Difference between revisions of "BCH364C BCH394P 2017"

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(Syllabus & course outline)
(Lectures & Handouts)
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** Links to various applications of SOMs: [http://en.wikipedia.org/wiki/Self-organizing_map 1], [http://www.bentley.edu/centers/sites/www.bentley.edu.centers/files/csbigs/hua.pdf 2], [http://vizier.u-strasbg.fr/kohonen.htx 3], [http://wn.com/Self_Organizing_Maps_Application 4]. You can run SOMs on the [http://www.math.le.ac.uk/people/ag153/homepage/PCA_SOM/PCA_SOM.html following web site]. You can also run SOM clustering with the Open Source Clustering package from problem set 3 with the '-s' option, or GUI option. See [http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/SOM.html#SOM the manual] for details. (FYI, it also supports PCA). If you are not happy with Cluster's SOM function, the statistical package R also provides a package for calculating SOMs (http://cran.r-project.org/web/packages/som/index.html).  
 
** Links to various applications of SOMs: [http://en.wikipedia.org/wiki/Self-organizing_map 1], [http://www.bentley.edu/centers/sites/www.bentley.edu.centers/files/csbigs/hua.pdf 2], [http://vizier.u-strasbg.fr/kohonen.htx 3], [http://wn.com/Self_Organizing_Maps_Application 4]. You can run SOMs on the [http://www.math.le.ac.uk/people/ag153/homepage/PCA_SOM/PCA_SOM.html following web site]. You can also run SOM clustering with the Open Source Clustering package from problem set 3 with the '-s' option, or GUI option. See [http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/SOM.html#SOM the manual] for details. (FYI, it also supports PCA). If you are not happy with Cluster's SOM function, the statistical package R also provides a package for calculating SOMs (http://cran.r-project.org/web/packages/som/index.html).  
  
'''Mar 24, 2016 - Functional Genomics & Data Mining - Clustering I'''
+
'''Mar 23, 2017 - Functional Genomics & Data Mining - Clustering I'''
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_LargeScaleExperiments_Spring2016.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_LargeScaleExperiments_Spring2016.pdf Today's slides]
 
* [http://en.wikipedia.org/wiki/Cluster_analysis Clustering]
 
* [http://en.wikipedia.org/wiki/Cluster_analysis Clustering]
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* [http://www.marcottelab.org/users/BCH339N_2016/yeast_microarraydata2.txt Yeast mRNA expression profiles]
 
* [http://www.marcottelab.org/users/BCH339N_2016/yeast_microarraydata2.txt Yeast mRNA expression profiles]
  
'''Mar 22, 2016 - Motifs'''
+
'''Mar 21, 2017 - Motifs'''
 
* Homework #3 (worth 10% of your final course grade) is due on Rosalind '''by 11:59PM tonight'''.  There were apparently problems with the [http://meme-suite.org/ Meme web server], but it appears to working now.  Also, a [http://alternate.meme-suite.org/ mirror Meme server] has been set up as an alternative.
 
* Homework #3 (worth 10% of your final course grade) is due on Rosalind '''by 11:59PM tonight'''.  There were apparently problems with the [http://meme-suite.org/ Meme web server], but it appears to working now.  Also, a [http://alternate.meme-suite.org/ mirror Meme server] has been set up as an alternative.
 
* Go ahead and start mini-assignment 2, and try to finish it within a week.   
 
* Go ahead and start mini-assignment 2, and try to finish it within a week.   
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* [http://www.marcottelab.org/users/BCH339N_2016/AlignAce.pdf AlignAce]
 
* [http://www.marcottelab.org/users/BCH339N_2016/AlignAce.pdf AlignAce]
  
'''Mar 15-17, 2016 - SPRING BREAK'''
+
'''Mar 14-16, 2017 - SPRING BREAK'''
 
* Finish HW3 and and the first mini-assignment (#1) for your gene project.
 
* Finish HW3 and and the first mini-assignment (#1) for your gene project.
  
'''Mar 10, 2016 - Genomes II'''<br>
+
'''Mar 14, 2017 - Genomes II'''<br>
 
* For those of you interested in doing your homework/research with more experienced coders in the room, there is a weekly Open Coding Hour in the CCBB conference room / collaboratorium (GDC 7.514) each Tuesday from 5-6 PM. [http://ccbb.biosci.utexas.edu/community.html#opencoding].
 
* For those of you interested in doing your homework/research with more experienced coders in the room, there is a weekly Open Coding Hour in the CCBB conference room / collaboratorium (GDC 7.514) each Tuesday from 5-6 PM. [http://ccbb.biosci.utexas.edu/community.html#opencoding].
 
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 22'''.
 
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 22'''.
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* [http://www.marcottelab.org/users/BCH339N_2016/Spellman.pdf Cell cycle data]
 
* [http://www.marcottelab.org/users/BCH339N_2016/Spellman.pdf Cell cycle data]
  
'''Mar 8, 2016 - Genome Assembly'''
+
'''Mar 9, 2017 - Genome Assembly'''
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_GenomeAssembly_Spring2016.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_GenomeAssembly_Spring2016.pdf Today's slides]
 
* 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 tonight'''<br>
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* Here are a few explanations of using the BWT for indexing: [http://blog.avadis-ngs.com/2012/04/elegant-exact-string-match-using-bwt-2/ 1] [http://www.di.unipi.it/~ferragin/Libraries/fmindexV2/index.html 2]
 
* Here are a few explanations of using the BWT for indexing: [http://blog.avadis-ngs.com/2012/04/elegant-exact-string-match-using-bwt-2/ 1] [http://www.di.unipi.it/~ferragin/Libraries/fmindexV2/index.html 2]
  
'''Mar 3, 2016 - Gene finding II'''
+
'''Mar 7, 2017 - Gene finding II'''
 
* We're finishing up the slides from Feb. 25, then moving on into [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_GenomeAssembly_Spring2016.pdf Genome Assembly]
 
* We're finishing up the slides from Feb. 25, then moving on into [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_GenomeAssembly_Spring2016.pdf Genome Assembly]
  
'''Mar 2, 2016''' - TA office hours canceled due to illness, rescheduled tomorrow, Mar 3, 3-4PM
+
'''Mar 2, 2017''' - TA office hours canceled due to illness, rescheduled tomorrow, Mar 3, 3-4PM
  
'''Mar 1, 2016 - Next-generation Sequencing (NGS)'''
+
'''Feb 28, 2017 - Next-generation Sequencing (NGS)'''
 
* Guest speaker: [http://cssb.utexas.edu/members/scott-hunicke-smith/ Dr. Scott Hunicke-Smith], former director of the [https://wikis.utexas.edu/display/GSAF/Home+Page Genome Sequencing and Analysis Facility], and current director of commercial NextGen sequencing diagnostics.
 
* Guest speaker: [http://cssb.utexas.edu/members/scott-hunicke-smith/ Dr. Scott Hunicke-Smith], former director of the [https://wikis.utexas.edu/display/GSAF/Home+Page Genome Sequencing and Analysis Facility], and current director of commercial NextGen sequencing diagnostics.
 
* [http://www.youtube.com/watch?v=77r5p8IBwJk Illumina/Solexa Sequencing (Youtube Video)]
 
* [http://www.youtube.com/watch?v=77r5p8IBwJk Illumina/Solexa Sequencing (Youtube Video)]
 
* [http://www.youtube.com/watch?v=45vNetkGspo Genome Analyzer (Youtube Video)]
 
* [http://www.youtube.com/watch?v=45vNetkGspo Genome Analyzer (Youtube Video)]
  
'''Feb 25, 2015 - Gene finding'''
+
'''Feb 23, 2016 - Gene finding'''
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-GeneFinding-Spring2016.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-GeneFinding-Spring2016.pdf Today's slides]
 
* [http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A61755389-61788517&hgsid=477602291_ccTRfcOcZIQHnMkBKGzbQLBRc6HL The UCSC genome browser]
 
* [http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A61755389-61788517&hgsid=477602291_ccTRfcOcZIQHnMkBKGzbQLBRc6HL The UCSC genome browser]
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* [http://www.marcottelab.org/users/BCH339N_2016/EukGeneAnnotation.pdf Eukaryotic gene finding], [http://www.marcottelab.org/users/BCH339N_2016/GeneMark.hmm.pdf GeneMark.hmm], and [http://www.marcottelab.org/users/BCH339N_2016/BurgeKarlin-main.pdf GENSCAN]
 
* [http://www.marcottelab.org/users/BCH339N_2016/EukGeneAnnotation.pdf Eukaryotic gene finding], [http://www.marcottelab.org/users/BCH339N_2016/GeneMark.hmm.pdf GeneMark.hmm], and [http://www.marcottelab.org/users/BCH339N_2016/BurgeKarlin-main.pdf GENSCAN]
  
'''Feb 23, 2016 - HMMs II'''
+
'''Feb 21, 2017 - HMMs II'''
 
* We're finishing up the slides from Feb. 18.  
 
* We're finishing up the slides from Feb. 18.  
 
Problem Set 2, due before midnight Mar. 8, 2016:<br>
 
Problem Set 2, due before midnight Mar. 8, 2016:<br>
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* You'll need these 3 files: [http://www.marcottelab.org/users/BCH339N_2016/state_sequences State sequences], [http://www.marcottelab.org/users/BCH339N_2016/soluble_sequences Soluble sequences], [http://www.marcottelab.org/users/BCH339N_2016/transmembrane_sequences Transmembrane sequences]
 
* You'll need these 3 files: [http://www.marcottelab.org/users/BCH339N_2016/state_sequences State sequences], [http://www.marcottelab.org/users/BCH339N_2016/soluble_sequences Soluble sequences], [http://www.marcottelab.org/users/BCH339N_2016/transmembrane_sequences Transmembrane sequences]
  
'''Feb 18, 2015 - Hidden Markov Models'''
+
'''Feb 16, 2017 - Hidden Markov Models'''
 
* Don't forget: Homework #2 (worth 10% of your final course grade) is due on Rosalind '''by 11:59PM today'''.
 
* Don't forget: Homework #2 (worth 10% of your final course grade) is due on Rosalind '''by 11:59PM today'''.
 
* It's also time to get started with our major class project.  [http://www.marcottelab.org/users/BCH339N_2016/GeneDossierAssignment.pdf Here] are the instructions.  Go ahead and start mini-assignment 1, and try to finish it within a week. There will be 5 of these from now until the end of the semester. '''By classtime Tuesday, Feb. 23, email the TA the name of the gene you selected and a link to the web page you are creating for your project.'''  (You can find instructions for how to create a google web site at the bottom of this page.)  
 
* It's also time to get started with our major class project.  [http://www.marcottelab.org/users/BCH339N_2016/GeneDossierAssignment.pdf Here] are the instructions.  Go ahead and start mini-assignment 1, and try to finish it within a week. There will be 5 of these from now until the end of the semester. '''By classtime Tuesday, Feb. 23, email the TA the name of the gene you selected and a link to the web page you are creating for your project.'''  (You can find instructions for how to create a google web site at the bottom of this page.)  
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* Care to practice your [http://en.wikipedia.org/wiki/Regular_expression regular expressions]? (In [http://www.tutorialspoint.com/python/python_reg_expressions.htm python?])
 
* Care to practice your [http://en.wikipedia.org/wiki/Regular_expression regular expressions]? (In [http://www.tutorialspoint.com/python/python_reg_expressions.htm python?])
  
'''Feb 16, 2016 - Biological databases'''
+
'''Feb 14, 2017 - Biological databases'''
 
* Just a note that we'll be seeing ever more statistics as go on. Here's a [http://www.marcottelab.org/users/BCH339N_2016/StatisticsPrimer.pdf good primer] from [http://www.bio.utexas.edu/research/meyers/LaurenM/index.html Prof. Lauren Myers] 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/BCH339N_2016/StatisticsPrimer.pdf good primer] from [http://www.bio.utexas.edu/research/meyers/LaurenM/index.html Prof. Lauren Myers] to refresh/explain basic concepts.
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-BiologicalDatabases-Spring2016.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-BiologicalDatabases-Spring2016.pdf Today's slides]<br>
  
'''Feb 11, 2016 - 3D Protein Structure Modeling'''
+
'''Feb 9, 2017 - 3D Protein Structure Modeling'''
 
* Guest speaker: [https://scholar.google.com/citations?hl=en&user=zJ8L0GcAAAAJ&view_op=list_works Dr. Kevin Drew], formerly of New York University and now at the UT Center for Systems and Synthetic Biology
 
* Guest speaker: [https://scholar.google.com/citations?hl=en&user=zJ8L0GcAAAAJ&view_op=list_works Dr. Kevin Drew], formerly of New York University and now at the UT Center for Systems and Synthetic Biology
 
* [http://www.marcottelab.org/users/BCH339N_2016/structbio_lecture_BCH339N_2016.pptx Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2016/structbio_lecture_BCH339N_2016.pptx Today's slides]<br>
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* The [http://www.rcsb.org/pdb/ Protein Data Bank], [http://toolkit.tuebingen.mpg.de/hhpred HHPRED], [https://salilab.org/modeller/ MODELLER], and [http://www.pymol.org/ Pymol]
 
* The [http://www.rcsb.org/pdb/ Protein Data Bank], [http://toolkit.tuebingen.mpg.de/hhpred HHPRED], [https://salilab.org/modeller/ MODELLER], and [http://www.pymol.org/ Pymol]
  
'''Feb 9, 2016 - BLAST'''
+
'''Feb 7, 2017 - BLAST'''
 
* News of the day: [http://www.nature.com/nbt/journal/v34/n2/full/nbt0216-117.html?WT.ec_id=NBT-201602&spMailingID=50636844&spUserID=MTc3MTg5MDc0MQS2&spJobID=860630483&spReportId=ODYwNjMwNDgzS0 ''farmaceuticals'' from transgenic chickens]
 
* News of the day: [http://www.nature.com/nbt/journal/v34/n2/full/nbt0216-117.html?WT.ec_id=NBT-201602&spMailingID=50636844&spUserID=MTc3MTg5MDc0MQS2&spJobID=860630483&spReportId=ODYwNjMwNDgzS0 ''farmaceuticals'' from transgenic chickens]
 
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 18'''.
 
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 18'''.
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* [http://www.marcottelab.org/paper-pdfs/jmb-lgl.pdf The protein homology graph paper]. Just for fun, here's a link to a [http://www.moma.org/interactives/exhibitions/2008/elasticmind/#/211/ stylized version] we exhibited in the engaging [http://www.moma.org/interactives/exhibitions/2008/elasticmind/ Design and the Elastic Mind] show at New York's Museum of Modern Art.  
 
* [http://www.marcottelab.org/paper-pdfs/jmb-lgl.pdf The protein homology graph paper]. Just for fun, here's a link to a [http://www.moma.org/interactives/exhibitions/2008/elasticmind/#/211/ stylized version] we exhibited in the engaging [http://www.moma.org/interactives/exhibitions/2008/elasticmind/ Design and the Elastic Mind] show at New York's Museum of Modern Art.  
  
'''Feb 4, 2016 - Guest lecture: Homologs, orthologs, and evolutionary trees'''  
+
'''Feb 2, 2017 - Guest lecture: Homologs, orthologs, and evolutionary trees'''  
 
* '''*** HEADS UP FOR THE PROBLEM SET ***'''  If you're trying 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're trying 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.
 
* We'll have a guest lecture by [http://bliebeskind.github.io/ Ben Liebeskind], a postdoctoral fellow in the Center for Systems and Synthetic Biology, on decoding the evolutionary relationships among genes.  
 
* We'll have a guest lecture by [http://bliebeskind.github.io/ Ben Liebeskind], a postdoctoral fellow in the Center for Systems and Synthetic Biology, on decoding the evolutionary relationships among genes.  
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* For those of you pre-med or health-focused students, you might be interested in [https://oneheartsource.org/volunteer_programs/health-innovation/ volunteer opportunities in South Africa] ([https://oneheartsource.typeform.com/to/m79wDs?refcode=KMedero%28B%29 application])
 
* For those of you pre-med or health-focused students, you might be interested in [https://oneheartsource.org/volunteer_programs/health-innovation/ volunteer opportunities in South Africa] ([https://oneheartsource.typeform.com/to/m79wDs?refcode=KMedero%28B%29 application])
  
'''Feb 2, 2016 - Sequence Alignment II'''
+
'''Jan 31, 2017 - Sequence Alignment II'''
 
* We're finishing up the slides from Jan. 28.  
 
* We're finishing up the slides from Jan. 28.  
 
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-DynamicProgramming.pdf Dynamic programming primer]
 
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-DynamicProgramming.pdf Dynamic programming primer]
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* A few examples of proteins with internally repetitive sequences: [http://www.pdb.org/pdb/explore/explore.do?structureId=1QYY 1], [http://www.pdb.org/pdb/explore/explore.do?structureId=2BEX 2], [http://www.pdb.org/pdb/explore/explore.do?structureId=1BKV 3]
 
* A few examples of proteins with internally repetitive sequences: [http://www.pdb.org/pdb/explore/explore.do?structureId=1QYY 1], [http://www.pdb.org/pdb/explore/explore.do?structureId=2BEX 2], [http://www.pdb.org/pdb/explore/explore.do?structureId=1BKV 3]
  
'''Jan 28, 2016 - Sequence Alignment I'''
+
'''Jan 26, 2017 - Sequence Alignment I'''
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-Spring2016-SequenceAlignmentI.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-Spring2016-SequenceAlignmentI.pdf Today's slides]<br>
 
Problem Set I, due before midnight Feb. 4, 2016:<br>
 
Problem Set I, due before midnight Feb. 4, 2016:<br>
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* There is a good discussion of the alignment algorithms and different scoring schemes [http://www.bioinformaticsonline.org/ch/ch03/supp-all.html here]
 
* There is a good discussion of the alignment algorithms and different scoring schemes [http://www.bioinformaticsonline.org/ch/ch03/supp-all.html here]
  
'''Jan 26, 2016 - Rosalind help & programming Q/A'''
+
'''Jan 24, 2017 - Rosalind help & programming Q/A'''
 
* The TA office hours have changed to better accommodate conflicts. The new office hours have shifted forward 1 hour, to Wed/Thurs 3-4.
 
* The TA office hours have changed to better accommodate conflicts. The new office hours have shifted forward 1 hour, to Wed/Thurs 3-4.
 
* [http://www.bbc.co.uk/news/science-environment-25576718 One of my favorite news items of the last few last years: China cloning on an 'industrial scale'.] Favorite quote: "If it tastes good you should sequence it..."  BGI is one of the biggest (the biggest?) genome sequencing centers in the world and employs >2,000 bioinformatics researchers.<br>
 
* [http://www.bbc.co.uk/news/science-environment-25576718 One of my favorite news items of the last few last years: China cloning on an 'industrial scale'.] Favorite quote: "If it tastes good you should sequence it..."  BGI is one of the biggest (the biggest?) genome sequencing centers in the world and employs >2,000 bioinformatics researchers.<br>
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* We'll be finishing Python slides from last time.
 
* We'll be finishing Python slides from last time.
  
'''Jan 21, 2016 - Intro to Python'''
+
'''Jan 19, 2017 - Intro to Python'''
 
* News of the day/Science in action:  There's a huge ongoing debate raging about the development of CRISPR genome editing technology, stemming in part from an [https://www.washingtonpost.com/news/wonk/wp/2016/01/13/control-of-crispr-biotechs-most-promising-breakthrough-is-up-for-grabs/ ongoing patent contest] over who made key innovations in characterizing, engineering, and applying CRISPR. You can read some of the debate [http://www.the-scientist.com/?articles.view/articleNo/45072/title/Who-Owns-CRISPR--Cont-d/ here], [http://www.the-scientist.com/?articles.view/articleNo/45119/title/-Heroes-of-CRISPR--Disputed/ here], and [http://genotopia.scienceblog.com/579/landergate-a-link-list/ here], among many other sites.
 
* News of the day/Science in action:  There's a huge ongoing debate raging about the development of CRISPR genome editing technology, stemming in part from an [https://www.washingtonpost.com/news/wonk/wp/2016/01/13/control-of-crispr-biotechs-most-promising-breakthrough-is-up-for-grabs/ ongoing patent contest] over who made key innovations in characterizing, engineering, and applying CRISPR. You can read some of the debate [http://www.the-scientist.com/?articles.view/articleNo/45072/title/Who-Owns-CRISPR--Cont-d/ here], [http://www.the-scientist.com/?articles.view/articleNo/45119/title/-Heroes-of-CRISPR--Disputed/ here], and [http://genotopia.scienceblog.com/579/landergate-a-link-list/ here], among many other sites.
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-PythonPrimer-Spring2016.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-PythonPrimer-Spring2016.pdf Today's slides]<br>
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-->
 
-->
  
'''Jan 19, 2016 - Introduction'''
+
'''Jan 17, 2017 - Introduction'''
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-IntroAndRosalind-Spring2016.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-IntroAndRosalind-Spring2016.pdf Today's slides]<br>
 
* Some warm-up videos to get you started on Python: [http://www.codecademy.com/tracks/python Code Academy's Python coding for beginners]<br>
 
* Some warm-up videos to get you started on Python: [http://www.codecademy.com/tracks/python Code Academy's Python coding for beginners]<br>

Revision as of 20:48, 16 January 2017

BCH364C/BCH394P Systems Biology & Bioinformatics

Course unique #: 55120/55210
Lectures: Tues/Thurs 11 – 12:30 PM in GDC 4.302
Instructor: Edward Marcotte, marcotte @ icmb.utexas.edu

  • Office hours: Wed 11 AM – 12 noon in MBB 3.148BA

TA: Azat Akhmetov, azat @ utexas.edu

  • TA Office hours: Mon/Wed 3 PM - 4 PM in MBB 3.128A Phone: on syllabus

Lectures & Handouts

Jan 17, 2017 - Introduction

  • Today's slides
  • Some warm-up videos to get you started on Python: Code Academy's Python coding for beginners
  • We'll be conducting homework using the online environment Rosalind. Go ahead and register on the site, and enroll specifically for BCH339N 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 28.
  • A useful online resource if you get bogged down: Python for Biologists. (& just a heads-up that some of their instructions for running code relate to a command line environment that's a bit different from the default one you install following the Rosalind instructions. It won't affect the programs, just the way they are run or how you specific where files are located.) However, if you've never programmed before, definitely check this out!!!
  • An oldie (by recent bioinformatics standards) but goodie: Computers are from Mars, Organisms are from Venus

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. UGs 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.

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
Assorted bioinformatics resources on the web: Assorted links
Online probability texts: #1, #2, #3

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). 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 27, 2017. The last two classes will be spent presenting your projects to each other. (The presentation will account for 5% of the project.)

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, and written solutions should be performed independently. Students are expected to follow the UT honor code. Cheating, plagiarism, copying, & reuse of prior homework or programs from CourseHero, Github, or other sources are all strictly forbidden and constitute breaches of academic integrity (UT academic integrity policy) and cause for dismissal with a failing grade.

The final project web site is due by midnight April 27, 2017.