Difference between revisions of "BCH394P BCH364C 2022"

From Marcotte Lab
Jump to: navigation, search
(Lectures & Handouts)
(Lectures & Handouts)
Line 245: Line 245:
 
* 3 mystery genes (for Problem 5): [http://www.marcottelab.org/users/BCH394P_364C_2022/MysteryGene1.txt MysteryGene1], [http://www.marcottelab.org/users/BCH394P_364C_2022/MysteryGene2.txt MysteryGene2], [http://www.marcottelab.org/users/BCH394P_364C_2022/MysteryGene3.txt MysteryGene3]<br>
 
* 3 mystery genes (for Problem 5): [http://www.marcottelab.org/users/BCH394P_364C_2022/MysteryGene1.txt MysteryGene1], [http://www.marcottelab.org/users/BCH394P_364C_2022/MysteryGene2.txt MysteryGene2], [http://www.marcottelab.org/users/BCH394P_364C_2022/MysteryGene3.txt MysteryGene3]<br>
 
* '''*** HEADS UP FOR THE PROBLEM SET ***'''  If you try to use the Python string.count function to count dinucleotides, Python counts '''non-overlapping''' instances, not '''overlapping''' instances.  So, ''AAAA'' is counted as 2, not 3, dinucleotides.  You want '''overlapping''' dinucleotides instead, so will have to try something else, such as the python string[counter:counter+2] command, as explained in the Rosalind homework assignment on strings.
 
* '''*** HEADS UP FOR THE PROBLEM SET ***'''  If you try to use the Python string.count function to count dinucleotides, Python counts '''non-overlapping''' instances, not '''overlapping''' instances.  So, ''AAAA'' is counted as 2, not 3, dinucleotides.  You want '''overlapping''' dinucleotides instead, so will have to try something else, such as the python string[counter:counter+2] command, as explained in the Rosalind homework assignment on strings.
 
+
-->
 +
<!--
 
Announcements:<br>
 
Announcements:<br>
* The UT Center for Biomedical Research Support is offering [https://research.utexas.edu/cbrs/classes/short-courses/spring-2022/ short (1 day) online courses in bioinformatics and biocomputing]  
+
* The UT Center for Biomedical Research Support is offering [https://research.utexas.edu/cbrs/classes/short-courses/spring-2022/ short (1 day) online courses in bioinformatics and biocomputing]
* For those of you who could use more tips on programming, there's a weekly peer-led open coding hour happening every Wednesday on zoom. The zoom link will be posted to Slack & Canvas. It's a very informal setting where you can work and ask questions of more experienced programmers.
+
* For those of you who could use more tips on programming, there's usually (modulo pandemic) a weekly peer-led open coding hour happening every Wednesday on zoom. The zoom link will be posted to Slack & Canvas. It's a very informal setting where you can work and ask questions of more experienced programmers.
 
+
-->
 +
<!--
 
Extra reading, if you're curious:<br>
 
Extra reading, if you're curious:<br>
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/NBTPrimer-BLOSUM.pdf BLOSUM primer]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/NBTPrimer-BLOSUM.pdf BLOSUM primer]
Line 265: Line 267:
 
* REMINDER:  My email inbox is always fairly backlogged (e.g., my median time between non-spam emails was 11 minutes when I measured it some time ago, and it's gotten much worse since then), so please copy the TA on any emails to me to make sure they get taken care of.
 
* REMINDER:  My email inbox is always fairly backlogged (e.g., my median time between non-spam emails was 11 minutes when I measured it some time ago, and it's gotten much worse since then), so please copy the TA on any emails to me to make sure they get taken care of.
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C-PythonPrimer-Spring2022.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C-PythonPrimer-Spring2022.pdf Today's slides]<br>
* [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C_Lecture2-Python_primer-Spring2022.pdf Python primer]
 
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/Ecoli_genome.txt E. coli genome]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/Ecoli_genome.txt E. coli genome]
* [http://astrofrog.github.io/blog/2015/05/09/2015-survey-results/ Python 2 vs 3?]. We'll use Python 3 (the latest version is 3.8), but Rosalind and some materials are only available in Python 2.7, so we'll generally try to be version agnostic for compatibility. Use whichever you wish, but be aware that support for Python 2.7 has officially been stopped. For beginners, the [http://www.practicepython.org/blog/2017/02/09/python2-and-3.html differences are quite minimal] and are [https://www.guru99.com/python-2-vs-python-3.html summarized in a table here].  There's also a great [https://python-future.org/compatible_idioms.html cheat sheet here] for writing code compatible with both versions.
+
* [http://astrofrog.github.io/blog/2015/05/09/2015-survey-results/ Python 2 vs 3?]. We'll use Python 3 (the latest version is 3.8; any recent version will be fine), but Rosalind and some materials are only available in Python 2.7, so we'll generally try to be version agnostic for compatibility. Use whichever you wish, but be aware that support for Python 2.7 has officially been stopped. For beginners, the [http://www.practicepython.org/blog/2017/02/09/python2-and-3.html differences are quite minimal] and are [https://www.guru99.com/python-2-vs-python-3.html summarized in a table here].  There's also a great [https://python-future.org/compatible_idioms.html cheat sheet here] for writing code compatible with both versions.
-->
+
 
<!--
+
 
 
'''Jan 18, 2022 - Introduction'''
 
'''Jan 18, 2022 - Introduction'''
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C-IntroAndRosalind-Spring2022.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH394P_364C_2022/BCH394P-364C-IntroAndRosalind-Spring2022.pdf Today's slides]<br>
Line 278: Line 279:
 
* Khan Academy has archived their older intro videos on Python [https://www.youtube.com/user/khanacademy/search?query=python here]<br>
 
* Khan Academy has archived their older intro videos on Python [https://www.youtube.com/user/khanacademy/search?query=python here]<br>
 
* & very, very useful if you're a complete Python newbie:  Eric Matthes's [https://nostarch.com/pythoncrashcourse2e Python Crash Course book]. He made some GREAT, free [https://github.com/ehmatthes/pcc/releases/download/v1.0.0/beginners_python_cheat_sheet_pcc_all.pdf Python command cheat sheets] to support the book.
 
* & very, very useful if you're a complete Python newbie:  Eric Matthes's [https://nostarch.com/pythoncrashcourse2e Python Crash Course book]. He made some GREAT, free [https://github.com/ehmatthes/pcc/releases/download/v1.0.0/beginners_python_cheat_sheet_pcc_all.pdf Python command cheat sheets] to support the book.
-->
 
  
 
== Syllabus & course outline ==
 
== Syllabus & course outline ==

Revision as of 17:45, 12 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