Difference between revisions of "BCH339N 2016"

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* '''Office hours:'''  Mon 4 PM – 5 PM in MBB 3.148BA<br>
 
* '''Office hours:'''  Mon 4 PM – 5 PM in MBB 3.148BA<br>
 
'''TA:''' Claire McWhite, claire.mcwhite@utexas.edu<br>
 
'''TA:''' Claire McWhite, claire.mcwhite@utexas.edu<br>
*'''TA Office hours:''' Wed/Thurs 3 PM - 4 PM in MBB 3.128A '''Phone:''' listed on the syllabus<br>
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*'''TA Office hours:''' Wed/Thurs 4 PM - 5 PM in MBB 3.128A '''Phone:''' listed on the syllabus<br>
  
 
== Lectures & Handouts ==
 
== Lectures & Handouts ==
'''May 5 - 7, 2015 - Gene Pages'''
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'''Apr 28 - May 5, 2016 - Gene Presentations'''
 
* Note: There are some great [http://ccbb.biosci.utexas.edu/summerschool.html short summer courses in computational biology] being offered at UT. Of particular note, introductions to [http://ccbb.biosci.utexas.edu/summerschool.html#corengs core NextGen sequencing tools] and [http://ccbb.biosci.utexas.edu/summerschool.html#rosetta protein modeling using Rosetta]
 
* Note: There are some great [http://ccbb.biosci.utexas.edu/summerschool.html short summer courses in computational biology] being offered at UT. Of particular note, introductions to [http://ccbb.biosci.utexas.edu/summerschool.html#corengs core NextGen sequencing tools] and [http://ccbb.biosci.utexas.edu/summerschool.html#rosetta protein modeling using Rosetta]
  
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[http://www.nationalgeographic.com/deextinction De-extinction I], [http://science.kqed.org/quest/video/reawakening-extinct-species/ II], and [http://www.popsci.com/woolly-mammoth-dna-brought-life-elephant-cells III]
 
[http://www.nationalgeographic.com/deextinction De-extinction I], [http://science.kqed.org/quest/video/reawakening-extinct-species/ II], and [http://www.popsci.com/woolly-mammoth-dna-brought-life-elephant-cells III]
  
'''April 28, 2015 - Phenologs'''
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'''April 26, 2016 - Phenologs'''
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_Phenologs_Spring2015.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_Phenologs_Spring2015.pdf Today's slides]
 
* [http://www.marcottelab.org/paper-pdfs/PNAS_Phenologs_2010.pdf Phenologs] and the [http://www.marcottelab.org/paper-pdfs/PLoSBiology_TBZ_2012.pdf drug discovery story] we'll discuss in class
 
* [http://www.marcottelab.org/paper-pdfs/PNAS_Phenologs_2010.pdf Phenologs] and the [http://www.marcottelab.org/paper-pdfs/PLoSBiology_TBZ_2012.pdf drug discovery story] we'll discuss in class
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* [http://www.marcottelab.org/users/BCH339N_2016/Sonnhammer2002TiG.pdf All your ortholog definition questions answered!]
 
* [http://www.marcottelab.org/users/BCH339N_2016/Sonnhammer2002TiG.pdf All your ortholog definition questions answered!]
  
'''April 23, 2015 - Networks II'''
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'''April 21, 2016 - Networks II'''
 
* We're finishing up the slides from Apr. 21.  
 
* We're finishing up the slides from Apr. 21.  
 
* Worth noting: [http://ccbb.biosci.utexas.edu/summerschool.html UT Summer school for big data in biology]
 
* Worth noting: [http://ccbb.biosci.utexas.edu/summerschool.html UT Summer school for big data in biology]
  
'''April 21, 2015 - Networks'''
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'''April 19, 2016 - Networks'''
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_Networks_Spring2015.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_Networks_Spring2015.pdf Today's slides]
 
* Metabolic networks: [http://ca.expasy.org/cgi-bin/show_thumbnails.pl The wall chart] (it's interactive, e.g. here's [http://web.expasy.org/cgi-bin/pathways/show_image?E5&left enolase]), the current state of the [http://www.marcottelab.org/users/BCH339N_2016/HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network], and older but still relevant review of [http://www.marcottelab.org/users/BCH339N_2016/ChIP-chipReview.pdf transcriptional networks] (with the current record holder in this regard held by [http://www.genome.gov/10005107 ENCODE]), and an early review of [http://www.marcottelab.org/users/BCH339N_2016/vonmering.pdf protein interaction extent and quality] whose lessons still hold.
 
* Metabolic networks: [http://ca.expasy.org/cgi-bin/show_thumbnails.pl The wall chart] (it's interactive, e.g. here's [http://web.expasy.org/cgi-bin/pathways/show_image?E5&left enolase]), the current state of the [http://www.marcottelab.org/users/BCH339N_2016/HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network], and older but still relevant review of [http://www.marcottelab.org/users/BCH339N_2016/ChIP-chipReview.pdf transcriptional networks] (with the current record holder in this regard held by [http://www.genome.gov/10005107 ENCODE]), and an early review of [http://www.marcottelab.org/users/BCH339N_2016/vonmering.pdf protein interaction extent and quality] whose lessons still hold.
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* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]
 
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]
  
'''Apr 16, 2015 - Genome Engineering'''
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'''Apr 14, 2016 - Genome Engineering'''
 
* Guest speaker: [http://cssb.utexas.edu/fellows/christopher-yellman/ Dr. Chris Yellman]
 
* Guest speaker: [http://cssb.utexas.edu/fellows/christopher-yellman/ Dr. Chris Yellman]
 
<!--* [http://www.marcottelab.org/users/BCH339N_2016/synthetic-biology-genome-engineering-2-2014.ppt Today's slides]-->
 
<!--* [http://www.marcottelab.org/users/BCH339N_2016/synthetic-biology-genome-engineering-2-2014.ppt Today's slides]-->
  
'''Apr 14, 2015 - Principal Component Analysis (& the curious case of European genotypes)'''
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'''Apr 12, 2016 - Principal Component Analysis (& the curious case of European genotypes)'''
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_PCA_Spring2015.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_PCA_Spring2015.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2016/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
 
* [http://www.marcottelab.org/users/BCH339N_2016/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
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* Python code for [http://sebastianraschka.com/Articles/2015_pca_in_3_steps.html performing PCA yourself]
 
* Python code for [http://sebastianraschka.com/Articles/2015_pca_in_3_steps.html performing PCA yourself]
  
'''Apr 9, 2015 - Classifiers I'''
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'''Apr 7, 2016 - Classifiers I'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_Classifiers_Spring2015.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Classifiers_Spring2016.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2016/AMLALLclassification.pdf Classifying leukemias]
 
* [http://www.marcottelab.org/users/BCH339N_2016/AMLALLclassification.pdf Classifying leukemias]
 
* For those of you using classifiers for your projects, here's the best open software for do-it-yourself classifiers and data mining: [http://www.cs.waikato.ac.nz/ml/weka/ Weka]
 
* For those of you using classifiers for your projects, here's the best open software for do-it-yourself classifiers and data mining: [http://www.cs.waikato.ac.nz/ml/weka/ Weka]
  
'''Apr 7, 2015 - Clustering II
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'''Apr 5, 2016 - Clustering II
* We're finishing up the slides from Apr2.<br>
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* We're finishing up the slides from Mar31.<br>
 
* [http://www.marcottelab.org/users/BCH339N_2016/FuzzyK-Means.pdf Fuzzy k-means]
 
* [http://www.marcottelab.org/users/BCH339N_2016/FuzzyK-Means.pdf Fuzzy k-means]
 
* [http://www.marcottelab.org/users/BCH339N_2016/SOM-geneexpression.pdf SOM gene expression]
 
* [http://www.marcottelab.org/users/BCH339N_2016/SOM-geneexpression.pdf SOM gene expression]
 
** 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 (an alternative to Eisen's Cluster) with '-s' option, or GUI option. See http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/SOM.html#SOM for detail. (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 (an alternative to Eisen's Cluster) with '-s' option, or GUI option. See http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/SOM.html#SOM for detail. (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).  
  
'''Apr 2, 2015 - Functional Genomics & Data Mining - Clustering I'''
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'''Mar 31, 2016 - Functional Genomics & Data Mining - Clustering I'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_LargeScaleExperiments_Spring2015.pdf Today's slides]
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* [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]
 
* [http://www.marcottelab.org/users/BCH339N_2016/nature_review_2000.pdf Review of phylogenetic profiles]
 
* [http://www.marcottelab.org/users/BCH339N_2016/nature_review_2000.pdf Review of phylogenetic profiles]
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* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-MicroarrayClustering.pdf Primer on clustering]
 
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-MicroarrayClustering.pdf Primer on clustering]
 
* [http://www.marcottelab.org/users/BCH339N_2016/K-means-Example.ppt K-means example (.ppt)]
 
* [http://www.marcottelab.org/users/BCH339N_2016/K-means-Example.ppt K-means example (.ppt)]
[http://www.marcottelab.org/users/BCH339N_2016/ProblemSet3_2015.pdf '''Problem Set 3], due before midnight Apr. 14, 2015'''.  You will need the following software and datasets:<br>
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[http://www.marcottelab.org/users/BCH339N_2016/ProblemSet3_2016.pdf '''Problem Set 3], due before midnight Apr. 12, 2016'''.  You will need the following software and datasets:<br>
 
* The clustering and treeview software is available [http://rana.lbl.gov/EisenSoftware.htm here]. Previous students have said the Mac/Linux versions of the tree viewing program can be a bit buggy; however, the Windows version (TreeView) seems to be fine.<br>  
 
* The clustering and treeview software is available [http://rana.lbl.gov/EisenSoftware.htm here]. Previous students have said the Mac/Linux versions of the tree viewing program can be a bit buggy; however, the Windows version (TreeView) seems to be fine.<br>  
 
* [http://www.marcottelab.org/users/BCH339N_2016/yeast_aaseqs Yeast protein sequences]
 
* [http://www.marcottelab.org/users/BCH339N_2016/yeast_aaseqs Yeast protein sequences]
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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 31, 2015 - Motifs'''
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'''Mar 29, 2016 - Motifs'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_Motifs_Spring2015.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Motifs_Spring2016.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2016/nbt0406-423-primer-whataremotifs.pdf NBT Primer - What are motifs?]
 
* [http://www.marcottelab.org/users/BCH339N_2016/nbt0406-423-primer-whataremotifs.pdf NBT Primer - What are motifs?]
 
* [http://www.marcottelab.org/users/BCH339N_2016/nbt0806-959-primer-howdoesmotifdiscoverywork.pdf NBT Primer - How does motif discovery work?]
 
* [http://www.marcottelab.org/users/BCH339N_2016/nbt0806-959-primer-howdoesmotifdiscoverywork.pdf NBT Primer - How does motif discovery work?]
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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 26, 2015 - Mapping protein complexes'''
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'''Mar 24, 2016 - Mapping protein complexes'''
 
* Guest speaker: [http://www.blakeb.org/ Blake Borgeson]
 
* Guest speaker: [http://www.blakeb.org/ Blake Borgeson]
  
'''Mar 24, 2015 - Mass spectrometry proteomics'''
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'''Mar 22, 2016 - Mass spectrometry proteomics'''
 
* Welcome back from Spring Break. Apparently, we had some down time on Rosalind, so I'm extending the HW3 deadline to '''11:59PM March 26'''...
 
* Welcome back from Spring Break. Apparently, we had some down time on Rosalind, so I'm extending the HW3 deadline to '''11:59PM March 26'''...
 
* Guest speaker: [http://www.researchgate.net/profile/Daniel_Boutz/ Dr. Daniel Boutz]
 
* Guest speaker: [http://www.researchgate.net/profile/Daniel_Boutz/ Dr. Daniel Boutz]
  
'''Mar 17-19, 2015 - SPRING BREAK'''
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'''Mar 15-17, 2016 - SPRING BREAK'''
  
'''Mar 12, 2015 - Genomes II, Gene Expression'''<br>
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'''Mar 10, 2016 - Genomes II, Gene Expression'''<br>
 
* For those of you interested in doing your homework/research with more experienced coders in the room, there will be a weekly Open Coding Hour in the CCBB conference room / collaboratorium (GDC 7.514) each Tuesday ?from 5-7 PM.  Scott Hunicke-Smith will begin each Open Coding Hour with 10 minutes of computing tricks. [https://groups.google.com/forum/#!forum/utbiocomputing Accompanying google group in-house programming question and answer forum].
 
* For those of you interested in doing your homework/research with more experienced coders in the room, there will be a weekly Open Coding Hour in the CCBB conference room / collaboratorium (GDC 7.514) each Tuesday ?from 5-7 PM.  Scott Hunicke-Smith will begin each Open Coding Hour with 10 minutes of computing tricks. [https://groups.google.com/forum/#!forum/utbiocomputing Accompanying google group in-house programming question and answer forum].
 
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 24'''.
 
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 24'''.
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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 10, 2015 - Genome Assembly'''
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'''Mar 8, 2016 - Genome Assembly'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_GenomeAssembly_Spring2015.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_GenomeAssembly_Spring2016.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2016/DeBruijnPrimer.pdf DeBruijn Primer] and [http://www.marcottelab.org/users/BCH339N_2016/DeBruijnSupplement.pdf Supplement]
 
* [http://www.marcottelab.org/users/BCH339N_2016/DeBruijnPrimer.pdf DeBruijn Primer] and [http://www.marcottelab.org/users/BCH339N_2016/DeBruijnSupplement.pdf Supplement]
 
* 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] [http://www.cbcb.umd.edu/~langmead/UMD_Bioscience_Nov2008.ppt 3]
 
* 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] [http://www.cbcb.umd.edu/~langmead/UMD_Bioscience_Nov2008.ppt 3]
  
'''Mar 5, 2015 - *** ICE STORM 2015***, UT classes cancelled'''
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'''Mar 3, 2016 - *** ICE STORM 2015***, UT classes cancelled'''
  
'''Mar 3, 2015 - Gene finding II'''
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'''Mar 1, 2016 - Gene finding II'''
* We're finishing up the slides from Feb. 26, then moving on into [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_GenomeAssembly_Spring2015.pdf Genome Assembly]
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* 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]
* '''Due March 12 by email''' - One to two (full) paragraphs describing your plans for a final project, along with the names of your collaborators.  This assignment 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: [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]<br>
+
  
'''Feb 26, 2015 - Gene finding'''
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'''Feb 25, 2015 - Gene finding'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L-GeneFinding-Spring2015.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-GeneFinding-Spring2016.pdf Today's slides]
 
* [http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr21%3A33031597-33041570 The UCSC genome browser]
 
* [http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr21%3A33031597-33041570 The UCSC genome browser]
 
Reading:<br>
 
Reading:<br>
 
* [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 24, 2015 - HMMs II'''
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'''Feb 23, 2016 - HMMs II'''
* We're finishing up the slides from Feb. 19.  
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* We're finishing up the slides from Feb. 18.  
Problem Set 2, due before midnight Mar. 10, 2015:<br>
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Problem Set 2, due before midnight Mar. 8, 2016:<br>
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_ProblemSet2_Spring2015.pdf '''Problem Set 2'''].   
+
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_ProblemSet2_Spring2016.pdf '''Problem Set 2'''].   
 
* 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 19, 2015 - Hidden Markov Models'''
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'''Feb 18, 2015 - Hidden Markov Models'''
* re: our discussion of databases, another view of the remarkable growth of data, e.g. [http://www.ebi.ac.uk/uniprot/TrEMBLstats/ UniProt]
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* Another view of the remarkable growth of data, e.g. [http://www.ebi.ac.uk/uniprot/TrEMBLstats/ UniProt]
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L-HMMs-Spring2015.pdf Today's slides]<br>
+
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-HMMs-Spring2016.pdf Today's slides]<br>
 
Reading:<br>
 
Reading:<br>
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-HMMs.pdf HMM primer] and [http://www.marcottelab.org/users/BIO337_2014/NBTPrimer-Bayes.pdf Bayesian statistics primer], [http://en.wikipedia.org/wiki/Bayes'_theorem Wiki Bayes]
+
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-HMMs.pdf HMM primer] and [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-Bayes.pdf Bayesian statistics primer], [http://en.wikipedia.org/wiki/Bayes'_theorem Wiki Bayes]
 
* 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 17, 2015 - Next-generation Sequencing (NGS)'''
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'''Feb 16, 2016 - Next-generation Sequencing (NGS)'''
* Guest speaker: [http://cssb.utexas.edu/members/scott-hunicke-smith/ Dr. Scott Hunicke-Smith], director of the [https://wikis.utexas.edu/display/GSAF/Home+Page Genome Sequencing and Analysis Facility].
+
* 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 NextGen sequencing diagnostics at [].
 
* [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 12, 2015 - 3D Protein Structure Modeling'''
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'''Feb 11, 2016 - 3D Protein Structure Modeling'''
* Congratulations to this year's [http://en.wikipedia.org/wiki/Dan_David_Prize Dan David Prize] winners, awarded in bioinformatics (!) to [http://www.jpost.com/Israel-News/Dan-David-Foundation-to-award-three-prizes-of-1-million-to-six-world-renowned-laureates-390602 David Haussler, Cyrus Chothia, and Michael Waterman] !!!
+
 
* Guest speaker: [http://bonneaulab.bio.nyu.edu/people.html#kevin Dr. Kevin Drew], formerly of New York University and now at the UT Center for Systems and Synthetic Biology
 
* Guest speaker: [http://bonneaulab.bio.nyu.edu/people.html#kevin 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_BCH391L_20150212.ppt Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2016/structbio_lecture_BCH391L_20150212.ppt Today's slides]<br>
Line 171: Line 168:
 
* 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 10, 2015 - Biological databases'''
+
'''Feb 9, 2016 - Biological databases'''
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 19'''.
+
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 18'''.
 
* 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/BCH364C-391L-BiologicalDatabases-Spring2015.pdf Today's slides]<br>
+
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-BiologicalDatabases-Spring2016.pdf Today's slides]<br>
  
'''Feb 5, 2015 - Guest lecture: Intro to Appsoma'''   
+
'''Feb 4, 2016 - Guest lecture: Homologs, orthologs, and evolutionary trees'''   
* We'll have a guest lecture by [http://www.mine-control.com/zack/ Zack Simpson], a Fellow of the [http://web.cssb.utexas.edu/ UT Center for Systems and Synthetic Biology]. For the curious, ''Science'' magazine wrote a nice feature on Zack several years ago ([http://www.marcottelab.org/users/BCH339N_2016/Science_Zack.pdf posted here]).  Zack co-founded the bioinformatics startup company [http://www.traitwise.com/ Traitwise] (full disclosure: I'm on their scientific advisory board) and is the lead developer of [https://appsoma.com/home Appsoma], a web-based scientific cloud computing platform that has a number of enhancements (and dedicated computer clusters) specifically for UT students.
+
* We'll have a guest lecture on evolutionary relationships among genes.  
  
'''Feb 3, 2015 - BLAST'''
+
'''Feb 2, 2016 - BLAST'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L-BLAST-Spring2015.pdf Our slides today] are modified from a paper on [http://dx.doi.org/10.1371/journal.pbio.1001014 Teaching BLAST] by Cheryl Kerfeld & Kathleen Scott.
+
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-BLAST-Spring2016.pdf Our slides today] are modified from a paper on [http://dx.doi.org/10.1371/journal.pbio.1001014 Teaching BLAST] by Cheryl Kerfeld & Kathleen Scott.
 
* [http://www.marcottelab.org/users/BCH339N_2016/BLAST.pdf The original BLAST paper]
 
* [http://www.marcottelab.org/users/BCH339N_2016/BLAST.pdf The original BLAST paper]
 
* [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.  
 
* Repeats in the human genome, tallied [http://www.biochem.arizona.edu/classes/bioc471/pages/Lecture7/a6GenomeRepeats.jpg here]
 
* Repeats in the human genome, tallied [http://www.biochem.arizona.edu/classes/bioc471/pages/Lecture7/a6GenomeRepeats.jpg here]
  
'''Jan 29, 2015 - Sequence Alignment II'''
+
'''Jan 28, 2016 - Sequence Alignment II'''
* We're finishing up the slides from Jan. 27.  Note that I added a few more slides.
+
* We're finishing up the slides from Jan. 26.  Note that I added a few more slides.
 
* [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]
 
* [http://www.marcottelab.org/users/BCH339N_2016/GALPAS.xls An example of dynamic programming using Excel], created by [http://www.thepmcf.ca/News-Media/Blog/The-PMCF-Blog/January-2014/Meet-Michael-Hoffman Michael Hoffman] (a former UT undergraduate who took the prior incarnation of this class)
 
* [http://www.marcottelab.org/users/BCH339N_2016/GALPAS.xls An example of dynamic programming using Excel], created by [http://www.thepmcf.ca/News-Media/Blog/The-PMCF-Blog/January-2014/Meet-Michael-Hoffman Michael Hoffman] (a former UT undergraduate who took the prior incarnation of this class)
 
* 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 27, 2015 - Sequence Alignment I'''
+
'''Jan 26, 2016 - Sequence Alignment I'''
* [http://www.bbc.co.uk/news/science-environment-25576718 One of my favorite news items last year: 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>
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L-Spring2015-SequenceAlignmentI.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L-Spring2015-SequenceAlignmentI.pdf Today's slides]<br>
 
Problem Set I, due before midnight Feb. 5, 2015:<br>
 
Problem Set I, due before midnight Feb. 5, 2015:<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 22, 2015 - Intro to Python'''
+
'''Jan 21, 2016 - Intro to Python'''
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L-PythonPrimer-Spring2015.pptx Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L-PythonPrimer-Spring2015.pptx Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_Lecture2-Python_primer-Spring2015.pdf Python primer]
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_Lecture2-Python_primer-Spring2015.pdf Python primer]
 
* [http://www.marcottelab.org/users/BCH339N_2016/Ecoli_genome.txt E. coli genome]
 
* [http://www.marcottelab.org/users/BCH339N_2016/Ecoli_genome.txt E. coli genome]
  
'''Jan 20, 2015 - Introduction'''
+
'''Jan 19, 2016 - Introduction'''
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-IntroAndRosalind-Spring2016.pptx Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-IntroAndRosalind-Spring2016.pptx 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>
* We'll be conducting homework using the online environment [http://rosalind.info/faq/ Rosalind].  Go ahead and register on the site, and enroll specifically for BCH339N using [http://rosalind.info/classes/enroll/c5be9c4629/ ''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'''.
+
* We'll be conducting homework using the online environment [http://rosalind.info/faq/ Rosalind].  Go ahead and register on the site, and enroll specifically for BCH339N using [http://rosalind.info/classes/enroll/c5be9c4629/ ''this link''].  Homework #1 (worth 10% of your final course grade) has already been assigned on Rosalind and is '''due by 11:59PM January 26'''.
 
* A useful online resource if you get bogged down: [http://pythonforbiologists.com/index.php/introduction-to-python-for-biologists/ 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!!!'''<br>
 
* A useful online resource if you get bogged down: [http://pythonforbiologists.com/index.php/introduction-to-python-for-biologists/ 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!!!'''<br>
 
* An oldie (by recent bioinformatics standards) but goodie:  [http://www.marcottelab.org/users/BCH339N_2016/ComputersMarsOrganismsVenus.pdf Computers are from Mars, Organisms are from Venus]
 
* An oldie (by recent bioinformatics standards) but goodie:  [http://www.marcottelab.org/users/BCH339N_2016/ComputersMarsOrganismsVenus.pdf Computers are from Mars, Organisms are from Venus]
Line 218: Line 215:
 
== Syllabus & course outline ==
 
== Syllabus & course outline ==
  
[http://www.marcottelab.org/users/BCH339N_2016/BCH364C-391L_2015_syllabus.pdf Course syllabus]
+
[http://www.marcottelab.org/users/BCH339N_2016/BCH339N_2016_syllabus.pdf 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.<br>
 
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.<br>
Line 249: Line 246:
 
Students are welcome to discuss ideas and problems with each other, but '''all programs, Rosalind homework, and written solutions should be performed independently''' (except the final collaborative project).<br>
 
Students are welcome to discuss ideas and problems with each other, but '''all programs, Rosalind homework, and written solutions should be performed independently''' (except the final collaborative project).<br>
  
'''The final project is due by midnight May 4, 2015.'''
+
'''The final project is due by midnight April 27, 2016.'''
  
  

Revision as of 14:51, 17 January 2016

BCH339N Systems Biology & Bioinformatics

Course unique #: 54040
Lectures: Tues/Thurs 11 – 12:30 PM in BUR 212
Instructor: Edward Marcotte, marcotte@icmb.utexas.edu

  • Office hours: Mon 4 PM – 5 PM in MBB 3.148BA

TA: Claire McWhite, claire.mcwhite@utexas.edu

  • TA Office hours: Wed/Thurs 4 PM - 5 PM in MBB 3.128A Phone: listed on the syllabus

Lectures & Handouts

Apr 28 - May 5, 2016 - Gene Presentations


April 30, 2015 - Synthetic Biology

A collection of further reading, if you're so inclined:

Food for thought:
De-extinction I, II, and III

April 26, 2016 - Phenologs

  • Today's slides
  • Phenologs and the drug discovery story we'll discuss in class
  • Search for phenologs here. You can get started by rediscovering the plant model of Waardenburg syndrome. Search among the known diseases for "Waardenburg", or enter the human genes linked to Waardenburg (Entrez gene IDs 4286, 5077, 6591, 7299) to get a feel for how this works. Also, here's Carl Zimmer's NYT article about phenologs and the scientific process.

Tools for finding orthologs:

April 21, 2016 - Networks II

April 19, 2016 - Networks

  • Today's slides
  • Metabolic networks: The wall chart (it's interactive, e.g. here's enolase), the current state of the human metabolic reaction network, and older but still relevant review of transcriptional networks (with the current record holder in this regard held by ENCODE), and an early review of protein interaction extent and quality whose lessons still hold.
  • Useful gene network resources include:
    • FunctionalNet, which links to human, worm, Arabidopsis, mouse and yeast gene networks. Not the prettiest web site, but useful, and helped my own group find genes for a wide variety of biological processes. Try searching HumanNet for the myelin regulatory factor MYRF (Entrez gene ID 745) and predicting its function, which is now known but wasn't when the network was made.
    • STRING is available for many organisms, including large numbers of prokaryotes. Try searching on the E. coli enolase (Eno) as an example.
    • GeneMania, which aggregates many individual gene networks.
    • MouseFunc, a collection of network and classifier-based predictions of gene function from an open contest to predict gene function in the mouse.
    • The best interactive tool for network visualization is Cytoscape. You can download and install it locally on your computer, then visualize and annotated any gene network, such as are output by the network tools linked above. There is also a web-based network viewer that can be incorporated into your own pages (e.g., as used in YeastNet).

Reading:

Apr 14, 2016 - Genome Engineering

Apr 12, 2016 - Principal Component Analysis (& the curious case of European genotypes)

A smattering of links on PCA:

Apr 7, 2016 - Classifiers I

Apr 5, 2016 - Clustering II

Mar 31, 2016 - Functional Genomics & Data Mining - Clustering I

Problem Set 3, due before midnight Apr. 12, 2016. You will need the following software and datasets:

Mar 29, 2016 - Motifs

Mar 24, 2016 - Mapping protein complexes

Mar 22, 2016 - Mass spectrometry proteomics

  • Welcome back from Spring Break. Apparently, we had some down time on Rosalind, so I'm extending the HW3 deadline to 11:59PM March 26...
  • Guest speaker: Dr. Daniel Boutz

Mar 15-17, 2016 - SPRING BREAK

Mar 10, 2016 - Genomes II, Gene Expression

Mar 8, 2016 - Genome Assembly

Mar 3, 2016 - *** ICE STORM 2015***, UT classes cancelled

Mar 1, 2016 - Gene finding II

  • We're finishing up the slides from Feb. 25, then moving on into Genome Assembly

Feb 25, 2015 - Gene finding

Reading:

Feb 23, 2016 - HMMs II

  • We're finishing up the slides from Feb. 18.

Problem Set 2, due before midnight Mar. 8, 2016:

Feb 18, 2015 - Hidden Markov Models

Reading:

Feb 16, 2016 - Next-generation Sequencing (NGS)

Feb 11, 2016 - 3D Protein Structure Modeling

Feb 9, 2016 - Biological databases

  • Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is due by 11:59PM February 18.
  • Just a note that we'll be seeing ever more statistics as go on. Here's a good primer from Prof. Lauren Myers to refresh/explain basic concepts.
  • Today's slides

Feb 4, 2016 - Guest lecture: Homologs, orthologs, and evolutionary trees

  • We'll have a guest lecture on evolutionary relationships among genes.

Feb 2, 2016 - BLAST

Jan 28, 2016 - Sequence Alignment II

Jan 26, 2016 - Sequence Alignment I

Problem Set I, due before midnight Feb. 5, 2015:

Reading:

Jan 21, 2016 - Intro to Python

Jan 19, 2016 - 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 26.
  • 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 biochemistry majors. Prerequisites: Biochemistry 339F or Chemistry 339K with a grade of at least C-.
Requires basic familiarity with molecular biology & basic statistics, although varied backgrounds are expected.


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
Beginning Python for Bioinformatics
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 a course project (25% of final grade), which will be collaborative. Cross-discipline collaborations will be encouraged. The course project will consist of a research project on a bioinformatics topic chosen by the students (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.

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 (except the final collaborative project).

The final project is due by midnight April 27, 2016.