Difference between revisions of "BCH394P BCH364C 2019"

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'''April 30, 2019 - Synthetic Biology II'''
 
'''April 30, 2019 - Synthetic Biology II'''
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* '''Reminder: All projects are due by midnight, April 25'''.  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 29'''.  Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR.   
 
* We'll be finishing the slides from Apr. 19.
 
* We'll be finishing the slides from Apr. 19.
  
 
'''April 25, 2019 - Synthetic Biology I'''
 
'''April 25, 2019 - Synthetic Biology I'''
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* '''Reminder: All projects are due by midnight, April 25'''.  Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR.   
+
* '''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.   
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_SyntheticBio_Spring2019.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_SyntheticBio_Spring2019.pdf Today's slides]
 
A collection of further reading, if you're so inclined:
 
A collection of further reading, if you're so inclined:
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'''April 18, 2019 - Networks II'''
 
'''April 18, 2019 - Networks II'''
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* We're finishing up the slides from Apr. 5.
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* We're finishing up the slides from Apr. 16.
 
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'''Apr 16, 2019 - Cryo-electron microscopy'''
 
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* Guest speaker: [http://cryoem.cns.utexas.edu/ Prof. David Taylor]
 
  
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'''Apr 11, 2019 - Networks'''
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'''Apr 16, 2019 - Networks'''
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_Networks_Spring2019.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_Networks_Spring2019.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.
 
* 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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* [http://www.marcottelab.org/users/BCH394P_364C_2019/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]
  
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'''Apr 9, 2019 - Principal Component Analysis (& the curious case of European genotypes)'''
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'''Apr 11, 2019 - 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]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_PCA_Spring2019.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
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* Python code for [http://sebastianraschka.com/Articles/2015_pca_in_3_steps.html performing PCA yourself]. 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.
  
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'''Apr 4, 2019 - Classifiers I'''
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'''Apr 9, 2019 - Classifiers I'''
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_Classifiers_Spring2019.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_Classifiers_Spring2019.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]
 
* [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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* 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].  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 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].
  
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'''Apr 2, 2019 - 3D Protein Structure Modeling'''
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'''Apr 4, 2019 - Clustering II'''
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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_2019/structbio_lecture_BCH394P_364C_2019.pptx Today's slides]<br>
+
−
* 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]
+
−
* 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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−
 
+
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'''Mar 28, 2019 - Clustering II'''
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* 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]
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* We're finishing up the slides from Mar.  20.<br>
+
* We're finishing up the slides from April 2.<br>
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/FuzzyK-Means.pdf Fuzzy k-means]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/FuzzyK-Means.pdf Fuzzy k-means]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/SOM-geneexpression.pdf SOM gene expression]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/SOM-geneexpression.pdf SOM gene expression]
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** 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].  
  
−
[http://www.marcottelab.org/users/BCH394P_364C_2019/ProblemSet3_2019.pdf '''Problem Set 3], due before midnight Apr. 16, 2019'''.  You will need the following software and datasets:<br>
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'''Apr 2, 2019 - Functional Genomics & Data Mining - Clustering I'''
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* 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>
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* [http://www.marcottelab.org/users/BCH394P_364C_2019/yeast_aaseqs Yeast protein sequences]
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* [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_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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'''Mar 26, 2019 - Functional Genomics & Data Mining - Clustering I'''
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* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_LargeScaleExperiments_Spring2019.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_LargeScaleExperiments_Spring2019.pdf Today's slides]
 
* [http://en.wikipedia.org/wiki/Cluster_analysis Clustering]
 
* [http://en.wikipedia.org/wiki/Cluster_analysis Clustering]
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* [http://www.marcottelab.org/users/BCH394P_364C_2019/nature_review_2000.pdf Review of phylogenetic profiles]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/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. 15, 2019'''.  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>
 +
* [http://www.marcottelab.org/users/BCH394P_364C_2019/yeast_aaseqs Yeast protein sequences]
 +
* [http://www.marcottelab.org/users/BCH394P_364C_2019/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].
 +
 +
'''Mar 28, 2019 - Guest Lecture'''<br>
 +
 +
'''Mar 26, 2019 - 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/BCH394P_364C_2019/structbio_lecture_BCH394P_364C_2019.pptx Today's slides]<br>
 +
* 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]
 +
* 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 19-21, 2019 - SPRING BREAK'''
 
'''Mar 19-21, 2019 - SPRING BREAK'''
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'''Mar 14, 2019 - Motifs'''
 
'''Mar 14, 2019 - Motifs'''
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_Motifs_Spring2019.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_Motifs_Spring2019.pdf Today's slides]
−
* '''Due March 19 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>  
+
* '''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>  
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/nbt0406-423-primer-whataremotifs.pdf NBT Primer - What are motifs?]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/nbt0406-423-primer-whataremotifs.pdf NBT Primer - What are motifs?]
 
* [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_2019/nbt0806-959-primer-howdoesmotifdiscoverywork.pdf NBT Primer - How does motif discovery work?]
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'''Mar 12, 2019 - Live Demo: Next-next-...-generation Sequencing (NGS) by nanopore'''
 
'''Mar 12, 2019 - Live Demo: Next-next-...-generation Sequencing (NGS) by nanopore'''
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* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 19'''.
+
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 25'''.
 
* We're trying an experiment this year to see if we can sequence a genome (or at least some reasonable portion of it) in the space/time of a single class (!).  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 trying an experiment this year to see if we can sequence a genome (or at least some reasonable portion of it) in the space/time of a single class (!).  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
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'''Mar 7, 2019 - Genomes II'''<br>
 
'''Mar 7, 2019 - Genomes II'''<br>
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* We're finishing up the slides from Mar. 5. 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.]
+
* 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.]
 
* The [http://www.marcottelab.org/users/BCH394P_364C_2019/BWApaper.pdf BWA paper] gives a clear introduction to how the Burrows–Wheeler transform can be used to construct an index.
 
* The [http://www.marcottelab.org/users/BCH394P_364C_2019/BWApaper.pdf BWA paper] gives a clear introduction to how the Burrows–Wheeler transform can be used to construct an index.
 +
* 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 5, 2019 - Guest Lecture: [https://sites.cns.utexas.edu/cbrs/bioinformatics/staff Anna Battenhouse], NGS Analysis Best Practices'''<br>
 +
* Practical advice and best practices for NGS mapping and analysis
  
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'''Mar 5, 2019 - Genome Assembly'''
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'''Feb 28, 2019 - Genome Assembly'''
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* Follow up from the last lecture: [https://www.biorxiv.org/content/early/2018/02/09/262964 1/3 of known E. coli operons were just extended by at least 1 gene]
+
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_GenomeAssembly_Spring2019.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_GenomeAssembly_Spring2019.pdf Today's slides]
−
* A gentle reminder that Problem Set 2 is '''due by 11:59PM March 5'''<br>
+
* A gentle reminder that Problem Set 2 is '''due by 11:59PM March 6'''<br>
 
* [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_2019/DeBruijnPrimer.pdf DeBruijn Primer] and [http://www.marcottelab.org/users/BCH394P_364C_2019/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]
 
 
* 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].
  
−
'''Feb 28, 2019 - Gene finding II'''
+
'''Feb 26, 2019 - Gene finding II'''
−
* We're finishing up the slides from Feb. 26, then moving on into [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_GenomeAssembly_Spring2019.pdf Genome Assembly]
+
* We're finishing up the slides from Feb. 21, then moving on into [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_GenomeAssembly_Spring2019.pdf Genome Assembly]
  
−
'''Feb 26, 2019 - Gene finding'''
+
'''Feb 21, 2019 - Gene finding'''
−
* We'll finish slides from Feb 21, then start [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C-GeneFinding-Spring2019.pdf today's slides on gene finding]
+
* We'll finish 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]
 
* [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. 11, 2019:<br>
+
Problem Set 2, due before midnight Mar. 6, 2019:<br>
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_ProblemSet2_Spring2019.pdf '''Problem Set 2'''].   
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C_ProblemSet2_Spring2019.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_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]
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* [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_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]
  
−
'''Feb 21, 2019 - HMMs II'''
+
'''Feb 19, 2019 - HMMs II'''
−
* We're finishing up the slides from Feb. 19.  
+
* We're finishing up the slides from Feb. 14.  
 
* News of the day: (1) A group in San Diego [https://www.rchsd.org/about-us/newsroom/press-releases/new-guinness-world-records-title-set-for-fastest-genetic-diagnosis/ was just recognized by the Guinness Book of World Records] for sequencing a newborn infant's genome and diagnosing a genetic disease in <20 hours. The particular sequencing platform they used [https://www.illumina.com/systems/sequencing-platforms/novaseq.html claims a throughput of 6 Tb and 20 B reads in < 2 days].  (2) Relevant to today's lecture, [https://arstechnica.com/science/2018/01/pocket-sized-dna-reader-used-to-scan-entire-human-genome-sequence/ researchers at Nottingham University reported sequencing and assembling a near-complete human genome using a nanopore sequencer].  The data interpretation relied heavily on hidden Markov models.  [http://www.marcottelab.org/users/BCH394P_364C_2019/MinionHumanGenome.pdf Here's the paper].
 
* News of the day: (1) A group in San Diego [https://www.rchsd.org/about-us/newsroom/press-releases/new-guinness-world-records-title-set-for-fastest-genetic-diagnosis/ was just recognized by the Guinness Book of World Records] for sequencing a newborn infant's genome and diagnosing a genetic disease in <20 hours. The particular sequencing platform they used [https://www.illumina.com/systems/sequencing-platforms/novaseq.html claims a throughput of 6 Tb and 20 B reads in < 2 days].  (2) Relevant to today's lecture, [https://arstechnica.com/science/2018/01/pocket-sized-dna-reader-used-to-scan-entire-human-genome-sequence/ researchers at Nottingham University reported sequencing and assembling a near-complete human genome using a nanopore sequencer].  The data interpretation relied heavily on hidden Markov models.  [http://www.marcottelab.org/users/BCH394P_364C_2019/MinionHumanGenome.pdf Here's the paper].
  
−
'''Feb 19, 2019 - Hidden Markov Models'''
+
'''Feb 14, 2019 - Hidden Markov Models'''
−
* Don't forget: Homework #2 (worth 10% of your final course grade) is due on Rosalind '''by 11:59PM February 19'''.
+
* Happy Valentine's Day!
 +
* Don't forget: Rosalind Homework #2 (worth 10% of your final course grade) is due '''by 11:59PM February 20'''.
 
* Linking out to [http://www.uniprot.org/ UniProt], discussed last time
 
* Linking out to [http://www.uniprot.org/ UniProt], discussed last time
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C-HMMs-Spring2019.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C-HMMs-Spring2019.pdf Today's slides]<br>
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* Care to practice your [http://en.wikipedia.org/wiki/Regular_expression regular expressions]? (In [http://www.tutorialspoint.com/python/python_reg_expressions.htm python?])
 
* Care to practice your [http://en.wikipedia.org/wiki/Regular_expression regular expressions]? (In [http://www.tutorialspoint.com/python/python_reg_expressions.htm python?])
  
−
'''Feb 14, 2019 - Biological databases'''
+
'''Feb 12, 2019 - Biological databases'''
 +
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 20'''.
 
* 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.
 
* 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_2019/BCH394P-364C-BiologicalDatabases-Spring2019.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P-364C-BiologicalDatabases-Spring2019.pdf Today's slides]<br>
−
 
+
-->
−
'''Feb 12, 2019 - BLAST'''
+
'''Feb 7, 2019 - BLAST'''
−
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 19'''.
+
 
* [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_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_2019/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 7, 2019 - Guest lecture: Homologs, orthologs, and evolutionary trees'''
 
−
* 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/BCH394P_364C_2019/BioinformaticsClass_sp2018.pdf Today's slides]<br>
 
−
-->
 
−
<!--
 
 
'''Feb 5, 2019 - Sequence Alignment II'''
 
'''Feb 5, 2019 - Sequence Alignment II'''
−
* News of the day: [https://www.sciencealert.com/naked-mole-rats-nonageing-gompertz-law-longevity-calico Naked mole rats apparently don't age!?!]
+
* We're finishing up the slides from Jan. 31.  
−
* We're finishing up the slides from Jan. 25.  
+
* [http://www.marcottelab.org/users/BCH394P_364C_2019/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_2019/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_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)
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'''Jan 29, 2019 - Finishing Python intro, plus Rosalind help & programming Q/A, maybe a glimpse of next lecture'''
 
'''Jan 29, 2019 - Finishing Python intro, plus Rosalind help & programming Q/A, maybe a glimpse of next lecture'''
−
* [https://www.theatlantic.com/science/archive/2018/01/brain-cells-can-share-information-using-a-gene-that-came-from-viruses/550403/ news of the day--your neurons communicate with proteins related to retroviruses], reporting on 2 very nice back-to-back papers in cell: [http://www.cell.com/cell/fulltext/S0092-8674(17)31504-0 1], [http://www.cell.com/cell/fulltext/S0092-8674(17)31502-7 2]
 
 
* [http://www.scipy-lectures.org/packages/statistics/index.html Statistics in Python]
 
* [http://www.scipy-lectures.org/packages/statistics/index.html Statistics in Python]
 
* We'll be finishing Python slides from last time.
 
* We'll be finishing Python slides from last time.
−
-->
+
 
 
'''Jan 24, 2019 - Intro to Python'''
 
'''Jan 24, 2019 - 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.
 
* 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.

Revision as of 17:50, 20 January 2019

BCH394P/BCH364C Systems Biology & Bioinformatics

Course unique #: 54044/53945
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: Caitie McCaffery, clmccafferty @ utexas.edu

  • TA Office hours: Mon 11-12/Fri 2-3 in NHB 3.400B atrium (or MBB 3.128B) Phone: 512-232-3919

Lectures & Handouts

Feb 7, 2019 - BLAST

Feb 5, 2019 - Sequence Alignment II

Jan 31, 2019 - Sequence Alignment I

  • For those of you who might be interested, Rosalind is having a 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!
  • Today's slides

Problem Set I, due before midnight Feb. 11, 2019:

  • 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 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.

Reading:

Jan 29, 2019 - Finishing Python intro, plus Rosalind help & programming Q/A, maybe a glimpse of next lecture

Jan 24, 2019 - 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.
  • Today's slides
  • Python primer
  • E. coli genome
  • 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, 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 differences are quite minimal.

Jan 22, 2019 - 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-BCH364C-Spring2019 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 31.
  • 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 29, 2019. 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 cause for dismissal with a failing grade.

The final project web site is due by midnight April 29, 2019.

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