Difference between revisions of "BCH394P BCH364C 2020"

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== Lectures & Handouts ==
 
== Lectures & Handouts ==
 
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'''Apr 30 - May 7, 2019 - Final Project Presentations'''
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'''Mar 26, 2020 - 3D Protein Structure Modeling'''
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* 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
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/stuctbio_lecture_final2020.pptx Today's slides]
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* The [https://www.rosettacommons.org/software Rosetta] software suite for 3D protein modeling, and [http://www.marcottelab.org/users/BCH394P_364C_2020/RosettaOverview.pdf what it can do for you]
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* The [http://www.rcsb.org/pdb/ Protein Data Bank], [http://toolkit.tuebingen.mpg.de/hhpred HHPRED], [https://salilab.org/modeller/ MODELLER], and [http://www.pymol.org/ Pymol]
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'''Mar 24, 2020 - Proteomics'''
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* Guest speaker: [https://scholar.google.com/citations?hl=en&user=sYCFT1YAAAAJ&view_op=list_works Dr. Daniel Boutz], formerly of UCLA and now at the UT Center for Systems and Synthetic Biology
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* Reminder: the Center for Biomedical Research Support offers [http://ccbb.utexas.edu/shortcourses.html one-day courses in bioinformatics and biocomputing] in April/May. Topics include Unix, bash, and single cell data analysis.  There is also an Annual (4 day long!) [http://ccbb.utexas.edu/summerschool.html Summer School for Big Data in Biology] offered May 28-31, 2020. Topics there include genome/RNA seq, python, proteomics, machine learning, R, etc.
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'''Apr 28 - May 5, 2020 - Final Project 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#ngs core NextGen sequencing tools] and [http://ccbb.biosci.utexas.edu/summerschool.html#rna RNA-seq], also machine learning & proteomics.
 
* 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#ngs core NextGen sequencing tools] and [http://ccbb.biosci.utexas.edu/summerschool.html#rna RNA-seq], also machine learning & proteomics.
 
* We'll spend 5 minutes on the [https://utdirect.utexas.edu/ctl/ecis/ Course - Instructor Survey] Thursday morning.
 
* We'll spend 5 minutes on the [https://utdirect.utexas.edu/ctl/ecis/ Course - Instructor Survey] Thursday morning.
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'''April 23-25, 2019 - Synthetic Biology I'''
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'''April 21-23, 2020 - Synthetic Biology I'''
* '''Reminder: All projects are due by midnight, April 29'''.  Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR.   
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* '''Reminder: All 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/BCH394P_364C_2019/BCH394P-364C_SyntheticBio_Spring2019.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C_SyntheticBio_Spring2020.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/BCH394P_364C_2019/MinimalMycoplasma.pdf Minimal Mycoplasma]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/MinimalMycoplasma.pdf Minimal Mycoplasma]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/GenomeTransplantation.pdf Genome Transplantation]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/GenomeTransplantation.pdf Genome Transplantation]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/JCVI-1.0.pdf JCVI-1.0]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/JCVI-1.0.pdf JCVI-1.0]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/OneStepAssemblyInYeast.pdf One step genome assembly in yeast]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/OneStepAssemblyInYeast.pdf One step genome assembly in yeast]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/StrainsFromYeastGenomicClones.pdf New cells from yeast genomic clones]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/StrainsFromYeastGenomicClones.pdf New cells from yeast genomic clones]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/NewCellFromChemicalGenome.pdf A new cell from a chemically synthesized genome], [http://www.marcottelab.org/users/BCH394P_364C_2019/NewCellFromChemicalGenome.SOM.pdf SOM]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/NewCellFromChemicalGenome.pdf A new cell from a chemically synthesized genome], [http://www.marcottelab.org/users/BCH394P_364C_2020/NewCellFromChemicalGenome.SOM.pdf SOM]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/YeastSynthCsome.pdf 1/2 a synthetic yeast chromosome] and [http://syntheticyeast.org/ Build-A-Genome]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/YeastSynthCsome.pdf 1/2 a synthetic yeast chromosome] and [http://syntheticyeast.org/ Build-A-Genome]
*  [http://www.marcottelab.org/users/BCH394P_364C_2019/Science-2014-Annaluru-55-8.pdf Entire synthetic yeast chromosome]  
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*  [http://www.marcottelab.org/users/BCH394P_364C_2020/Science-2014-Annaluru-55-8.pdf Entire synthetic yeast chromosome]  
 
* [http://science.sciencemag.org/content/355/6329/1040.long Sc 2.0, as of 2017], with the [http://science.sciencemag.org/content/355/6329/1038 computational genome design]
 
* [http://science.sciencemag.org/content/355/6329/1040.long Sc 2.0, as of 2017], with the [http://science.sciencemag.org/content/355/6329/1038 computational genome design]
 
* [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/BCH394P_364C_2019/repressilator.pdf The infamous repressilator]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/repressilator.pdf The infamous repressilator]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BacterialPhotography.pdf Bacterial photography], and [http://www.marcottelab.org/users/BIO337_2014/UTiGEM2012.pdf UT's 2012 iGEM entry]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/BacterialPhotography.pdf Bacterial photography], and [http://www.marcottelab.org/users/BIO337_2014/UTiGEM2012.pdf UT's 2012 iGEM entry]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/EdgeDetector.pdf Edge detector]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/EdgeDetector.pdf Edge detector]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/nbt.2510.pdf A nice example of digital logic]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/nbt.2510.pdf A nice 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]
 
[http://www.popsci.com/woolly-mammoth-dna-brought-life-elephant-cells Food for thought]
 
[http://www.popsci.com/woolly-mammoth-dna-brought-life-elephant-cells Food for thought]
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'''April 18, 2019 - Phenologs'''
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'''April 16, 2020 - Phenologs'''
 
* [https://www.nytimes.com/2019/04/14/health/gene-editing-babies.html More on ethics, CRISPR babies] & [https://www.nytimes.com/2019/04/16/health/stanford-gene-editing-babies.html Stanford's response]
 
* [https://www.nytimes.com/2019/04/14/health/gene-editing-babies.html More on ethics, CRISPR babies] & [https://www.nytimes.com/2019/04/16/health/stanford-gene-editing-babies.html Stanford's response]
* '''Remember: The final project web page is due by midnight April 29, 2019, turned in as a URL emailed to the TA+Professor.  Please indicate in the email if you are willing to let us post the project to the course web site.  Also, note that ''late days can't be used for the final project'' '''  
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* '''Remember: The final project web page is due by midnight April 27, 2020, turned in as a URL emailed to the TA+Professor.  Please indicate in the email if you are willing to let us post the project to the course web site.  Also, note that ''late days can't be used for the final project'' '''  
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_Phenologs_Spring2019.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C_Phenologs_Spring2020.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. This is a fun example of the power of opportunistic data mining aka [http://researchparasite.com/ "research parasitism"] in biomedical research.
 
* [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. This is a fun example of the power of opportunistic data mining aka [http://researchparasite.com/ "research parasitism"] in biomedical research.
 
* 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.
 
* 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.
 
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/BCH394P_364C_2019/OMA.pdf this paper]), [http://phylomedb.org/ PhylomeDB], and [http://eggnogdb.embl.de/#/app/home EggNOG].  The various algorithms basically have different trade-offs with regard to precision vs recall, and ease of use.  For example, we use EggNOG in the lab for annotating genes in new genomes/transcriptomes because the EggNOG HMM ortholog models are easily downloadable/re-run on any set of genes you happen to be interested in.
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* 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/BCH394P_364C_2020/OMA.pdf this paper]), [http://phylomedb.org/ PhylomeDB], and [http://eggnogdb.embl.de/#/app/home EggNOG].  The various algorithms basically have different trade-offs with regard to precision vs recall, and ease of use.  For example, we use EggNOG in the lab for annotating genes in new genomes/transcriptomes because the EggNOG HMM ortholog models are easily downloadable/re-run on any set of genes you happen to be interested in.
* All (well, at least some) of [http://www.marcottelab.org/users/BCH394P_364C_2019/Sonnhammer2002TiG.pdf your ortholog definition questions answered!]
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* All (well, at least some) of [http://www.marcottelab.org/users/BCH394P_364C_2020/Sonnhammer2002TiG.pdf your ortholog definition questions answered!]
  
  
'''Apr 16, 2019 - Networks'''
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'''Apr 14, 2020 - Networks'''
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_Networks_Spring2019.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C_Networks_Spring2020.pdf Today's slides]
* Metabolic networks: [http://ca.expasy.org/cgi-bin/show_thumbnails.pl The wall chart] (it's interactive. For example, can you find enolase?), the current state of the [http://www.marcottelab.org/users/BCH394P_364C_2019/HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network], a review of [http://www.marcottelab.org/users/BCH394P_364C_2019/ChiPSeqReview.pdf mapping transcriptional networks by Chip-SEQ] (with the current record holder in this regard held by [https://www.encodeproject.org/ ENCODE]), and a recent review of [http://www.marcottelab.org/users/BCH394P_364C_2019/PPIsAndDiseaseReview.pdf protein interaction mapping in humans] and how it is informing disease genetics.
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* Metabolic networks: [http://ca.expasy.org/cgi-bin/show_thumbnails.pl The wall chart] (it's interactive. For example, can you find enolase?), the current state of the [http://www.marcottelab.org/users/BCH394P_364C_2020/HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network], a review of [http://www.marcottelab.org/users/BCH394P_364C_2020/ChiPSeqReview.pdf mapping transcriptional networks by Chip-SEQ] (with the current record holder in this regard held by [https://www.encodeproject.org/ ENCODE]), and a recent review of [http://www.marcottelab.org/users/BCH394P_364C_2020/PPIsAndDiseaseReview.pdf protein interaction mapping in humans] and how it is informing disease genetics.
 
* Useful gene network resources include:
 
* Useful gene network resources include:
 
** [http://www.reactome.org/ Reactome]), which we've seen before, links human genes according to reactions and pathways, and also calculated functional linkages from various high-throughput data.
 
** [http://www.reactome.org/ Reactome]), which we've seen before, links human genes according to reactions and pathways, and also calculated functional linkages from various high-throughput data.
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** The best interactive tool for network visualization is [http://www.cytoscape.org/ 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 [http://www.inetbio.org/yeastnet/ YeastNet]).  Here's an example file to visualize, the [http://proteincomplexes.org/static/downloads/human_protein_complex_map.cys latest version] of the [http://proteincomplexes.org/ human protein complex map].
 
** The best interactive tool for network visualization is [http://www.cytoscape.org/ 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 [http://www.inetbio.org/yeastnet/ YeastNet]).  Here's an example file to visualize, the [http://proteincomplexes.org/static/downloads/human_protein_complex_map.cys latest version] of the [http://proteincomplexes.org/ human protein complex map].
 
Reading:<br>
 
Reading:<br>
* [http://www.marcottelab.org/users/BCH394P_364C_2019/YeastSGA-2016.pdf The Yeast SGA map]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/YeastSGA-2016.pdf The Yeast SGA map]
 
* [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/BCH394P_364C_2019/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]
  
  
'''Apr 11, 2019 - Principal Component Analysis (& the curious case of European genotypes)'''
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'''Apr 9, 2020 - Principal Component Analysis (& the curious case of European genotypes)'''
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_PCA_Spring2019.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C_PCA_Spring2020.pdf Today's slides]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
 
* [http://projector.tensorflow.org/ The tSNE interactive visualization tool also performs PCA]
 
* [http://projector.tensorflow.org/ The tSNE interactive visualization tool also performs PCA]
 
* Relevant to today's lecture for his eponymous distance measure: [http://en.wikipedia.org/wiki/Prasanta_Chandra_Mahalanobis Mahalanobis]
 
* Relevant to today's lecture 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/BCH394P_364C_2019/NBT_primer_PCA.pdf NBT Primer on PCA]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/NBT_primer_PCA.pdf NBT Primer on PCA]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/PrincipalComponentAnalysis.docx A PCA overview (.docx format)] & the [http://horicky.blogspot.com/2009/11/principal-component-analysis.html original post]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/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/BCH394P_364C_2019/IntroToPCA.pdf here] (with [http://www.marcottelab.org/users/BCH394P_364C_2019/2001967Slides-FINAL.ppt slides])
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* 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/BCH394P_364C_2020/IntroToPCA.pdf here] (with [http://www.marcottelab.org/users/BCH394P_364C_2020/2001967Slides-FINAL.ppt slides])
 
* Python code for [http://sebastianraschka.com/Articles/2015_pca_in_3_steps.html performing PCA yourself]. This example gives a great intro to several important numerical/statistical/data mining packages in Python, including pandas and numpy.
 
* Python code for [http://sebastianraschka.com/Articles/2015_pca_in_3_steps.html performing PCA yourself]. This example gives a great intro to several important numerical/statistical/data mining packages in Python, including pandas and numpy.
  
  
'''Apr 9, 2019 - Classifiers'''
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'''Apr 7, 2020 - Classifiers'''
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_Classifiers_Spring2019.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C_Classifiers_Spring2020.pdf Today's slides]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/MachineLearningReview.pdf A nice recent review explaining Support Vector Machines and k-NN classifiers]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/MachineLearningReview.pdf A nice recent review explaining Support Vector Machines and k-NN classifiers]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/AMLALLclassification.pdf Classifying leukemias]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/AMLALLclassification.pdf Classifying leukemias]
 
* For those of you interesting in trying out classifiers on your own, here's the best stand alone open software for do-it-yourself classifiers and data mining: [http://www.cs.waikato.ac.nz/ml/weka/ Weka].  There is a great introduction to using Weka in this book chapter [http://link.springer.com/protocol/10.1007/978-1-4939-3578-9_17 Introducing Machine Learning Concepts with WEKA], as well as the very accessible Weka-produced book [http://www.cs.waikato.ac.nz/ml/weka/book.html Data Mining: Practical Machine Learning Tools and Techniques].
 
* For those of you interesting in trying out classifiers on your own, here's the best stand alone open software for do-it-yourself classifiers and data mining: [http://www.cs.waikato.ac.nz/ml/weka/ Weka].  There is a great introduction to using Weka in this book chapter [http://link.springer.com/protocol/10.1007/978-1-4939-3578-9_17 Introducing Machine Learning Concepts with WEKA], as well as the very accessible Weka-produced book [http://www.cs.waikato.ac.nz/ml/weka/book.html Data Mining: Practical Machine Learning Tools and Techniques].
 
* There's a particularly nice Python library of simple, easy-to-use, classification, regression, machine learning and data mining tools called [https://scikit-learn.org/stable/ scikit-learn]
 
* There's a particularly nice Python library of simple, easy-to-use, classification, regression, machine learning and data mining tools called [https://scikit-learn.org/stable/ scikit-learn]
  
  
'''Apr 4, 2019 - Clustering II'''
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'''Apr 2, 2020 - Clustering II'''
 
* Fun article: [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2002050 All biology is computational biology]
 
* Fun article: [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2002050 All biology is computational biology]
* We're finishing up the slides from April 2.<br>
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* We're finishing up the slides from last time.<br>
* [http://www.marcottelab.org/users/BCH394P_364C_2019/FuzzyK-Means.pdf Fuzzy k-means]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/FuzzyK-Means.pdf Fuzzy k-means]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/SOM-geneexpression.pdf SOM gene expression]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/SOM-geneexpression.pdf SOM gene expression]
 
** Links to various applications of SOMs: [http://en.wikipedia.org/wiki/Self-organizing_map 1], [http://vizier.u-strasbg.fr/kohonen.htx 2], [http://wn.com/Self_Organizing_Maps_Application 3]. 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 [http://bonsai.hgc.jp/~mdehoon/software/cluster Open Source Clustering package] with the '-s' option, or GUI option (here's the [http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/SOM.html#SOM manual]). (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://vizier.u-strasbg.fr/kohonen.htx 2], [http://wn.com/Self_Organizing_Maps_Application 3]. 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 [http://bonsai.hgc.jp/~mdehoon/software/cluster Open Source Clustering package] with the '-s' option, or GUI option (here's the [http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/SOM.html#SOM manual]). (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).  
* [http://www.marcottelab.org/users/BCH394P_364C_2019/tSNE.pdf t-SNE]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/tSNE.pdf t-SNE]
 
** Links to various applications of t-SNE: [https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding 1], [http://lvdmaaten.github.io/tsne/ 2], [https://www.youtube.com/watch?v=RJVL80Gg3lA 3], [http://distill.pub/2016/misread-tsne/ 4]. You can run t-SNE on the [http://projector.tensorflow.org/ following web site].  
 
** Links to various applications of t-SNE: [https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding 1], [http://lvdmaaten.github.io/tsne/ 2], [https://www.youtube.com/watch?v=RJVL80Gg3lA 3], [http://distill.pub/2016/misread-tsne/ 4]. You can run t-SNE on the [http://projector.tensorflow.org/ following web site].  
  
 
+
-->
'''Apr 2, 2019 - Functional Genomics & Data Mining - Clustering I'''
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'''Apr 2, 2020 - Functional Genomics & Data Mining - Clustering I'''
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P_364C_LargeScaleExperiments_Spring2019.pdf Today's slides]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P_364C_LargeScaleExperiments_Spring2020.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/BCH394P_364C_2019/NBTPrimer-MicroarrayClustering.pdf Primer on clustering]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/NBTPrimer-MicroarrayClustering.pdf Primer on clustering]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/K-means-Example.ppt K-means example (.ppt)]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/K-means-Example.ppt K-means example (.ppt)]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/Bcelllymphoma.pdf B cell lymphomas]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/Bcelllymphoma.pdf B cell lymphomas]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/nature_review_2000.pdf Review of phylogenetic profiles]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/nature_review_2000.pdf Review of phylogenetic profiles]
 
* [http://en.wikipedia.org/wiki/RNA-Seq RNA-Seq]
 
* [http://en.wikipedia.org/wiki/RNA-Seq RNA-Seq]
  
[http://www.marcottelab.org/users/BCH394P_364C_2019/ProblemSet3_2019.pdf '''Problem Set 3], due before midnight Apr. 11, 2019'''.  You will need the following software and datasets:<br>
+
[http://www.marcottelab.org/users/BCH394P_364C_2020/ProblemSet3_2020.pdf '''Problem Set 3], due before midnight Apr. 13, 2020'''.  You will need the following software and datasets:<br>
 
* The clustering software is available [https://software.broadinstitute.org/morpheus/ here]. There is an alternative package [http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm here] that you can download and install on your local computer if you prefer.<br>  
 
* The clustering software is available [https://software.broadinstitute.org/morpheus/ here]. There is an alternative package [http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm here] that you can download and install on your local computer if you prefer.<br>  
* [http://www.marcottelab.org/users/BCH394P_364C_2019/yeast_aaseqs Yeast protein sequences]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/yeast_aaseqs Yeast protein sequences]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/yeast_phyloprofiles2.txt Yeast protein phylogenetic profiles]
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/yeast_phyloprofiles2.txt Yeast protein phylogenetic profiles]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/yeast_cofractionationdata.txt Yeast protein fractionation/mass spectrometry profiles].  These additionally have common gene names (LocusID_commonname_location) which may help with the interpretation. These data come from [http://www.marcottelab.org/paper-pdfs/Nature_AnimalComplexes_2015.pdf this paper].
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* [http://www.marcottelab.org/users/BCH394P_364C_2020/yeast_cofractionationdata.txt Yeast protein fractionation/mass spectrometry profiles].  These additionally have common gene names (LocusID_commonname_location) which may help with the interpretation. These data come from [http://www.marcottelab.org/paper-pdfs/Nature_AnimalComplexes_2015.pdf this paper].
  
  
'''Mar 28, 2019 - 3D Protein Structure Modeling'''
+
'''Mar 31, 2020 - Motifs'''
* 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
+
* I hope that you're all safe & healthy, under the circumstances, and will be able to join class by zoom today. You should have received a zoom invitation by Canvas and email for class today, regular time. Your TA will record the class & we'll post it later to the Canvas in case you need to go back to it (or miss it). Slides will be from the Mar 12 posting below.
* [http://www.marcottelab.org/users/BCH394P_364C_2019/stuctbio_lecture_final2019.pptx Today's slides]
+
* Rosalind is reactivated for those of you who didn't finish yet.
* The [https://www.rosettacommons.org/software Rosetta] software suite for 3D protein modeling, and [http://www.marcottelab.org/users/BCH394P_364C_2019/RosettaOverview.pdf what it can do for you]
+
* Please send project write-ups ASAP. Besides problem set #3 (to be assigned next lecture), this project will be your major course grade, so it's important to nail down the subject now. This write-up is 5 points out of the 25 points assigned to the project.
* 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 26, 2019 - Proteomics'''
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'''Mar 26, 2020 Heads Up'''
* Guest speaker: [https://scholar.google.com/citations?hl=en&user=sYCFT1YAAAAJ&view_op=list_works Dr. Daniel Boutz], formerly of UCLA and now at the UT Center for Systems and Synthetic Biology
+
* Just some info to get organized for the upcoming restart of class. We'll use the plan we worked out in the last class, at least at first to see how it goes. (We will obviously have to be a bit flexible here!) The plan is to hold lectures by Zoom during the normally scheduled class time. We'll be trying to record the lectures & post the recordings afterward on Canvas so any of you who might be in other timezones or otherwise be unable to make class will have the opportunity to watch them. As always, slides will be posted before class so you can follow along with the material. The Mar 31 lecture will cover the motif-finding lecture we skipped on Mar 12 in favor of the COVID19 response modeling (rather more important at the time!). We will be flexible on deadlines under the circumstances, but do please try to wrap up Rosalind and think about a project, which obviously needs to be one that can be done from available online resources.
* Reminder: the Center for Biomedical Research Support offers [http://ccbb.utexas.edu/shortcourses.html one-day courses in bioinformatics and biocomputing] in April/May. Topics include Unix, bash, and single cell data analysis. There is also an Annual (4 day long!) [http://ccbb.utexas.edu/summerschool.html Summer School for Big Data in Biology] offered May 28-31, 2019. Topics there include genome/RNA seq, python, proteomics, machine learning, R, etc.
+
* We will email the class zoom link to everyone registered in Canvas. If you're auditing & you didn't get it, drop the TA an email & we will send to you too.
  
  
'''Mar 19-21, 2019 - SPRING BREAK'''
+
'''Mar 17-26, 2020 - SPRING BREAK'''
* Don't forget to finish HW3 and turn in the proposal for your course project by March 25th.
+
* Don't forget to finish HW3 and turn in the proposal for your course project by "March 30th".  Under the circumstances, we're going to suspend late penalties, but do please make a good effort, where possible, to get it in on time.  Also, FYI, I updated the Rosalind problem set as noted below (March 10).
  
  
'''Mar 14, 2019 - Motifs'''
+
'''Mar 12, 2020 - Motifs'''
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_Motifs_Spring2019.pdf Today's slides]
+
* News of the day, COVID-19: This is a [https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca detailed writeup] from a data modeler trying to make some scaling arguments on the virus spread and how many cases are undiagnosed in the US and elsewhere. The key point is that early interventions in "social distancing" (including closing schools, etc) have a disproportionate impact down the line, as you would expect on any exponential process. The virus is a near-perfect exponential fit right now.  [https://twitter.com/MarkJHandley/status/1237119688578138112 Here's the plot] from a few days ago (note the log scale y axis).
* '''Due March 25 by email''' - One to two (full) paragraphs describing your plans for a final project, along with the names of your collaborators.  This assignment (planning out your project) will account for 5 points out of your 25 total points for your course project. Here are a few examples of final projects from previous years: [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>  
+
* The [https://coronavirus.jhu.edu/map.html Johns Hopkins Univ Coronavirus Map] is a phenomenal example of bio data sciences in a crisis.
* [http://www.marcottelab.org/users/BCH394P_364C_2019/nbt0406-423-primer-whataremotifs.pdf NBT Primer - What are motifs?]
+
* In light of COVID-19 preparations, I'm going to suspend late penalties for the remainder of the semester.  We'll talk in class about the likely transitioning online after our now 2-week spring break, but stay tuned to this page for continuing updates.
* [http://www.marcottelab.org/users/BCH394P_364C_2019/nbt0806-959-primer-howdoesmotifdiscoverywork.pdf NBT Primer - How does motif discovery work?]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C_Motifs_Spring2020.pdf Today's slides]
 +
* '''Due March 30 by email''' - One to two (full) paragraphs describing your plans for a final project, along with the names of your collaborators.  This assignment (planning out your project) will account for 5 points out of your 25 total points for your course project. Here are a few examples of final projects from previous years: [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>  
 +
* [http://www.marcottelab.org/users/BCH394P_364C_2020/nbt0406-423-primer-whataremotifs.pdf NBT Primer - What are motifs?]
 +
* [http://www.marcottelab.org/users/BCH394P_364C_2020/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/BCH394P_364C_2019/GibbsSampling.pdf Gibbs Sampling]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/GibbsSampling.pdf Gibbs Sampling]
* FYI, we stopped last class's nanopore sequencing run pretty soon after class ended. Even in that relatively short time (<30 min), our longest read (sequencing randomly shorter DNA fragments from a 40kb phage genome) was >20 kb.
+
* FYI, last class's nanopore sequencing run (+ the test run on the same pore) gave ~500Mb sequencing, now low by nanopore standards, but still respectable, with the longest reads >30kb.
  
  
'''Mar 12, 2019 - Live Demo: Next-next-...-generation Sequencing (NGS) by nanopore'''
+
'''Mar 10, 2020 - Live Demo: Next-next-...-generation Sequencing (NGS) by nanopore'''
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 25'''.
+
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM <s>March 23</s>, extended to March 30'''.  Also, note that one of the original problems assigned using the Uniprot database appears to be broken in Rosalind, so I've substituted a problem using the Meme motif finding site. In the past, we've run into problems with Rosalind timing out before Meme completes (although it just performed fine in tests in I ran), so be warned you may have to try it a couple of times.
 
* We're going to be live-demoing a nanopore single molecule DNA sequencer in class, assuming all goes well. Specifically, we'll be using an [https://www.youtube.com/watch?v=CGWZvHIi3i0 Oxford Nanopore MinION sequencer], which differs substantially from these major alternatives:
 
* We're going to be live-demoing a nanopore single molecule DNA sequencer in class, assuming all goes well. Specifically, we'll be using an [https://www.youtube.com/watch?v=CGWZvHIi3i0 Oxford Nanopore MinION sequencer], which differs substantially from these major alternatives:
 
* [https://www.youtube.com/watch?v=fCd6B5HRaZ8 Youtube video] of Illumina/Solexa Sequencing by Synthesis
 
* [https://www.youtube.com/watch?v=fCd6B5HRaZ8 Youtube video] of Illumina/Solexa Sequencing by Synthesis
Line 155: Line 170:
  
  
'''Mar 7, 2019 - Genomes II'''<br>
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'''Mar 5, 2020 - Guest Lecture: [https://sites.cns.utexas.edu/cbrs/bioinformatics/staff Anna Battenhouse], NGS Analysis Best Practices'''<br>
* We're finishing up the slides from Feb. 28. Note that we give short shrift to read mapping/alignment algorithms, of which there are now [https://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment a very long list]. Here's an interesting discussion by Lior Pachter of the [https://liorpachter.wordpress.com/2015/11/01/what-is-a-read-mapping/ major developments in that field.]
+
* Practical advice and best practices for NGS mapping and analysis
* Here is [http://blog.thegrandlocus.com/2016/07/a-tutorial-on-burrows-wheeler-indexing-methods an excellent explanation of how the BWT relates to a suffix tree and enables fast read mapping to a genome]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/2020-03-NGS_IntroForEdM.pdf Today's slides]
* If you want a more detailed explanation, the [http://www.marcottelab.org/users/BCH394P_364C_2019/BWApaper.pdf BWA paper] more formally describes how the Burrows–Wheeler transform can be used to construct an index.
+
* & here are two more examples 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]
+
* Plus:  [https://www.slideshare.net/AdamPhillippy/telomeretotelomere-assembly-of-a-complete-human-x-chromosome "I have some troubling news...the human reference genome is incomplete"], breaking prepublication results on the telomere-to-telomere assembly of a complete human X chromosome from Karen Miga and Adam Phillippy, presented at the AGBT 2019 conference last week.
+
  
  
'''Mar 5, 2019 - Guest Lecture: [https://sites.cns.utexas.edu/cbrs/bioinformatics/staff Anna Battenhouse], NGS Analysis Best Practices'''<br>
+
'''Mar 3, 2020 - Genomes II'''<br>
* Practical advice and best practices for NGS mapping and analysis
+
* We had to swap the guest lecture to Thursday, so today we're finishing up the slides from Feb. 27. Note that we give short shrift to read mapping/alignment algorithms, of which there are now [https://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment a very long list]. Here's an interesting discussion by Lior Pachter of the [https://liorpachter.wordpress.com/2015/11/01/what-is-a-read-mapping/ major developments in that field.]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/2019-03-NGS_IntroForEdM.pdf Today's slides]
+
* Here is [http://blog.thegrandlocus.com/2016/07/a-tutorial-on-burrows-wheeler-indexing-methods an excellent explanation of how the BWT relates to a suffix tree and enables fast read mapping to a genome]
 +
* If you want a more detailed explanation, the [http://www.marcottelab.org/users/BCH394P_364C_2020/BWApaper.pdf BWA paper] more formally describes how the Burrows–Wheeler transform can be used to construct an index.
 +
* & here are two more examples 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]
  
  
'''Feb 28, 2019 - Genome Assembly'''
+
'''Feb 27, 2020 - Genome Assembly'''
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C-GenomeAssembly_Spring2019.pdf Today's slides]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C-GenomeAssembly_Spring2020.pdf Today's slides]
* A gentle reminder that Problem Set 2 is '''due by 11:59PM March 6'''<br>
+
* A gentle reminder that Problem Set 2 is '''due by 11:59PM March 4'''<br>
* Also, next Tuesday will be the first of our guest lecturers, [https://sites.cns.utexas.edu/cbrs/bioinformatics/staff Anna Battenhouse], on practical aspects of genome sequencing/assembly
+
* Also, next Tuesday will be the first of our guest lecturers, [https://research.utexas.edu/cbrs/cores/cbb/staff/ Anna Battenhouse], on practical aspects of genome sequencing/assembly
* [http://www.marcottelab.org/users/BCH394P_364C_2019/DeBruijnPrimer.pdf DeBruijn Primer] and [http://www.marcottelab.org/users/BCH394P_364C_2019/DeBruijnSupplement.pdf Supplement]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/DeBruijnPrimer.pdf DeBruijn Primer] and [http://www.marcottelab.org/users/BCH394P_364C_2020/DeBruijnSupplement.pdf Supplement]
 
* If you would like a few examples of proteins annotated with their transmembrane and soluble regions (according to UniProt) to help troubleshoot your homework, here are some [http://www.marcottelab.org/images/5/5a/Annotated_peptides.txt example yeast protein sequences].
 
* If you would like a few examples of proteins annotated with their transmembrane and soluble regions (according to UniProt) to help troubleshoot your homework, here are some [http://www.marcottelab.org/images/5/5a/Annotated_peptides.txt example yeast protein sequences].
 
* From last time, some definitions of [https://en.wikipedia.org/wiki/Sensitivity_and_specificity sensitivity/specificity] & [https://en.wikipedia.org/wiki/Precision_and_recall precision/recall]. Note that the gene finding community settled early on to a different definition of specificity that corresponds to the precision or PPV in other fields. Other fields define specificity as the true negative rate.
 
* From last time, some definitions of [https://en.wikipedia.org/wiki/Sensitivity_and_specificity sensitivity/specificity] & [https://en.wikipedia.org/wiki/Precision_and_recall precision/recall]. Note that the gene finding community settled early on to a different definition of specificity that corresponds to the precision or PPV in other fields. Other fields define specificity as the true negative rate.
  
  
'''Feb 26, 2019 - Gene finding II'''
+
'''Feb 25, 2020 - Gene finding II'''
* We're finishing up the slides from Feb. 21
+
* We're finishing up the slides from last time.
* Peer-led open coding hour has been resurrected!  Wed 12:30-1:30 in the MBB 2nd floor student lounge (the newly revamped eating space)
+
  
  
'''Feb 21, 2019 - Gene finding'''
+
'''Feb 20, 2020 - Gene finding'''
* We'll finish HMM slides from Feb 19, then start [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C-GeneFinding-Spring2019.pdf today's slides on gene finding]
+
* Science news of the day: Kudos to the McLellan lab for solving the coronavirus spike protein 3D structure in 12 days (!), with a paper in the bioRxiv and now [https://science.sciencemag.org/content/early/2020/02/19/science.abb2507 Science] in record-breaking time
* Some science news of the day:  [https://amp.economist.com/graphic-detail/2018/07/26/python-is-becoming-the-worlds-most-popular-coding-language "In the past 12 months Americans have searched for Python on Google more often than for Kim Kardashian"]
+
* [https://research.utexas.edu/cbrs/classes/short-courses/spring-2020/ Short classes at UT] in genome sequencing, proteomics, and bioinformatics
* For a few more examples of HMMs in action, here's the [http://www.marcottelab.org/users/BCH394P_364C_2019/MinionHumanGenome.pdf recent paper on sequencing the human genome by nanopore], which used HMMs in 3-4 different ways for polishing, contig inspection, repeat analysis and 5-methylcytosine detection.
+
* We'll finish HMM slides from last time, then start [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C-GeneFinding-Spring2020.pdf today's slides on gene finding]
 +
* [https://amp.economist.com/graphic-detail/2018/07/26/python-is-becoming-the-worlds-most-popular-coding-language "In the past 12 months Americans have searched for Python on Google more often than for Kim Kardashian"]
 +
* For a few more examples of HMMs in action, here's a [http://www.marcottelab.org/users/BCH394P_364C_2020/MinionHumanGenome.pdf paper on sequencing the human genome by nanopore], which used HMMs in 3-4 different ways for polishing, contig inspection, repeat analysis and 5-methylcytosine detection.
 
* [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]
'''Problem Set 2, due before midnight Mar. 6, 2019''':<br>
+
'''Problem Set 2, due before midnight Mar. 4, 2020''':<br>
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_ProblemSet2_Spring2019.pdf '''Problem Set 2'''].   
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C_ProblemSet2_Spring2020.pdf '''Problem Set 2'''].   
* You'll need these 3 files: [http://www.marcottelab.org/users/BCH394P_364C_2019/state_sequences State sequences], [http://www.marcottelab.org/users/BCH394P_364C_2019/soluble_sequences Soluble sequences], [http://www.marcottelab.org/users/BCH394P_364C_2019/transmembrane_sequences Transmembrane sequences]
+
* You'll need these 3 files: [http://www.marcottelab.org/users/BCH394P_364C_2020/state_sequences State sequences], [http://www.marcottelab.org/users/BCH394P_364C_2020/soluble_sequences Soluble sequences], [http://www.marcottelab.org/users/BCH394P_364C_2020/transmembrane_sequences Transmembrane sequences]
 
Reading (a couple of old classics + a review):<br>
 
Reading (a couple of old classics + a review):<br>
* [http://www.marcottelab.org/users/BCH394P_364C_2019/EukGeneAnnotation.pdf Eukaryotic gene finding], [http://www.marcottelab.org/users/BCH394P_364C_2019/GeneMark.hmm.pdf GeneMark.hmm], and [http://www.marcottelab.org/users/BCH394P_364C_2019/BurgeKarlin-main.pdf GENSCAN]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/EukGeneAnnotation.pdf Eukaryotic gene finding], [http://www.marcottelab.org/users/BCH394P_364C_2020/GeneMark.hmm.pdf GeneMark.hmm], and [http://www.marcottelab.org/users/BCH394P_364C_2020/BurgeKarlin-main.pdf GENSCAN]
  
  
'''Feb 19, 2019 - HMMs II'''
+
'''Feb 18, 2020 - HMMs II'''
* We're finishing up the slides from Feb. 14.  
+
* We're finishing up the slides from last time.  
* I was just pointed to [http://setosa.io/blog/2014/07/26/markov-chains/ this great interactive visualization of Markov Chains], by Victor Powell & Lewis Lehe. It's worth checking out to build some intuition.
+
* Link to [http://setosa.io/blog/2014/07/26/markov-chains/ a great interactive visualization of Markov Chains], by Victor Powell & Lewis Lehe. It's worth checking out to build some intuition.
 
* A non-biological example of using log odds ratios & Bayesian stats [https://priceonomics.com/how-statistics-solved-a-175-year-old-mystery-about/ to learn the authors of the Federalist Papers]
 
* A non-biological example of using log odds ratios & Bayesian stats [https://priceonomics.com/how-statistics-solved-a-175-year-old-mystery-about/ to learn the authors of the Federalist Papers]
  
  
'''Feb 14, 2019 - Hidden Markov Models'''
+
'''Feb 13, 2020 - Hidden Markov Models'''
* Happy Valentine's Day!
+
* Happy Day-Before-Valentine's Day!
* Don't forget: Rosalind Homework #2 (worth 10% of your final course grade) is due '''by 11:59PM February 20'''.
+
* Don't forget: Rosalind Homework #2 (worth 10% of your final course grade) is due '''by 11:59PM February 19'''.
* [https://www.huber.embl.de/msmb/ Modern Statistic for Modern Biology], by Susan Holmes and Wolfgang Huber, discussed last time. It's currently available online and due to be [https://www.amazon.com/Modern-Statistics-Biology-Susan-Holmes/dp/1108705294/ released on dead tree in the US in April]. (FYI, all code is in R.)
+
* More stats for comp biologists worth checking out:  [https://www.huber.embl.de/msmb/ Modern Statistic for Modern Biology], by Susan Holmes and Wolfgang Huber. It's currently available online and [https://www.amazon.com/Modern-Statistics-Biology-Susan-Holmes/dp/1108705294/ available on dead tree]. (FYI, all code is in R.)
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C-HMMs-Spring2019.pdf Today's slides]<br>
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C-HMMs-Spring2020.pdf Today's slides]<br>
 
Reading:<br>
 
Reading:<br>
* [http://www.marcottelab.org/users/BCH394P_364C_2019/NBTPrimer-HMMs.pdf HMM primer] and [http://www.marcottelab.org/users/BCH394P_364C_2019/NBTPrimer-Bayes.pdf Bayesian statistics primer #1], [http://www.marcottelab.org/users/BCH394P_364C_2019/BayesPrimer-NatMethods.pdf Bayesian statistics primer #2], [http://en.wikipedia.org/wiki/Bayes'_theorem Wiki Bayes]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/NBTPrimer-HMMs.pdf HMM primer] and [http://www.marcottelab.org/users/BCH394P_364C_2020/NBTPrimer-Bayes.pdf Bayesian statistics primer #1], [http://www.marcottelab.org/users/BCH394P_364C_2020/BayesPrimer-NatMethods.pdf Bayesian statistics primer #2], [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 12, 2019 - Biological databases'''
+
'''Feb 11, 2020 - Biological databases'''
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 20'''.
+
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 19'''.
* Science news of the day: [http://www.sciencemag.org/news/2019/01/gum-disease-causing-bacteria-could-spur-alzheimer-s Does gum disease cause Alzheimer's?]
+
* Just a note that we'll be seeing ever more statistics as go on. Here's a [http://www.marcottelab.org/users/BCH394P_364C_2020/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/BCH394P_364C_2019/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/BCH394P_364C_2020/BCH394P-364C-BiologicalDatabases-Spring2020.pdf Today's slides]<br>
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C-BiologicalDatabases-Spring2019.pdf Today's slides]<br>
+
  
  
'''Feb 7, 2019 - BLAST'''
+
'''Feb 6, 2020 - BLAST'''
* Science news of the day: Yet more [http://dev.biologists.org/content/146/3/dev175778 CRISPR] [https://www.statnews.com/2019/01/31/crispr-babies-michael-deem-rice-he-jiankui/ baby] [https://www.technologyreview.com/s/612892/crispr-baby-stanford-investigation/ news]!
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C-BLAST-Spring2020.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/BCH394P_364C_2019/BCH394P-364C-BLAST-Spring2019.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/BCH394P_364C_2020/BLAST.pdf The original BLAST paper]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/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.  
  
  
'''Feb 5, 2019 - Sequence Alignment II'''
+
'''Feb 4, 2020 - Sequence Alignment II'''
* We're finishing up the slides from Jan. 31.
+
* Science news of the day: [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH364C-394P-Spring2020-WuhanCoronavirus.pptx Wuhan coronavirus, DNA sequencing, bioinformatics, and bioRxiv!]. The genome papers have already been published at Nature [https://doi.org/10.1038/s41586-020-2008-3 1] [https://doi.org/10.1038/s41586-020-2012-7 2]! For the record, I consider this a huge win for biology, medicine, and the new trend in bio publishing of depositing preprints + public discussion/pre-publication peer review, often well in advance (but not this time!) of the more traditional peer review & publication at a journal.
* Science-ish news of the day: [http://www.sciencemag.org/news/2019/02/choose-your-champion-year-s-dance-your-phd-contest The Dance Your Ph.D. contest is on!]
+
* We're finishing up the slides from last time.  
* [http://www.marcottelab.org/users/BCH394P_364C_2019/FactAndFictionInAlignment.png Fact and Fiction in Sequence Alignments]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/FactAndFictionInAlignment.png Fact and Fiction in Sequence Alignments]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/NBTPrimer-DynamicProgramming.pdf Dynamic programming primer]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/NBTPrimer-DynamicProgramming.pdf Dynamic programming primer]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/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 U Texas undergraduate, now U Toronto professor, who took a prior incarnation of this class)
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/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 U Texas undergraduate, now U Toronto professor, 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 31, 2019 - Sequence Alignment I'''
+
'''Jan 30, 2020 - Sequence Alignment I'''
* For those of you who might be interested, Rosalind is having a [http://bioinf.me/contest Bioinformatics Contest].  Sign up runs until Feb. 2, the qualification round is Feb. 2-10, and Feb. 23 is the final round, with 24 hours to solve as many problems as you can. First prize in 2019 is to get your genome (exome) sequenced or get your own nanopore sequencer!
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH364C-394P-Spring2020-SequenceAlignment.pdf Today's slides]<br>
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH364C-394P-Spring2019-SequenceAlignment.pdf Today's slides]<br>
+
Problem Set I, due before midnight Feb. 10, 2020:<br>
Problem Set I, due before midnight Feb. 11, 2019:<br>
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH364C-394P_ProblemSet1_Spring2020.pdf Problem Set 1]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH364C-394P_ProblemSet1_Spring2019.pdf Problem Set 1]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/Hinfluenzae.txt H. influenzae genome]. [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenza] was the first free living organism to have its genome sequenced. '''NOTE: there are some additional characters in this file from ambiguous sequence calls.  For simplicity's sake, when calculating your nucleotide and dinucleotide frequencies, you can just ignore anything other than A, C, T, and G.'''
* [http://www.marcottelab.org/users/BCH394P_364C_2019/Hinfluenzae.txt H. influenzae genome]. [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenza] was the first free living organism to have its genome sequenced. '''NOTE: there are some additional characters in this file from ambiguous sequence calls.  For simplicity's sake, when calculating your nucleotide and dinucleotide frequencies, you can just ignore anything other than A, C, T, and G.'''
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/Taquaticus.txt T. aquaticus genome]. [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] helped spawn the genomic revolution as the source of heat-stable Taq polymerase for PCR.
* [http://www.marcottelab.org/users/BCH394P_364C_2019/Taquaticus.txt T. aquaticus genome]. [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] helped spawn the genomic revolution as the source of heat-stable Taq polymerase for PCR.
+
* 3 mystery genes (for Problem 5): [http://www.marcottelab.org/users/BCH394P_364C_2020/MysteryGene1.txt MysteryGene1], [http://www.marcottelab.org/users/BCH394P_364C_2020/MysteryGene2.txt MysteryGene2], [http://www.marcottelab.org/users/BCH394P_364C_2020/MysteryGene3.txt MysteryGene3]<br>
* 3 mystery genes (for Problem 5): [http://www.marcottelab.org/users/BCH394P_364C_2019/MysteryGene1.txt MysteryGene1], [http://www.marcottelab.org/users/BCH394P_364C_2019/MysteryGene2.txt MysteryGene2], [http://www.marcottelab.org/users/BCH394P_364C_2019/MysteryGene3.txt MysteryGene3]<br>
+
 
* '''*** HEADS UP FOR THE PROBLEM SET ***'''  If you try to use the Python string.count function to count dinucleotides, Python counts '''non-overlapping''' instances, not '''overlapping''' instances.  So, ''AAAA'' is counted as 2, not 3, dinucleotides.  You want '''overlapping''' dinucleotides instead, so will have to try something else, such as the python string[counter:counter+2] command, as explained in the Rosalind homework assignment on strings.
 
* '''*** HEADS UP FOR THE PROBLEM SET ***'''  If you try to use the Python string.count function to count dinucleotides, Python counts '''non-overlapping''' instances, not '''overlapping''' instances.  So, ''AAAA'' is counted as 2, not 3, dinucleotides.  You want '''overlapping''' dinucleotides instead, so will have to try something else, such as the python string[counter:counter+2] command, as explained in the Rosalind homework assignment on strings.
  
* For those of you who could use more tips on programming, there's a peer-led open coding hour happening on Tuesdays 3-4pm in MBB 2.232 (2nd floor lounge). It's a very informal setting where you can ask questions of more experienced programmers.
+
* For those of you who could use more tips on programming, there's a weekly peer-led open coding hour happening on Wednesday 12:30-1:30pm in MBB 2.232 (2nd floor lounge). It's a very informal setting where you can work and ask questions of more experienced programmers.
  
 
Reading:<br>
 
Reading:<br>
* [http://www.marcottelab.org/users/BCH394P_364C_2019/NBTPrimer-BLOSUM.pdf BLOSUM primer]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/NBTPrimer-BLOSUM.pdf BLOSUM primer]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BLOSUM_paper.pdf The original BLOSUM paper] (hot off the presses from 1992!)
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/BLOSUM_paper.pdf The original BLOSUM paper] (hot off the presses from 1992!)
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BLOSUM62Miscalculations.pdf BLOSUM miscalculations improve performance]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/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 29, 2019 - Intro to Python #2'''
+
'''Jan 28, 2020 - Intro to Python #2'''
 
* We'll be finishing Python slides from last time, plus Rosalind help & programming Q/A, maybe a glimpse of next lecture.
 
* We'll be finishing Python slides from last time, plus Rosalind help & programming Q/A, maybe a glimpse of next lecture.
* Science news of the day: [https://doi.org/10.1371/journal.pone.0208425 A 500 year experiment], with a [https://www.theatlantic.com/science/archive/2019/01/500-year-long-science-experiment/581155/ nice commentary in The Atlantic]
 
 
* [http://www.scipy-lectures.org/packages/statistics/index.html Statistics in Python]
 
* [http://www.scipy-lectures.org/packages/statistics/index.html Statistics in Python]
  
  
'''Jan 24, 2019 - Intro to Python'''
+
'''Jan 23, 2020 - Intro to Python'''
* REMINDER:  My email inbox is always fairly backlogged (e.g., my median time between non-spam emails was 11 minutes when I measured last year), so please copy the TA on any emails to me to make sure they get taken care of.
+
* Recommended seminar! [http://eisenlab.org/ Mike Eisen (UC Berkeley)] will be [https://liberalarts.utexas.edu/psychology/events/neuroscience-dr-michael-eisen-model-zombies-robust-behavior-manipulation-of-lab-reared-drosophila-melanogaster-by-the-fungal-pathogen-entomophthora speaking Monday Jan 27, 3PM, NHB 1.720]
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C-PythonPrimer-Spring2019.pdf Today's slides]<br>
+
* REMINDER:  My email inbox is always fairly backlogged (e.g., my median time between non-spam emails was 11 minutes when I measured it some time ago, and it's gotten much worse since then), so please copy the TA on any emails to me to make sure they get taken care of.
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_Lecture2-Python_primer-Spring2019.pdf Python primer]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C-PythonPrimer-Spring2020.pdf Today's slides]<br>
* [http://www.marcottelab.org/users/BCH394P_364C_2019/Ecoli_genome.txt E. coli genome]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C_Lecture2-Python_primer-Spring2020.pdf Python primer]
* [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. The current plan is for Python 2.7 support to be halted in 2020, but there is some hope (wishful thinking?) that Python 4 will be backwards compatible, [http://astrofrog.github.io/blog/2016/01/12/stop-writing-python-4-incompatible-code/ unlike Python 3]. Regardless, you're welcome to use whichever version you prefer, but we'll use 2.7 for all class explanations in the interests of simplicity and consistency. For beginners, the [http://www.practicepython.org/blog/2017/02/09/python2-and-3.html differences are quite minimal].
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/Ecoli_genome.txt E. coli genome]
 +
* [http://astrofrog.github.io/blog/2015/05/09/2015-survey-results/ Python 2 vs 3?]. We'll use Python 3 (the latest version is 3.8), but Rosalind and some materials are only available in Python 2.7, so we'll generally try to be version agnostic for compatibility. Use whichever you wish, but be aware that support for Python 2.7 has officially been stopped. For beginners, the [http://www.practicepython.org/blog/2017/02/09/python2-and-3.html differences are quite minimal] and are [https://www.guru99.com/python-2-vs-python-3.html summarized in a table here].  There's also a great [https://python-future.org/compatible_idioms.html cheat sheet here] for writing code compatable with both versions.
  
-->
+
 
'''Jan 22, 2019 - Introduction'''
+
'''Jan 21, 2020 - Introduction'''
* Science news of the day (& a reminder of the importance of ethics in science!):  [https://www.cnn.com/2019/01/21/health/china-gene-editing-babies-intl/index.html Chinese authorities say world's first gene-edited babies were illegal]
+
* [http://www.marcottelab.org/users/BCH394P_364C_2020/BCH394P-364C-IntroAndRosalind-Spring2020.pdf Today's slides]<br>
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C-IntroAndRosalind-Spring2019.pdf Today's slides]<br>
+
 
* Some warm-up videos to get you started on Python (2 not 3, unless you pay for an upgrade): [https://www.codecademy.com/learn/learn-python Code Academy's Python coding for beginners]<br>
 
* Some warm-up videos to get you started on Python (2 not 3, unless you pay for an upgrade): [https://www.codecademy.com/learn/learn-python Code Academy's Python coding for beginners]<br>
 
* Khan Academy has archived their videos on Python [https://www.youtube.com/user/khanacademy/search?query=python here]<br>
 
* Khan Academy has archived their videos on Python [https://www.youtube.com/user/khanacademy/search?query=python here]<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 BCH394P-BCH364C-Spring2019 using [http://rosalind.info/classes/enroll/127bf319a3/ ''this link''].  Homework #1 (worth 10% of your final course grade) has already been assigned on Rosalind and is '''due by 11:59PM January 31'''.
+
* 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 BCH394P/364C (Spring 2020) Systems Biology/Bioinformatics using [http://rosalind.info/classes/enroll/deda74d0a0/ ''this link''].  Homework #1 (worth 10% of your final course grade) has already been assigned on Rosalind and is '''due by 11:59PM January 30'''.
 
* 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 Python 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 Python before, definitely check this out!!!'''<br>
  

Revision as of 09:08, 2 April 2020

BCH394P/BCH364C Systems Biology & Bioinformatics

Course unique #: 53545/53436
Lectures: Tues/Thurs 11 – 12:30 PM in JGB 2.202
Instructor: Edward Marcotte, marcotte @ icmb.utexas.edu

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

TA: Brendan Floyd, bmfloyd @ utexas.edu

  • TA Office hours: Mon 1-2/Fri 1:30-2:30 in NHB 3.400B atrium (or MBB 3.128B) Phone: 512-232-3919

Lectures & Handouts

Apr 2, 2020 - Functional Genomics & Data Mining - Clustering I

Problem Set 3, due before midnight Apr. 13, 2020. You will need the following software and datasets:


Mar 31, 2020 - Motifs

  • I hope that you're all safe & healthy, under the circumstances, and will be able to join class by zoom today. You should have received a zoom invitation by Canvas and email for class today, regular time. Your TA will record the class & we'll post it later to the Canvas in case you need to go back to it (or miss it). Slides will be from the Mar 12 posting below.
  • Rosalind is reactivated for those of you who didn't finish yet.
  • Please send project write-ups ASAP. Besides problem set #3 (to be assigned next lecture), this project will be your major course grade, so it's important to nail down the subject now. This write-up is 5 points out of the 25 points assigned to the project.


Mar 26, 2020 Heads Up

  • Just some info to get organized for the upcoming restart of class. We'll use the plan we worked out in the last class, at least at first to see how it goes. (We will obviously have to be a bit flexible here!) The plan is to hold lectures by Zoom during the normally scheduled class time. We'll be trying to record the lectures & post the recordings afterward on Canvas so any of you who might be in other timezones or otherwise be unable to make class will have the opportunity to watch them. As always, slides will be posted before class so you can follow along with the material. The Mar 31 lecture will cover the motif-finding lecture we skipped on Mar 12 in favor of the COVID19 response modeling (rather more important at the time!). We will be flexible on deadlines under the circumstances, but do please try to wrap up Rosalind and think about a project, which obviously needs to be one that can be done from available online resources.
  • We will email the class zoom link to everyone registered in Canvas. If you're auditing & you didn't get it, drop the TA an email & we will send to you too.


Mar 17-26, 2020 - SPRING BREAK

  • Don't forget to finish HW3 and turn in the proposal for your course project by "March 30th". Under the circumstances, we're going to suspend late penalties, but do please make a good effort, where possible, to get it in on time. Also, FYI, I updated the Rosalind problem set as noted below (March 10).


Mar 12, 2020 - Motifs

  • News of the day, COVID-19: This is a detailed writeup from a data modeler trying to make some scaling arguments on the virus spread and how many cases are undiagnosed in the US and elsewhere. The key point is that early interventions in "social distancing" (including closing schools, etc) have a disproportionate impact down the line, as you would expect on any exponential process. The virus is a near-perfect exponential fit right now. Here's the plot from a few days ago (note the log scale y axis).
  • The Johns Hopkins Univ Coronavirus Map is a phenomenal example of bio data sciences in a crisis.
  • In light of COVID-19 preparations, I'm going to suspend late penalties for the remainder of the semester. We'll talk in class about the likely transitioning online after our now 2-week spring break, but stay tuned to this page for continuing updates.
  • Today's slides
  • Due March 30 by email - One to two (full) paragraphs describing your plans for a final project, along with the names of your collaborators. This assignment (planning out your project) will account for 5 points out of your 25 total points for your course project. Here are a few examples of final projects from previous years: 1, 2, 3, 4, 5 6 7 8 9 10 11 12 13 14
  • NBT Primer - What are motifs?
  • NBT Primer - How does motif discovery work?
  • The biochemical basis of a particular motif
  • Gibbs Sampling
  • FYI, last class's nanopore sequencing run (+ the test run on the same pore) gave ~500Mb sequencing, now low by nanopore standards, but still respectable, with the longest reads >30kb.


Mar 10, 2020 - Live Demo: Next-next-...-generation Sequencing (NGS) by nanopore

  • Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is due by 11:59PM March 23, extended to March 30. Also, note that one of the original problems assigned using the Uniprot database appears to be broken in Rosalind, so I've substituted a problem using the Meme motif finding site. In the past, we've run into problems with Rosalind timing out before Meme completes (although it just performed fine in tests in I ran), so be warned you may have to try it a couple of times.
  • We're going to be live-demoing a nanopore single molecule DNA sequencer in class, assuming all goes well. Specifically, we'll be using an Oxford Nanopore MinION sequencer, which differs substantially from these major alternatives:
  • Youtube video of Illumina/Solexa Sequencing by Synthesis
  • Youtube video of Pacific Biosciences single molecule sequencing by synthesis in zero mode waveguides
  • Here's Oxford nanopore's own videos explaining the tech. DNA sequences are collected first as electrical traces. A big breakthrough was learning to convert these traces to DNA nucleotide sequences using hidden Markov model based algorithms very similar in spirit to those we've already talked about in class (e.g., as in this open source HMM-based nanopore base-caller). The latest base-callers are moving towards neural network algorithms.


Mar 5, 2020 - Guest Lecture: Anna Battenhouse, NGS Analysis Best Practices

  • Practical advice and best practices for NGS mapping and analysis
  • Today's slides


Mar 3, 2020 - Genomes II


Feb 27, 2020 - Genome Assembly

  • Today's slides
  • A gentle reminder that Problem Set 2 is due by 11:59PM March 4
  • Also, next Tuesday will be the first of our guest lecturers, Anna Battenhouse, on practical aspects of genome sequencing/assembly
  • DeBruijn Primer and Supplement
  • If you would like a few examples of proteins annotated with their transmembrane and soluble regions (according to UniProt) to help troubleshoot your homework, here are some example yeast protein sequences.
  • From last time, some definitions of sensitivity/specificity & precision/recall. Note that the gene finding community settled early on to a different definition of specificity that corresponds to the precision or PPV in other fields. Other fields define specificity as the true negative rate.


Feb 25, 2020 - Gene finding II

  • We're finishing up the slides from last time.


Feb 20, 2020 - Gene finding

Problem Set 2, due before midnight Mar. 4, 2020:

Reading (a couple of old classics + a review):


Feb 18, 2020 - HMMs II


Feb 13, 2020 - Hidden Markov Models

  • Happy Day-Before-Valentine's Day!
  • Don't forget: Rosalind Homework #2 (worth 10% of your final course grade) is due by 11:59PM February 19.
  • More stats for comp biologists worth checking out: Modern Statistic for Modern Biology, by Susan Holmes and Wolfgang Huber. It's currently available online and available on dead tree. (FYI, all code is in R.)
  • Today's slides

Reading:


Feb 11, 2020 - Biological databases

  • Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is due by 11:59PM February 19.
  • 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 6, 2020 - BLAST


Feb 4, 2020 - Sequence Alignment II


Jan 30, 2020 - Sequence Alignment I

Problem Set I, due before midnight Feb. 10, 2020:

  • Problem Set 1
  • H. influenzae genome. Haemophilus influenza was the first free living organism to have its genome sequenced. NOTE: there are some additional characters in this file from ambiguous sequence calls. For simplicity's sake, when calculating your nucleotide and dinucleotide frequencies, you can just ignore anything other than A, C, T, and G.
  • T. aquaticus genome. Thermus aquaticus helped spawn the genomic revolution as the source of heat-stable Taq polymerase for PCR.
  • 3 mystery genes (for Problem 5): MysteryGene1, MysteryGene2, MysteryGene3
  • *** HEADS UP FOR THE PROBLEM SET *** If you try to use the Python string.count function to count dinucleotides, Python counts non-overlapping instances, not overlapping instances. So, AAAA is counted as 2, not 3, dinucleotides. You want overlapping dinucleotides instead, so will have to try something else, such as the python string[counter:counter+2] command, as explained in the Rosalind homework assignment on strings.
  • For those of you who could use more tips on programming, there's a weekly peer-led open coding hour happening on Wednesday 12:30-1:30pm in MBB 2.232 (2nd floor lounge). It's a very informal setting where you can work and ask questions of more experienced programmers.

Reading:


Jan 28, 2020 - Intro to Python #2

  • We'll be finishing Python slides from last time, plus Rosalind help & programming Q/A, maybe a glimpse of next lecture.
  • Statistics in Python


Jan 23, 2020 - Intro to Python


Jan 21, 2020 - Introduction

  • Today's slides
  • Some warm-up videos to get you started on Python (2 not 3, unless you pay for an upgrade): Code Academy's Python coding for beginners
  • Khan Academy has archived their videos on Python here
  • We'll be conducting homework using the online environment Rosalind. Go ahead and register on the site, and enroll specifically for BCH394P/364C (Spring 2020) Systems Biology/Bioinformatics using this link. Homework #1 (worth 10% of your final course grade) has already been assigned on Rosalind and is due by 11:59PM January 30.
  • 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 Python before, definitely check this out!!!

Syllabus & course outline

Course syllabus

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

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

Note that this is not a course on practical sequence analysis or using web-based tools. Although we will use a number of these to help illustrate points, the focus of the course will be on learning the underlying algorithms and exploratory data analyses and their applications, esp. in high-throughput biology.

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, 2020. The last 2.5 classes will be spent presenting your projects to each other. (The presentation will account for 5/25 points for 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, problem sets, and written solutions should be performed independently . Students are expected to follow the UT honor code. Cheating, plagiarism, copying, & reuse of prior homework, projects, or programs from CourseHero, Github, or any other sources are all strictly forbidden and constitute breaches of academic integrity (UT academic integrity policy and Sec. 11–402. Academic Dishonesty) and cause for dismissal with a failing grade.

The final project web site is due by midnight April 27, 2020.