutations introduced to stabilize the spike protein.
+
* Science news of the day: We're just past exactly 2 years from publication of the SARS-CoV-2 genome papers [https://doi.org/10.1038/s41586-020-2008-3 1] [https://doi.org/10.1038/s41586-020-2012-7 2]. The release of the genome sequences immediately launched the COVID vaccine design process. [https://www.usatoday.com/in-depth/news/investigations/2021/01/26/moderna-covid-vaccine-science-fast/6555783002/ Here's a great write-up of the story of the vaccine development process], including the McLellan lab's key S2P double proline mutations introduced to stabilize the spike protein.
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/FactAndFictionInAlignment.png Fact and Fiction in Sequence Alignments]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/FactAndFictionInAlignment.png Fact and Fiction in Sequence Alignments]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/NBTPrimer-DynamicProgramming.pdf Dynamic programming primer]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/NBTPrimer-DynamicProgramming.pdf Dynamic programming primer]

Revision as of 15:36, 17 January 2022

BCH394P/BCH364C Systems Biology & Bioinformatics

Course unique #: 54540/54450
Lectures: Tues/Thurs 11 – 12:30 PM on Zoom until Jan 27 (log in to Canvas for the link), then in WEL 2.110
Instructor: Edward Marcotte, marcotte @ utexas.edu

  • Office hours: Wed 11 AM – 12 noon on Zoom

TA: Muyoung Lee, ml49649 @ utexas.edu

  • TA Office hours: Mon 1-2/Fri 11-12 on Zoom

Class Slack channel: ut-sp22-bioinfo.slack.com
Class Canvas site: https://utexas.instructure.com/courses/1325179

Lectures & Handouts

Jan 18, 2022 - Introduction

  • Today's slides
  • We'll be conducting homework using the online environment Rosalind. Go ahead and register on the site, and enroll specifically for BCH394P/364C (Spring 2022) Systems Biology/Bioinformatics using this link. Homework #1 (worth 10% of your final course grade) has already been assigned on Rosalind and is due by 11:59PM January 27.

Here are some online Python resources that you might find useful:

Syllabus & course outline

Course syllabus

An introduction to systems biology and bioinformatics, emphasizing quantitative analysis of high-throughput biological data, and covering typical data, data analysis, and computer algorithms. Topics will include introductory probability and statistics, basics of Python programming, protein and nucleic acid sequence analysis, genome sequencing and assembly, proteomics, synthetic biology, analysis of large-scale gene expression data, data clustering, biological pattern recognition, and gene and protein networks.

Open to graduate students and upper division undergrads (with permission) in natural sciences and engineering. Prerequisites: Basic familiarity with molecular biology, statistics & computing, but realistically, it is expected that students will have extremely varied backgrounds. Undergraduates have additional prerequisites, as listed in the catalog.

Note that this is not a course on practical sequence analysis or using web-based tools. Although we will use a number of these to help illustrate points, the focus of the course will be on learning the underlying algorithms and exploratory data analyses and their applications, esp. in high-throughput biology. By the end of the course, students will know the fundamentals of important algorithms in bioinformatics and systems biology, be able to design and implement computational studies in biology, and have performed an element of original computational biology research.

Most of the lectures will be from research articles and slides posted online, with some material from the...
Optional text (for sequence analysis): Biological sequence analysis, by R. Durbin, S. Eddy, A. Krogh, G. Mitchison (Cambridge University Press),

For biologists rusty on their stats, The Cartoon Guide to Statistics (Gonick/Smith) is very good. A reasonable online resource for beginners is Statistics Done Wrong.

Some online references:
An online bioinformatics course
Online probability & stats texts: #1, #2 (which has some lovely visualizations)

No exams will be given. Grades will be based on online homework (counting 30% of the grade), 3 problem sets (given every 2-3 weeks and counting 15% each towards the final grade) and an independent course project (25% of final grade), which can be collaborative (1-3 students/project). The course project will consist of a research project on a bioinformatics topic chosen by the student (with approval by the instructor) containing an element of independent computational biology research (e.g. calculation, programming, database analysis, etc.). This will be turned in as a link to a web page. The final project is due by midnight, April 25, 2022. The last 3 classes will be spent presenting your projects to each other. (The presentation will account for 5/25 points of the project grade.)

Since we will be in coronavirus lockdown at the start of this semester, this portion of the class will be web-based. We will hold lectures by Zoom during the normally scheduled class time. Log in to the UT Canvas class page for the link, or, if you are auditing, email the TA and he will send the link by return email. Slides will be posted before class on this web site so you can follow along with the material. We'll record the lectures & post the recordings afterward on Canvas so any of you who might be in other timezones or otherwise be unable to make class will have the opportunity to watch them. Note that the recordings will only be available on Canvas and are reserved only for students in this class for educational purposes and are protected under FERPA. The recordings should not be shared outside the class in any form. Violation of this restriction by a student could lead to Student Misconduct proceedings.

Online homework will be assigned and evaluated using the free bioinformatics web resource Rosalind.

All projects and homework will be turned in electronically and time-stamped. No makeup work will be given. Instead, all students have 5 days of free “late time” (for the entire semester, NOT per project, and counting weekends/holidays). For projects turned in late, days will be deducted from the 5 day total (or what remains of it) by the number of days late (in 1 day increments, rounding up, i.e. 10 minutes late = 1 day deducted). Once the full 5 days have been used up, assignments will be penalized 10 percent per day late (rounding up), i.e., a 50 point assignment turned in 1.5 days late would be penalized 20%, or 10 points.

Homework, problem sets, and the project total to a possible 100 points. There will be no curving of grades, nor will grades be rounded up. We’ll use the plus/minus grading system, so: A= 92 and above, A-=90 to 91.99, etc. Just for clarity's sake, here are the cutoffs for the grades: 92% = A, 90% = A- < 92%, 88% = B+ < 90%, 82% = B < 88%, 80% = B- < 82%, 78% = C+ < 80%, 72% = C < 78%, 70% = C- < 72%, 68% = D+ < 70%, 62% = D < 68%, 60% = D- < 62%, F < 60%.

Students are welcome to discuss ideas and problems with each other, but all programs, Rosalind homework, problem sets, and written solutions should be performed independently (except the final collaborative project). Students are expected to follow the UT honor code. Cheating, plagiarism, copying, & reuse of prior homework, projects, or programs from CourseHero, Github, or any other sources are all strictly forbidden and constitute breaches of academic integrity and cause for dismissal with a failing grade, possibly expulsion (UT's academic integrity policy). In particular, no materials used in this class, including, but not limited to, lecture hand-outs, videos, assessments (papers, projects, homework assignments), in-class materials, review sheets, and additional problem sets, may be shared online or with anyone outside of the class unless you have the instructor’s explicit, written permission. Any materials found online (e.g. in CourseHero) that are associated with you, or any suspected unauthorized sharing of materials, will be reported to Student Conduct and Academic Integrity in the Office of the Dean of Students. These reports can result in sanctions, including failure in the course.

The final project web site is due by midnight April 25, 2022.

Finally, between the pandemic and snowpocalypse, the last two years have really pushed our class schedule around a lot, so we’re going to reserve the last class day, May 5, as an emergency flex day. The current plan is for classes to end on May 3 and for there to be NO CLASS on May 5, but if weather, the pandemic, etc, leads to loss of lecture days, we’ll vote as a class to extend class to May 5.