Difference between revisions of "BCH364C BCH394P 2017"

From Marcotte Lab
Jump to: navigation, search
(Lectures & Handouts)
(Lectures & Handouts)
Line 10: Line 10:
 
== Lectures & Handouts ==
 
== Lectures & Handouts ==
 
<!--
 
<!--
'''Apr 28 - May 5, 2016 - Gene Presentations'''
+
'''May 2 - May 4, 2017 - 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].
 
* 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].
  
'''April 26, 2016 - Synthetic Biology'''
+
'''April 27, 2017 - Synthetic Biology II'''
 +
 
 +
'''Apr 25, 2017 - Genome Engineering'''
 +
* Problem Set 3 deadline has been pushed to midnight April 18, 2016.
 +
* Guest speaker: [http://www.yeastgenome.org/cgi-bin/colleague/colleagueSearch?rm=colleague_page&id=12102 Dr. Chris Yellman]
 +
 
 +
'''April 20, 2017 - Synthetic Biology I'''
 
* '''Reminder: All gene projects are due by midnight, April 27'''.  Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR.   
 
* '''Reminder: All gene projects are due by midnight, April 27'''.  Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR.   
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_SyntheticBio-Spring2016.pdf Today's slides]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_SyntheticBio-Spring2017.pdf Today's slides]
 
A collection of further reading, if you're so inclined:
 
A collection of further reading, if you're so inclined:
* [http://www.marcottelab.org/users/BCH339N_2016/MinimalMycoplasma.pdf Minimal Mycoplasma]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/MinimalMycoplasma.pdf Minimal Mycoplasma]
* [http://www.marcottelab.org/users/BCH339N_2016/GenomeTransplantation.pdf Genome Transplantation]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/GenomeTransplantation.pdf Genome Transplantation]
* [http://www.marcottelab.org/users/BCH339N_2016/JCVI-1.0.pdf JCVI-1.0]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/JCVI-1.0.pdf JCVI-1.0]
* [http://www.marcottelab.org/users/BCH339N_2016/OneStepAssemblyInYeast.pdf One step genome assembly in yeast]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/OneStepAssemblyInYeast.pdf One step genome assembly in yeast]
* [http://www.marcottelab.org/users/BCH339N_2016/StrainsFromYeastGenomicClones.pdf New cells from yeast genomic clones]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/StrainsFromYeastGenomicClones.pdf New cells from yeast genomic clones]
* [http://www.marcottelab.org/users/BCH339N_2016/NewCellFromChemicalGenome.pdf A new cell from a chemically synthesized genome], [http://www.marcottelab.org/users/BCH339N_2016/NewCellFromChemicalGenome.SOM.pdf SOM]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NewCellFromChemicalGenome.pdf A new cell from a chemically synthesized genome], [http://www.marcottelab.org/users/BCH364C_394P_2017/NewCellFromChemicalGenome.SOM.pdf SOM]
* [http://www.marcottelab.org/users/BCH339N_2016/YeastSynthCsome.pdf 1/2 a synthetic yeast chromosome] and [http://syntheticyeast.org/ Build-A-Genome]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/YeastSynthCsome.pdf 1/2 a synthetic yeast chromosome] and [http://syntheticyeast.org/ Build-A-Genome]
* & the latest: [http://www.marcottelab.org/users/BCH339N_2016/Science-2014-Annaluru-55-8.pdf Entire synthetic yeast chromosome]  
+
* & the latest: [http://www.marcottelab.org/users/BCH364C_394P_2017/Science-2014-Annaluru-55-8.pdf Entire synthetic yeast chromosome]  
 
* [http://en.wikipedia.org/wiki/Gillespie_algorithm The Gillespie algorithm]
 
* [http://en.wikipedia.org/wiki/Gillespie_algorithm The Gillespie algorithm]
 
* [https://www.igem.org/Main_Page iGEM], and an example part ([http://parts.igem.org/Featured_Parts:Light_Sensor the light sensor])
 
* [https://www.igem.org/Main_Page iGEM], and an example part ([http://parts.igem.org/Featured_Parts:Light_Sensor the light sensor])
 
* [http://www.popsci.com/diy/article/2013-08/grow-photo Take your own coliroids]
 
* [http://www.popsci.com/diy/article/2013-08/grow-photo Take your own coliroids]
* [http://www.marcottelab.org/users/BCH339N_2016/repressilator.pdf The infamous repressilator]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/repressilator.pdf The infamous repressilator]
* [http://www.marcottelab.org/users/BCH339N_2016/BacterialPhotography.pdf Bacterial photography], and [http://www.marcottelab.org/users/BIO337_2014/UTiGEM2012.pdf UT's 2012 iGEM entry]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BacterialPhotography.pdf Bacterial photography], and [http://www.marcottelab.org/users/BIO337_2014/UTiGEM2012.pdf UT's 2012 iGEM entry]
* [http://www.marcottelab.org/users/BCH339N_2016/EdgeDetector.pdf Edge detector]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/EdgeDetector.pdf Edge detector]
* [http://www.marcottelab.org/users/BCH339N_2016/nbt.2510.pdf A more recent example of digital logic]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/nbt.2510.pdf A more recent example of digital logic]
 
* An example of metabolic engineering: [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12051.html yeast making anti-malarial drugs]
 
* An example of metabolic engineering: [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12051.html yeast making anti-malarial drugs]
 
Food for thought:<br>
 
Food for thought:<br>
 
[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 21, 2016 - Phenologs'''
+
'''April 18, 2017 - Phenologs'''
* You should have started mini-assignment 5.  The web page is due by midnight April 27, 2016.   
+
* Remember: The final project web page is due by midnight April 27, 2016.   
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Phenologs_Spring2016.pdf Today's slides]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Phenologs_Spring2017.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
 
* Search for phenologs [http://www.phenologs.org/ 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 [http://www.nytimes.com/2010/04/27/science/27gene.html?_r=0 Carl Zimmer's NYT article] about phenologs and the scientific process.
 
* Search for phenologs [http://www.phenologs.org/ 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 [http://www.nytimes.com/2010/04/27/science/27gene.html?_r=0 Carl Zimmer's NYT article] about phenologs and the scientific process.
 
Tools for finding orthologs:<br>
 
Tools for finding orthologs:<br>
* One good tool for discovering orthologs is [http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid].  Note: InParanoid annotation lags a bit, so you'll need to find the [http://www.ensembl.org/index.html Ensembl] protein id, or try a text search for the common name. Or, just link there from [http://www.uniprot.org/ Uniprot]. InParanoid tends towards higher recall, lower precision for finding orthologs. Approaches with higher precision include [http://omabrowser.org/oma/home/ OMA] (introduced in [http://www.marcottelab.org/users/BCH339N_2016/OMA.pdf this paper]), [http://phylomedb.org/ PhylomeDB], and just released, [http://pythonhosted.org/bio-MOSAIC/ MOSAIC]
+
* One good tool for discovering orthologs is [http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid].  Note: InParanoid annotation lags a bit, so you'll need to find the [http://www.ensembl.org/index.html Ensembl] protein id, or try a text search for the common name. Or, just link there from [http://www.uniprot.org/ Uniprot]. InParanoid tends towards higher recall, lower precision for finding orthologs. Approaches with higher precision include [http://omabrowser.org/oma/home/ OMA] (introduced in [http://www.marcottelab.org/users/BCH364C_394P_2017/OMA.pdf this paper]), [http://phylomedb.org/ PhylomeDB], and just released, [http://pythonhosted.org/bio-MOSAIC/ MOSAIC]
* [http://www.marcottelab.org/users/BCH339N_2016/Sonnhammer2002TiG.pdf All your ortholog definition questions answered!]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Sonnhammer2002TiG.pdf All your ortholog definition questions answered!]
  
'''April 19, 2016 - Networks'''
+
'''April 13, 2017 - Networks II'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Networks_Spring2016.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.
+
'''April 11, 2017 - Networks'''
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Networks_Spring2017.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/BCH364C_394P_2017/HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network], and older but still relevant review of [http://www.marcottelab.org/users/BCH364C_394P_2017/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/BCH364C_394P_2017/vonmering.pdf protein interaction extent and quality] whose lessons still hold.
 
* Useful gene network resources include:
 
* Useful gene network resources include:
 
** [http://www.functionalnet.org 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.  
 
** [http://www.functionalnet.org 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.  
Line 57: Line 65:
 
* [http://www.marcottelab.org/paper-pdfs/ng-fraser-review.pdf Functional networks]
 
* [http://www.marcottelab.org/paper-pdfs/ng-fraser-review.pdf Functional networks]
 
* [http://www.marcottelab.org/paper-pdfs/JProteomics_GBAReview_2010.pdf Review of predicting gene function and phenotype from protein networks]
 
* [http://www.marcottelab.org/paper-pdfs/JProteomics_GBAReview_2010.pdf Review of predicting gene function and phenotype from protein networks]
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]
  
'''Apr 14, 2016 - Genome Engineering'''
+
'''Apr 6, 2017 - Principal Component Analysis (& the curious case of European genotypes)'''
* Go ahead and start mini-assignment 4, and try to finish it within a week. 
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_PCA_Spring2017.pdf Today's slides]
* Problem Set 3 deadline has been pushed to midnight April 18, 2016.
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
* Guest speaker: [http://www.yeastgenome.org/cgi-bin/colleague/colleagueSearch?rm=colleague_page&id=12102 Dr. Chris Yellman]
+
 
+
'''Apr 12, 2016 - Mass spectrometry proteomics'''
+
* Guest speaker: [http://www.researchgate.net/profile/Daniel_Boutz/ Dr. Daniel Boutz]
+
 
+
'''Apr 7, 2016 - IMPORTANT : PLAGIARISM'''
+
* [http://www.marcottelab.org/users/BCH339N_2016/PlagiarismInClass-Spring2016.pdf Plagiarism in the course and what we're going to do about it.]  I refer you to the [http://deanofstudents.utexas.edu/sjs/acadint_whatis.php official policies of UT Austin].
+
* Go ahead and start mini-assignment 3. 
+
 
+
'''Apr 5, 2016 - Principal Component Analysis (& the curious case of European genotypes)'''
+
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_PCA_Spring2016.pdf Today's slides]
+
* [http://www.marcottelab.org/users/BCH339N_2016/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
+
 
* Relevant to today's discussion for his eponymous distance measure: [http://en.wikipedia.org/wiki/Prasanta_Chandra_Mahalanobis Mahalanobis]
 
* Relevant to today's discussion for his eponymous distance measure: [http://en.wikipedia.org/wiki/Prasanta_Chandra_Mahalanobis Mahalanobis]
 
A smattering of links on PCA:<br>
 
A smattering of links on PCA:<br>
* [http://www.marcottelab.org/users/BCH339N_2016/NBT_primer_PCA.pdf NBT Primer on PCA]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBT_primer_PCA.pdf NBT Primer on PCA]
* [http://www.marcottelab.org/users/BCH339N_2016/PrincipalComponentAnalysis.docx A PCA overview (.docx format)] & the [http://horicky.blogspot.com/2009/11/principal-component-analysis.html original post]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/PrincipalComponentAnalysis.docx A PCA overview (.docx format)] & the [http://horicky.blogspot.com/2009/11/principal-component-analysis.html original post]
* Science Signaling (more specifically, Neil R. Clark and Avi Ma’ayan!) had a [http://stke.sciencemag.org/cgi/content/full/sigtrans;4/190/tr3/DC1 nice introduction to PCA] that I've reposted [http://www.marcottelab.org/users/BCH339N_2016/IntroToPCA.pdf here] (with [http://www.marcottelab.org/users/BCH339N_2016/2001967Slides-FINAL.ppt slides])
+
* Science Signaling (more specifically, Neil R. Clark and Avi Ma’ayan!) had a [http://stke.sciencemag.org/cgi/content/full/sigtrans;4/190/tr3/DC1 nice introduction to PCA] that I've reposted [http://www.marcottelab.org/users/BCH364C_394P_2017/IntroToPCA.pdf here] (with [http://www.marcottelab.org/users/BCH364C_394P_2017/2001967Slides-FINAL.ppt slides])
 
* 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]
  
'''Mar 31, 2016 - Classifiers I'''
+
'''Apr 4, 2017 - Classifiers I'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Classifiers_Spring2016.pdf Today's slides]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Classifiers_Spring2017.pdf Today's slides]
* [http://www.marcottelab.org/users/BCH339N_2016/AMLALLclassification.pdf Classifying leukemias]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/AMLALLclassification.pdf Classifying leukemias]
 
* For those of you interesting in trying out classifiers on your own, 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 interesting in trying out classifiers on your own, here's the best open software for do-it-yourself classifiers and data mining: [http://www.cs.waikato.ac.nz/ml/weka/ Weka]
  
'''Mar 29, 2016 - Clustering II'''
+
'''Mar 30, 2017 - Mass spectrometry proteomics'''
 +
* Guest speaker: [http://www.researchgate.net/profile/Daniel_Boutz/ Dr. Daniel Boutz]
 +
 
 +
'''Mar 28, 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
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/structbio_lecture_BCH364C-394P_2016.pptx Today's slides]<br>
 +
* The [https://www.rosettacommons.org/software Rosetta] software suite for 3D protein modeling, and [http://www.marcottelab.org/users/BCH364C_394P_2017/RosettaOverview.pdf what it can do for you]
 +
* 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]
 +
 
 +
'''Mar 23, 2017 - Clustering II'''
 
* We're finishing up the slides from Mar.  24.<br>
 
* We're finishing up the slides from Mar.  24.<br>
* [http://www.marcottelab.org/users/BCH339N_2016/FuzzyK-Means.pdf Fuzzy k-means]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/FuzzyK-Means.pdf Fuzzy k-means]
* [http://www.marcottelab.org/users/BCH339N_2016/SOM-geneexpression.pdf SOM gene expression]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/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 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 23, 2017 - Functional Genomics & Data Mining - Clustering I'''
+
'''Mar 21, 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/BCH364C_394P_2017/BCH364C-394P_LargeScaleExperiments_Spring2017.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/BCH364C_394P_2017/nature_review_2000.pdf Review of phylogenetic profiles]
* [http://www.marcottelab.org/users/BCH339N_2016/Bcelllymphoma.pdf B cell lymphomas]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Bcelllymphoma.pdf B cell lymphomas]
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-MicroarrayClustering.pdf Primer on clustering]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/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/BCH364C_394P_2017/K-means-Example.ppt K-means example (.ppt)]
  
[http://www.marcottelab.org/users/BCH339N_2016/ProblemSet3_2016.pdf '''Problem Set 3], due before midnight Apr. 14, 2016'''.  You will need the following software and datasets:<br>
+
[http://www.marcottelab.org/users/BCH364C_394P_2017/ProblemSet3_2016.pdf '''Problem Set 3], due before midnight Apr. 14, 2016'''.  You will need the following software and datasets:<br>
 
* The clustering and treeview software is available [http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm here].<br>  
 
* The clustering and treeview software is available [http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm here].<br>  
* [http://www.marcottelab.org/users/BCH339N_2016/yeast_aaseqs Yeast protein sequences]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/yeast_aaseqs Yeast protein sequences]
* [http://www.marcottelab.org/users/BCH339N_2016/yeast_phyloprofiles2.txt Yeast protein phylogenetic profiles]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/yeast_phyloprofiles2.txt Yeast protein phylogenetic profiles]
* [http://www.marcottelab.org/users/BCH339N_2016/yeast_microarraydata2.txt Yeast mRNA expression profiles]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/yeast_microarraydata2.txt Yeast mRNA expression profiles]
  
'''Mar 21, 2017 - Motifs'''
+
'''Mar 14-16, 2017 - SPRING BREAK'''
 +
* Finish HW3 and and the first mini-assignment (#1) for your gene project.
 +
 
 +
'''Mar 9, 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.   
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Motifs_Spring2016.pdf Today's slides]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Motifs_Spring2017.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/BCH364C_394P_2017/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/BCH364C_394P_2017/nbt0806-959-primer-howdoesmotifdiscoverywork.pdf NBT Primer - How does motif discovery work?]
 
* [http://www.rcsb.org/pdb/explore/explore.do?structureId=1L1M The biochemical basis of a particular motif]
 
* [http://www.rcsb.org/pdb/explore/explore.do?structureId=1L1M The biochemical basis of a particular motif]
* [http://www.marcottelab.org/users/BCH339N_2016/GibbsSampling.pdf Gibbs Sampling]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/GibbsSampling.pdf Gibbs Sampling]
* [http://www.marcottelab.org/users/BCH339N_2016/AlignAce.pdf AlignAce]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/AlignAce.pdf AlignAce]
 
+
'''Mar 14-16, 2017 - SPRING BREAK'''
+
* Finish HW3 and and the first mini-assignment (#1) for your gene project.
+
  
'''Mar 14, 2017 - Genomes II'''<br>
+
'''Mar 7, 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'''.
 
* We're finishing up the slides from Mar. 8, then on to motif-finding. Note: we'll increasingly be discussing primary papers in the lectures.  Here are a few classics and reviews that will come up after Spring Break if you want to start looking ahead.<br>
 
* We're finishing up the slides from Mar. 8, then on to motif-finding. Note: we'll increasingly be discussing primary papers in the lectures.  Here are a few classics and reviews that will come up after Spring Break if you want to start looking ahead.<br>
* [http://www.marcottelab.org/users/BCH339N_2016/ESTs.pdf Gene expression by ESTs]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/ESTs.pdf Gene expression by ESTs]
* [http://www.marcottelab.org/users/BCH339N_2016/SAGE.pdf Gene expression by SAGE]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/SAGE.pdf Gene expression by SAGE]
* [http://www.marcottelab.org/users/BCH339N_2016/Affy2.pdf Affy microarrays 1] & [http://www.marcottelab.org/users/BIO337_2014/Affy1.pdf Affy microarrays 2]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Affy2.pdf Affy microarrays 1] & [http://www.marcottelab.org/users/BIO337_2014/Affy1.pdf Affy microarrays 2]
* [http://www.marcottelab.org/users/BCH339N_2016/DeRisi.pdf cDNA microarrays]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/DeRisi.pdf cDNA microarrays]
 
* [http://en.wikipedia.org/wiki/RNA-Seq RNA-Seq]
 
* [http://en.wikipedia.org/wiki/RNA-Seq RNA-Seq]
* [http://www.marcottelab.org/users/BCH339N_2016/eisen.pdf Clustering by gene expression]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/eisen.pdf Clustering by gene expression]
* [http://www.marcottelab.org/users/BCH339N_2016/Spellman.pdf Cell cycle data]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Spellman.pdf Cell cycle data]
  
'''Mar 9, 2017 - Genome Assembly'''
+
'''Mar 2, 2017 - Genome Assembly'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_GenomeAssembly_Spring2016.pdf Today's slides]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_GenomeAssembly_Spring2017.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>
* [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/BCH364C_394P_2017/DeBruijnPrimer.pdf DeBruijn Primer] and [http://www.marcottelab.org/users/BCH364C_394P_2017/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]
 
* 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 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]
 
 
'''Mar 2, 2017''' - TA office hours canceled due to illness, rescheduled tomorrow, Mar 3, 3-4PM
 
  
 
'''Feb 28, 2017 - Next-generation Sequencing (NGS)'''
 
'''Feb 28, 2017 - Next-generation Sequencing (NGS)'''
Line 147: Line 147:
 
* [http://www.youtube.com/watch?v=45vNetkGspo Genome Analyzer (Youtube Video)]
 
* [http://www.youtube.com/watch?v=45vNetkGspo Genome Analyzer (Youtube Video)]
  
'''Feb 23, 2016 - Gene finding'''
+
'''Feb 23, 2017 - Gene finding II'''
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N-GeneFinding-Spring2016.pdf Today's slides]
+
* We're finishing up the slides from Feb. 25, then moving on into [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_GenomeAssembly_Spring2017.pdf Genome Assembly]
 +
 
 +
'''Feb 21, 2017 - Gene finding'''
 +
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-GeneFinding-Spring2017.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]
 
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/BCH364C_394P_2017/EukGeneAnnotation.pdf Eukaryotic gene finding], [http://www.marcottelab.org/users/BCH364C_394P_2017/GeneMark.hmm.pdf GeneMark.hmm], and [http://www.marcottelab.org/users/BCH364C_394P_2017/BurgeKarlin-main.pdf GENSCAN]
  
'''Feb 21, 2017 - HMMs II'''
+
'''Feb 16, 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>
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_ProblemSet2_Spring2016.pdf '''Problem Set 2'''].   
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_ProblemSet2_Spring2017.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/BCH364C_394P_2017/state_sequences State sequences], [http://www.marcottelab.org/users/BCH364C_394P_2017/soluble_sequences Soluble sequences], [http://www.marcottelab.org/users/BCH364C_394P_2017/transmembrane_sequences Transmembrane sequences]
  
'''Feb 16, 2017 - Hidden Markov Models'''
+
'''Feb 14, 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/BCH364C_394P_2017/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.)  
 
* Another view of the remarkable growth of data, e.g. [http://www.ebi.ac.uk/uniprot/TrEMBLstats/ UniProt]
 
* 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/BCH339N-HMMs-Spring2016.pdf Today's slides]<br>
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-HMMs-Spring2017.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/BCH339N_2016/NBTPrimer-Bayes.pdf Bayesian statistics primer], [http://en.wikipedia.org/wiki/Bayes'_theorem Wiki Bayes]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-HMMs.pdf HMM primer] and [http://www.marcottelab.org/users/BCH364C_394P_2017/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 14, 2017 - Biological databases'''
+
'''Feb 9, 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/BCH364C_394P_2017/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/BCH364C_394P_2017/BCH364C-394P-BiologicalDatabases-Spring2017.pdf Today's slides]<br>
 
+
'''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
+
* [http://www.marcottelab.org/users/BCH339N_2016/structbio_lecture_BCH339N_2016.pptx Today's slides]<br>
+
* The [https://www.rosettacommons.org/software Rosetta] software suite for 3D protein modeling, and [http://www.marcottelab.org/users/BCH339N_2016/RosettaOverview.pdf what it can do for you]
+
* 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 7, 2017 - 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'''.
* [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/BCH364C_394P_2017/BCH364C-394P-BLAST-Spring2017.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/BCH364C_394P_2017/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.  
  
Line 188: Line 185:
 
* '''*** 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.  
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Orthology_Spring2016.pdf Today's slides]<br>
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Orthology_Spring2017.pdf Today's slides]<br>
 
* 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])
  
 
'''Jan 31, 2017 - 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/BCH364C_394P_2017/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 a prior incarnation of this class)
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/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 a 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 26, 2017 - 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/BCH364C_394P_2017/BCH364C-394P-Spring2017-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>
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_ProblemSet1_Spring2016.pdf Problem Set 1]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_ProblemSet1_Spring2017.pdf Problem Set 1]
* [http://www.marcottelab.org/users/BCH339N_2016/Tvolcanium_genome.txt T. volcanium genome]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Tvolcanium_genome.txt T. volcanium genome]
* 3 mystery genes (for Problem 5): [http://www.marcottelab.org/users/BCH339N_2016/Mgene1 Mgene1], [http://www.marcottelab.org/users/BCH339N_2016/Mgene2 Mgene2], [http://www.marcottelab.org/users/BCH339N_2016/Mgene3 Mgene3]<br>
+
* 3 mystery genes (for Problem 5): [http://www.marcottelab.org/users/BCH364C_394P_2017/Mgene1 Mgene1], [http://www.marcottelab.org/users/BCH364C_394P_2017/Mgene2 Mgene2], [http://www.marcottelab.org/users/BCH364C_394P_2017/Mgene3 Mgene3]<br>
 
Reading:<br>
 
Reading:<br>
* [http://www.marcottelab.org/users/BCH339N_2016/NBTPrimer-BLOSUM.pdf BLOSUM primer]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-BLOSUM.pdf BLOSUM primer]
* [http://www.marcottelab.org/users/BCH339N_2016/BLOSUM_paper.pdf The original BLOSUM paper] (hot off the presses from 1992!)
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BLOSUM_paper.pdf The original BLOSUM paper] (hot off the presses from 1992!)
* [http://www.marcottelab.org/users/BCH339N_2016/BLOSUM62Miscalculations.pdf BLOSUM miscalculations improve performance]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BLOSUM62Miscalculations.pdf BLOSUM miscalculations improve performance]
 
* 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 24, 2017 - 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.
 
 
* [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>
 
* [http://www.scipy-lectures.org/packages/statistics/index.html Statistics in Python]
 
* [http://www.scipy-lectures.org/packages/statistics/index.html Statistics in Python]
Line 217: Line 213:
 
'''Jan 19, 2017 - 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/BCH364C_394P_2017/BCH364C-394P-PythonPrimer-Spring2017.pdf Today's slides]<br>
* [http://www.marcottelab.org/users/BCH339N_2016/BCH339N_Lecture2-Python_primer-Spring2016.pdf Python primer]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Lecture2-Python_primer-Spring2017.pdf Python primer]
* [http://www.marcottelab.org/users/BCH339N_2016/Ecoli_genome.txt E. coli genome]
+
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Ecoli_genome.txt E. coli genome]
 
* [http://astrofrog.github.io/blog/2015/05/09/2015-survey-results/ Python 2 vs 3?]. For compatibility with Rosalind and other materials, we'll use version 2.7.
 
* [http://astrofrog.github.io/blog/2015/05/09/2015-survey-results/ Python 2 vs 3?]. For compatibility with Rosalind and other materials, we'll use version 2.7.
  
Line 227: Line 223:
 
* [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>
* 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 28'''.
+
* 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 BCH364C/BCH394P using [http://rosalind.info/classes/enroll/b22533ccd7/ ''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/BCH364C_394P_2017/ComputersMarsOrganismsVenus.pdf Computers are from Mars, Organisms are from Venus]
  
 
== Syllabus & course outline ==
 
== Syllabus & course outline ==

Revision as of 21:08, 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 BCH364C/BCH394P 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 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.