Difference between revisions of "BCH394P BCH364C 2019"

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== Lectures & Handouts ==
 
== Lectures & Handouts ==
 
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'''Apr 26 - May 3, 2018 - Final Project Presentations'''
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'''May 2 - May 7, 2019 - 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].
 
* 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].
 
* We'll spend 5 minutes on the [https://utdirect.utexas.edu/ctl/ecis/ Course - Instructor Survey] this morning.
 
* We'll spend 5 minutes on the [https://utdirect.utexas.edu/ctl/ecis/ Course - Instructor Survey] this morning.
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** [https://sites.google.com/utexas.edu/bch339n-petbiodegradation/home PET Biodegradation, by Candice Chen, Nick Brzezniak, Max Rector]  
 
** [https://sites.google.com/utexas.edu/bch339n-petbiodegradation/home PET Biodegradation, by Candice Chen, Nick Brzezniak, Max Rector]  
  
'''April 24, 2018 - Synthetic Biology II'''
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'''April 30, 2019 - Synthetic Biology II'''
 
* '''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 25'''.  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 19, 2018 - Synthetic Biology I'''
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'''April 25, 2019 - Synthetic Biology I'''
 
* '''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 25'''.  Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR.   
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_SyntheticBio_Spring2018.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_SyntheticBio_Spring2018.pdf Today's slides]
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[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]
  
'''April 17, 2018 - Phenologs'''
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'''April 23, 2019 - Phenologs'''
 
* '''Remember: The final project web page is due by midnight April 25, 2018, 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.'''  
 
* '''Remember: The final project web page is due by midnight April 25, 2018, 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.'''  
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_Phenologs_Spring2018.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_Phenologs_Spring2018.pdf Today's slides]
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* [http://www.marcottelab.org/users/BCH339N_2018/Sonnhammer2002TiG.pdf All your ortholog definition questions answered!]
 
* [http://www.marcottelab.org/users/BCH339N_2018/Sonnhammer2002TiG.pdf All your ortholog definition questions answered!]
  
'''April 12, 2018 - Networks II'''
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'''April 18, 2019 - Networks II'''
 
* We're finishing up the slides from Apr. 5.
 
* We're finishing up the slides from Apr. 5.
 
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'''Apr 10, 2018 - Cryo-electron microscopy'''
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'''Apr 16, 2019 - Cryo-electron microscopy'''
 
* Guest speaker: [http://cryoem.cns.utexas.edu/ Prof. David Taylor]
 
* Guest speaker: [http://cryoem.cns.utexas.edu/ Prof. David Taylor]
  
'''April 5, 2018 - Networks'''
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'''Apr 11, 2019 - Networks'''
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_Networks_Spring2018.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_Networks_Spring2018.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/BCH339N_2018/HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network], a review of [http://www.marcottelab.org/users/BCH339N_2018/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/BCH339N_2018/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/BCH339N_2018/HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network], a review of [http://www.marcottelab.org/users/BCH339N_2018/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/BCH339N_2018/PPIsAndDiseaseReview.pdf protein interaction mapping in humans] and how it is informing disease genetics.
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* [http://www.marcottelab.org/users/BCH339N_2018/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]
 
* [http://www.marcottelab.org/users/BCH339N_2018/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]
  
'''Apr 3, 2018 - Principal Component Analysis (& the curious case of European genotypes)'''
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'''Apr 9, 2019 - Principal Component Analysis (& the curious case of European genotypes)'''
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_PCA_Spring2018.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_PCA_Spring2018.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2018/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
 
* [http://www.marcottelab.org/users/BCH339N_2018/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.
  
'''Mar 29, 2018 - Classifiers I'''
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'''Apr 4, 2019 - Classifiers I'''
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_Classifiers_Spring2018.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_Classifiers_Spring2018.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2018/MachineLearningReview.pdf A nice recent review explaining Support Vector Machines and k-NN classifiers]
 
* [http://www.marcottelab.org/users/BCH339N_2018/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].
  
'''Mar 27, 2018 - 3D Protein Structure Modeling'''
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'''Apr 2, 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
 
* Guest speaker: [https://scholar.google.com/citations?hl=en&user=zJ8L0GcAAAAJ&view_op=list_works Dr. Kevin Drew], formerly of New York University and now at the UT Center for Systems and Synthetic Biology
 
* [http://www.marcottelab.org/users/BCH339N_2018/structbio_lecture_BCH339N_2018.pptx Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2018/structbio_lecture_BCH339N_2018.pptx Today's slides]<br>
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* The [http://www.rcsb.org/pdb/ Protein Data Bank], [http://toolkit.tuebingen.mpg.de/hhpred HHPRED], [https://salilab.org/modeller/ MODELLER], and [http://www.pymol.org/ Pymol]
 
* The [http://www.rcsb.org/pdb/ Protein Data Bank], [http://toolkit.tuebingen.mpg.de/hhpred HHPRED], [https://salilab.org/modeller/ MODELLER], and [http://www.pymol.org/ Pymol]
  
'''Mar 22, 2018 - Clustering II'''
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'''Mar 28, 2019 - 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 Mar.  20.<br>
 
* We're finishing up the slides from Mar.  20.<br>
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* [http://www.marcottelab.org/users/BCH339N_2018/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].
 
* [http://www.marcottelab.org/users/BCH339N_2018/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 20, 2018 - Functional Genomics & Data Mining - Clustering I'''
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'''Mar 26, 2019 - Functional Genomics & Data Mining - Clustering I'''
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_LargeScaleExperiments_Spring2018.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_LargeScaleExperiments_Spring2018.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://en.wikipedia.org/wiki/RNA-Seq RNA-Seq]
 
* [http://en.wikipedia.org/wiki/RNA-Seq RNA-Seq]
  
'''Mar 13-15, 2018 - SPRING BREAK'''
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'''Mar 19-21, 2019 - SPRING BREAK'''
 
* Finish HW3 and turn in the proposal for your course project.
 
* Finish HW3 and turn in the proposal for your course project.
  
'''Mar 8, 2018 - Motifs'''
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'''Mar 14, 2019 - Motifs'''
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_Motifs_Spring2018.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_Motifs_Spring2018.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 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>  
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* FYI, The nanopore sequencing run we started in class ran for a day and collected >9000 basecalled reads, with average lengths of several thousand nucleotides. Our longest read was almost 70 kb! <s>We'll clean up the data and post it to the course web site so that some of you can use it for projects, if desired.</s>  Here are the nanopore reads if you'd like to play with them.  There are 3 fastq files, each gzipped and ~10-30GB in size:  [http://www.marcottelab.org/users/BCH339N_2018/fastq_runid_fbea4bea7410dfda4bf285ff8f07fef0c49a6b4f_0.fastq.gz 0], [http://www.marcottelab.org/users/BCH339N_2018/fastq_runid_fbea4bea7410dfda4bf285ff8f07fef0c49a6b4f_1.fastq.gz 1], [http://www.marcottelab.org/users/BCH339N_2018/fastq_runid_fbea4bea7410dfda4bf285ff8f07fef0c49a6b4f_2.fastq.gz 2]
 
* FYI, The nanopore sequencing run we started in class ran for a day and collected >9000 basecalled reads, with average lengths of several thousand nucleotides. Our longest read was almost 70 kb! <s>We'll clean up the data and post it to the course web site so that some of you can use it for projects, if desired.</s>  Here are the nanopore reads if you'd like to play with them.  There are 3 fastq files, each gzipped and ~10-30GB in size:  [http://www.marcottelab.org/users/BCH339N_2018/fastq_runid_fbea4bea7410dfda4bf285ff8f07fef0c49a6b4f_0.fastq.gz 0], [http://www.marcottelab.org/users/BCH339N_2018/fastq_runid_fbea4bea7410dfda4bf285ff8f07fef0c49a6b4f_1.fastq.gz 1], [http://www.marcottelab.org/users/BCH339N_2018/fastq_runid_fbea4bea7410dfda4bf285ff8f07fef0c49a6b4f_2.fastq.gz 2]
  
'''Mar 6, 2018 - Live Demo: Next-next-...-generation Sequencing (NGS) by nanopore'''
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'''Mar 12, 2019 - 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 19'''.
 
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 19'''.
 
* 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:
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* Here's [https://nanoporetech.com/resource-centre/videos/nanopore-dna-sequencing Oxford nanopore's own video] 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 [https://academic.oup.com/bioinformatics/article/33/1/49/2525680 this open source HMM-based nanopore base-caller]).  [https://nanoporetech.com/about-us/news/new-basecaller-now-performs-raw-basecalling-improved-sequencing-accuracy The latest base-callers] are moving towards neural network algorithms.
 
* Here's [https://nanoporetech.com/resource-centre/videos/nanopore-dna-sequencing Oxford nanopore's own video] 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 [https://academic.oup.com/bioinformatics/article/33/1/49/2525680 this open source HMM-based nanopore base-caller]).  [https://nanoporetech.com/about-us/news/new-basecaller-now-performs-raw-basecalling-improved-sequencing-accuracy The latest base-callers] are moving towards neural network algorithms.
  
'''Mar 1, 2018 - Genomes II'''<br>
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'''Mar 7, 2019 - Genomes II'''<br>
* 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.]
+
* 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.]
 
* The [http://www.marcottelab.org/users/BCH339N_2018/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/BCH339N_2018/BWApaper.pdf BWA paper] gives a clear introduction to how the Burrows–Wheeler transform can be used to construct an index.
  
'''Feb 27, 2018 - Genome Assembly'''
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'''Mar 5, 2019 - Genome Assembly'''
 
* 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]
 
* 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/BCH339N_2018/BCH339N_GenomeAssembly_Spring2018.pdf Today's slides]
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_GenomeAssembly_Spring2018.pdf Today's slides]
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* 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 22, 2018 - Gene finding II'''
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'''Feb 28, 2019 - Gene finding II'''
* We're finishing up the slides from Feb. 20, then moving on into [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_GenomeAssembly_Spring2018.pdf Genome Assembly]
+
* We're finishing up the slides from Feb. 26, then moving on into [http://www.marcottelab.org/users/BCH339N_2018/BCH339N_GenomeAssembly_Spring2018.pdf Genome Assembly]
  
'''Feb 20, 2018 - Gene finding'''
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'''Feb 26, 2019 - Gene finding'''
* We'll finish slides from Feb 15, then start [http://www.marcottelab.org/users/BCH339N_2018/BCH339N-GeneFinding-Spring2018.pdf today's slides on gene finding]
+
* We'll finish slides from Feb 21, then start [http://www.marcottelab.org/users/BCH339N_2018/BCH339N-GeneFinding-Spring2018.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. 5, 2018:<br>
 
Problem Set 2, due before midnight Mar. 5, 2018:<br>
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* [http://www.marcottelab.org/users/BCH339N_2018/EukGeneAnnotation.pdf Eukaryotic gene finding], [http://www.marcottelab.org/users/BCH339N_2018/GeneMark.hmm.pdf GeneMark.hmm], and [http://www.marcottelab.org/users/BCH339N_2018/BurgeKarlin-main.pdf GENSCAN]
 
* [http://www.marcottelab.org/users/BCH339N_2018/EukGeneAnnotation.pdf Eukaryotic gene finding], [http://www.marcottelab.org/users/BCH339N_2018/GeneMark.hmm.pdf GeneMark.hmm], and [http://www.marcottelab.org/users/BCH339N_2018/BurgeKarlin-main.pdf GENSCAN]
  
'''Feb 15, 2018 - HMMs II'''
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'''Feb 21, 2019 - HMMs II'''
* We're finishing up the slides from Feb. 13.  
+
* We're finishing up the slides from Feb. 19.  
 
* 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/BCH339N_2018/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/BCH339N_2018/MinionHumanGenome.pdf Here's the paper].
  
'''Feb 13, 2018 - Hidden Markov Models'''
+
'''Feb 19, 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'''.
 
* Don't forget: Homework #2 (worth 10% of your final course grade) is due on Rosalind '''by 11:59PM February 19'''.
 
* Linking out to [http://www.uniprot.org/ UniProt], discussed last time
 
* Linking out to [http://www.uniprot.org/ UniProt], discussed last time
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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 8, 2018 - Biological databases'''
+
'''Feb 14, 2019 - Biological databases'''
 
* Just a note that we'll be seeing ever more statistics as go on. Here's a [http://www.marcottelab.org/users/BCH339N_2018/StatisticsPrimer.pdf good primer] from [http://www.bio.utexas.edu/research/meyers/LaurenM/index.html Prof. Lauren Myers] to refresh/explain basic concepts.
 
* Just a note that we'll be seeing ever more statistics as go on. Here's a [http://www.marcottelab.org/users/BCH339N_2018/StatisticsPrimer.pdf good primer] from [http://www.bio.utexas.edu/research/meyers/LaurenM/index.html Prof. Lauren Myers] to refresh/explain basic concepts.
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N-BiologicalDatabases-Spring2018.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N-BiologicalDatabases-Spring2018.pdf Today's slides]<br>
  
'''Feb 6, 2018 - BLAST'''
+
'''Feb 12, 2019 - BLAST'''
 
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 19'''.
 
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 19'''.
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N-BLAST-Spring2018.pdf Our slides today] are modified from a paper on [http://dx.doi.org/10.1371/journal.pbio.1001014 Teaching BLAST] by Cheryl Kerfeld & Kathleen Scott.
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N-BLAST-Spring2018.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.
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* [http://www.marcottelab.org/paper-pdfs/jmb-lgl.pdf The protein homology graph paper]. Just for fun, here's a link to a [http://www.moma.org/interactives/exhibitions/2008/elasticmind/#/211/ stylized version] we exhibited in the engaging [http://www.moma.org/interactives/exhibitions/2008/elasticmind/ Design and the Elastic Mind] show at New York's Museum of Modern Art.  
 
* [http://www.marcottelab.org/paper-pdfs/jmb-lgl.pdf The protein homology graph paper]. Just for fun, here's a link to a [http://www.moma.org/interactives/exhibitions/2008/elasticmind/#/211/ stylized version] we exhibited in the engaging [http://www.moma.org/interactives/exhibitions/2008/elasticmind/ Design and the Elastic Mind] show at New York's Museum of Modern Art.  
  
'''Feb 1, 2018 - Guest lecture: Homologs, orthologs, and evolutionary trees'''  
+
'''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.  
 
* We'll have a guest lecture by [http://bliebeskind.github.io/ Ben Liebeskind], a postdoctoral fellow in the Center for Systems and Synthetic Biology, on decoding the evolutionary relationships among genes.  
 
-->
 
-->
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-->
 
-->
 
<!--
 
<!--
'''Jan 30, 2018 - 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!?!]
 
* 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. 25.  
 
* We're finishing up the slides from Jan. 25.  
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* A few examples of proteins with internally repetitive sequences: [http://www.pdb.org/pdb/explore/explore.do?structureId=1QYY 1], [http://www.pdb.org/pdb/explore/explore.do?structureId=2BEX 2], [http://www.pdb.org/pdb/explore/explore.do?structureId=1BKV 3]
 
* A few examples of proteins with internally repetitive sequences: [http://www.pdb.org/pdb/explore/explore.do?structureId=1QYY 1], [http://www.pdb.org/pdb/explore/explore.do?structureId=2BEX 2], [http://www.pdb.org/pdb/explore/explore.do?structureId=1BKV 3]
  
'''Jan 25, 2018 - Sequence Alignment I'''
+
'''Jan 31, 2019 - 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. 3, the qualification round is Feb. 3-11, and Feb. 24 is the final round, with 24 hours to solve as many problems as you can. First prize in 2017 was to get your genome (exome) sequenced!
 
* For those of you who might be interested, Rosalind is having a [http://bioinf.me/contest Bioinformatics Contest].  Sign up runs until Feb. 3, the qualification round is Feb. 3-11, and Feb. 24 is the final round, with 24 hours to solve as many problems as you can. First prize in 2017 was to get your genome (exome) sequenced!
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N-Spring2018-SequenceAlignmentI.pdf Today's slides]<br>
 
* [http://www.marcottelab.org/users/BCH339N_2018/BCH339N-Spring2018-SequenceAlignmentI.pdf Today's slides]<br>
Line 233: Line 233:
 
* 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 23, 2018 - 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]
 
* [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 18, 2018 - Intro to Python'''
+
'''Jan 24, 2019 - Intro to Python'''
 
* Given '''SNOWPOCALYPSE 2018''' and our lost first day of class, we'll pick up mid-stream: Today's lecture will combine the planned short intro from lecture 1 with a plunge right into Python...
 
* Given '''SNOWPOCALYPSE 2018''' and our lost first day of class, we'll pick up mid-stream: Today's lecture will combine the planned short intro from lecture 1 with a plunge right into Python...
 
-->
 
-->
Line 251: Line 251:
 
* [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://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].
 
-->
 
-->
'''Jan 16, 2018 - Introduction'''
+
'''Jan 22, 2019 - Introduction'''
 
* [http://www.marcottelab.org/users/BCH394P_364C_2019/BCH394P_364C-IntroAndRosalind-Spring2019.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>

Revision as of 14:48, 19 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 3.202 (or MBB 3.128AA) Phone: 512-232-3919

Lectures & Handouts

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
  • 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 25, 2018. The last three classes will be spent presenting your projects to each other. (The presentation will account for 5% of the project.)

Online homework will be assigned and evaluated using the free bioinformatics web resource Rosalind.

All projects and homework will be turned in electronically and time-stamped. No makeup work will be given. Instead, all students have 5 days of free “late time” (for the entire semester, NOT per project, and counting weekends/holidays). For projects turned in late, days will be deducted from the 5 day total (or what remains of it) by the number of days late (in 1 day increments, rounding up, i.e. 10 minutes late = 1 day deducted). Once the full 5 days have been used up, assignments will be penalized 10 percent per day late (rounding up), i.e., a 50 point assignment turned in 1.5 days late would be penalized 20%, or 10 points.

Homework, problem sets, and the project total to a possible 100 points. There will be no curving of grades, nor will grades be rounded up. We’ll use the plus/minus grading system, so: A= 92 and above, A-=90 to 91.99, etc. Just for clarity's sake, here are the cutoffs for the grades: 92% = A, 90% = A- < 92%, 88% = B+ < 90%, 82% = B < 88%, 80% = B- < 82%, 78% = C+ < 80%, 72% = C < 78%, 70% = C- < 72%, 68% = D+ < 70%, 62% = D < 68%, 60% = D- < 62%, F < 60%.

Students are welcome to discuss ideas and problems with each other, but all programs, Rosalind homework, 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 25, 2018.