View source for BCH364C BCH394P 2017

== BCH364C/BCH394P Systems Biology & Bioinformatics ==

'''Course unique #:''' 55120/55210<br>
'''Lectures:'''	Tues/Thurs 11 – 12:30 PM in GDC 4.302<br>
'''Instructor:'''  Edward Marcotte,		marcotte @ icmb.utexas.edu<br>
* '''Office hours:'''  		Wed 11 AM – 12 noon in MBB 3.148BA<br>
'''TA:''' Azat Akhmetov,	azat @ utexas.edu<br>
*'''TA Office hours:''' 	Mon/Wed 3 PM - 4 PM in MBB 3.204 '''Phone:''' on syllabus<br>

== Lectures & Handouts ==
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'''May 2 - May 4, 2017 - Gene Presentations'''
* Note: There are some great [http://ccbb.biosci.utexas.edu/summerschool.html short summer courses in computational biology] being offered at UT. Of particular note, introductions to [http://ccbb.biosci.utexas.edu/summerschool.html#corengs core NextGen sequencing tools].

'''April 27, 2017 - Synthetic Biology II'''

'''Apr 25, 2017 - Genome Engineering'''
* Problem Set 3 deadline has been pushed to midnight April 18, 2016.
* Guest speaker: [http://www.yeastgenome.org/cgi-bin/colleague/colleagueSearch?rm=colleague_page&id=12102 Dr. Chris Yellman]

'''April 20, 2017 - Synthetic Biology I'''
* '''Reminder: All gene projects are due by midnight, April 27'''.  Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR.  
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_SyntheticBio-Spring2017.pdf Today's slides]
A collection of further reading, if you're so inclined:
* [http://www.marcottelab.org/users/BCH364C_394P_2017/MinimalMycoplasma.pdf Minimal Mycoplasma]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/GenomeTransplantation.pdf Genome Transplantation]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/JCVI-1.0.pdf JCVI-1.0]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/OneStepAssemblyInYeast.pdf One step genome assembly in yeast]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/StrainsFromYeastGenomicClones.pdf New cells from yeast genomic clones]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NewCellFromChemicalGenome.pdf A new cell from a chemically synthesized genome], [http://www.marcottelab.org/users/BCH364C_394P_2017/NewCellFromChemicalGenome.SOM.pdf SOM]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/YeastSynthCsome.pdf 1/2 a synthetic yeast chromosome] and [http://syntheticyeast.org/ Build-A-Genome]
* & the latest: [http://www.marcottelab.org/users/BCH364C_394P_2017/Science-2014-Annaluru-55-8.pdf Entire synthetic yeast chromosome] 
* [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])
* [http://www.popsci.com/diy/article/2013-08/grow-photo Take your own coliroids]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/repressilator.pdf The infamous repressilator]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BacterialPhotography.pdf Bacterial photography], and [http://www.marcottelab.org/users/BIO337_2014/UTiGEM2012.pdf UT's 2012 iGEM entry]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/EdgeDetector.pdf Edge detector]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/nbt.2510.pdf A more recent example of digital logic]
* An example of metabolic engineering: [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12051.html yeast making anti-malarial drugs]
Food for thought:<br>
[http://www.nationalgeographic.com/deextinction De-extinction I], [http://science.kqed.org/quest/video/reawakening-extinct-species/ II], and [http://www.popsci.com/woolly-mammoth-dna-brought-life-elephant-cells III]

'''April 18, 2017 - Phenologs'''
* Remember: The final project web page is due by midnight April 27, 2016.  
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Phenologs_Spring2017.pdf Today's slides]
* [http://www.marcottelab.org/paper-pdfs/PNAS_Phenologs_2010.pdf Phenologs] and the [http://www.marcottelab.org/paper-pdfs/PLoSBiology_TBZ_2012.pdf drug discovery story] we'll discuss in class
* Search for phenologs [http://www.phenologs.org/ here].  You can get started by rediscovering the plant model of Waardenburg syndrome.  Search among the known diseases for "Waardenburg", or enter the human genes linked to Waardenburg (Entrez gene IDs 4286, 5077, 6591, 7299) to get a feel for how this works. Also, here's [http://www.nytimes.com/2010/04/27/science/27gene.html?_r=0 Carl Zimmer's NYT article] about phenologs and the scientific process.
Tools for finding orthologs:<br>
* One good tool for discovering orthologs is [http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid].  Note: InParanoid annotation lags a bit, so you'll need to find the [http://www.ensembl.org/index.html Ensembl] protein id, or try a text search for the common name. Or, just link there from [http://www.uniprot.org/ Uniprot]. InParanoid tends towards higher recall, lower precision for finding orthologs. Approaches with higher precision include [http://omabrowser.org/oma/home/ OMA] (introduced in [http://www.marcottelab.org/users/BCH364C_394P_2017/OMA.pdf this paper]), [http://phylomedb.org/ PhylomeDB], and just released, [http://pythonhosted.org/bio-MOSAIC/ MOSAIC]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Sonnhammer2002TiG.pdf All your ortholog definition questions answered!]

'''April 13, 2017 - Networks II'''

'''April 11, 2017 - Networks'''
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Networks_Spring2017.pdf Today's slides]
* Metabolic networks: [http://ca.expasy.org/cgi-bin/show_thumbnails.pl The wall chart] (it's interactive, e.g. here's [http://web.expasy.org/cgi-bin/pathways/show_image?E5&left enolase]), the current state of the [http://www.marcottelab.org/users/BCH364C_394P_2017/HumanMetabolicReactionNetwork-2013.pdf human metabolic reaction network], and older but still relevant review of [http://www.marcottelab.org/users/BCH364C_394P_2017/ChIP-chipReview.pdf transcriptional networks] (with the current record holder in this regard held by [http://www.genome.gov/10005107 ENCODE]), and an early review of [http://www.marcottelab.org/users/BCH364C_394P_2017/vonmering.pdf protein interaction extent and quality] whose lessons still hold.
* Useful gene network resources include:
** [http://www.functionalnet.org FunctionalNet], which links to human, worm, Arabidopsis, mouse and yeast gene networks. Not the prettiest web site, but useful, and helped my own group find genes for a wide variety of biological processes. Try searching HumanNet for the myelin regulatory factor MYRF (Entrez gene ID 745) and predicting its function, which is now known but wasn't when the network was made. 
** [http://string-db.org/ STRING] is available for many organisms, including large numbers of prokaryotes. Try searching on the <i>E. coli</i> enolase (Eno) as an example.
** [http://www.genemania.org/ GeneMania], which aggregates many individual gene networks.
** [http://func.mshri.on.ca/ MouseFunc], a collection of network and classifier-based predictions of gene function from [http://www.marcottelab.org/paper-pdfs/GenomeBiology_MouseFunc_2008.pdf an open contest to predict gene function in the mouse].
** 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]).
Reading:<br>
* [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/users/BCH364C_394P_2017/NBTPrimer-NetworkVisualization.pdf Primer on visualizing networks]

'''Apr 6, 2017 - Principal Component Analysis (& the curious case of European genotypes)'''
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_PCA_Spring2017.pdf Today's slides]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/EuropeanGenesPCA.pdf European men, their genomes, and their geography]
* [http://projector.tensorflow.org/ Nice interactive visualization tool using PCA]
* Relevant to today's discussion for his eponymous distance measure: [http://en.wikipedia.org/wiki/Prasanta_Chandra_Mahalanobis Mahalanobis]
A smattering of links on PCA:<br>
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBT_primer_PCA.pdf NBT Primer on PCA]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/PrincipalComponentAnalysis.docx A PCA overview (.docx format)] & the [http://horicky.blogspot.com/2009/11/principal-component-analysis.html original post]
* Science Signaling (more specifically, Neil R. Clark and Avi Ma’ayan!) had a [http://stke.sciencemag.org/cgi/content/full/sigtrans;4/190/tr3/DC1 nice introduction to PCA] that I've reposted [http://www.marcottelab.org/users/BCH364C_394P_2017/IntroToPCA.pdf here] (with [http://www.marcottelab.org/users/BCH364C_394P_2017/2001967Slides-FINAL.ppt slides])
* Python code for [http://sebastianraschka.com/Articles/2015_pca_in_3_steps.html performing PCA yourself]

'''Apr 4, 2017 - Classifiers I'''
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Classifiers_Spring2017.pdf Today's slides]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/AMLALLclassification.pdf Classifying leukemias]
* For those of you interesting in trying out classifiers on your own, here's the best open software for do-it-yourself classifiers and data mining: [http://www.cs.waikato.ac.nz/ml/weka/ Weka]

'''Mar 30, 2017 - Mass spectrometry proteomics'''
* Guest speaker: [http://www.researchgate.net/profile/Daniel_Boutz/ Dr. Daniel Boutz]

'''Mar 28, 2017 - 3D Protein Structure Modeling'''
* Guest speaker: [https://scholar.google.com/citations?hl=en&user=zJ8L0GcAAAAJ&view_op=list_works Dr. Kevin Drew], formerly of New York University and now at the UT Center for Systems and Synthetic Biology
* [http://www.marcottelab.org/users/BCH364C_394P_2017/structbio_lecture_BCH364C-394P_2016.pptx Today's slides]<br>
* The [https://www.rosettacommons.org/software Rosetta] software suite for 3D protein modeling, and [http://www.marcottelab.org/users/BCH364C_394P_2017/RosettaOverview.pdf what it can do for you]
* The [http://www.rcsb.org/pdb/ Protein Data Bank], [http://toolkit.tuebingen.mpg.de/hhpred HHPRED], [https://salilab.org/modeller/ MODELLER], and [http://www.pymol.org/ Pymol]

'''Mar 23, 2017 - Clustering II'''
* We're finishing up the slides from Mar.  24.<br>
* [http://www.marcottelab.org/users/BCH364C_394P_2017/FuzzyK-Means.pdf Fuzzy k-means]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/SOM-geneexpression.pdf SOM gene expression]
** Links to various applications of SOMs: [http://en.wikipedia.org/wiki/Self-organizing_map 1], [http://www.bentley.edu/centers/sites/www.bentley.edu.centers/files/csbigs/hua.pdf 2], [http://vizier.u-strasbg.fr/kohonen.htx 3], [http://wn.com/Self_Organizing_Maps_Application 4]. You can run SOMs on the [http://www.math.le.ac.uk/people/ag153/homepage/PCA_SOM/PCA_SOM.html following web site]. You can also run SOM clustering with the Open Source Clustering package from problem set 3 with the '-s' option, or GUI option. See [http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/SOM.html#SOM the manual] for details. (FYI, it also supports PCA). If you are not happy with Cluster's SOM function, the statistical package R also provides a package for calculating SOMs (http://cran.r-project.org/web/packages/som/index.html). 

'''Mar 21, 2017 - Functional Genomics & Data Mining - Clustering I'''
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_LargeScaleExperiments_Spring2017.pdf Today's slides]
* [http://en.wikipedia.org/wiki/Cluster_analysis Clustering]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/nature_review_2000.pdf Review of phylogenetic profiles]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Bcelllymphoma.pdf B cell lymphomas]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-MicroarrayClustering.pdf Primer on clustering]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/K-means-Example.ppt K-means example (.ppt)]

[http://www.marcottelab.org/users/BCH364C_394P_2017/ProblemSet3_2016.pdf '''Problem Set 3], due before midnight Apr. 14, 2016'''.  You will need the following software and datasets:<br>
* The clustering and treeview software is available [http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm here].<br> 
* [http://www.marcottelab.org/users/BCH364C_394P_2017/yeast_aaseqs Yeast protein sequences]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/yeast_phyloprofiles2.txt Yeast protein phylogenetic profiles]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/yeast_microarraydata2.txt Yeast mRNA expression profiles]

'''Mar 14-16, 2017 - SPRING BREAK'''
* Finish HW3 and and the first mini-assignment (#1) for your gene project.

'''Mar 9, 2017 - Motifs'''
* Homework #3 (worth 10% of your final course grade) is due on Rosalind '''by 11:59PM tonight'''.  There were apparently problems with the [http://meme-suite.org/ Meme web server], but it appears to working now.  Also, a [http://alternate.meme-suite.org/ mirror Meme server] has been set up as an alternative.
* Go ahead and start mini-assignment 2, and try to finish it within a week.  
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Motifs_Spring2017.pdf Today's slides]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/nbt0406-423-primer-whataremotifs.pdf NBT Primer - What are motifs?]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/nbt0806-959-primer-howdoesmotifdiscoverywork.pdf NBT Primer - How does motif discovery work?]
* [http://www.rcsb.org/pdb/explore/explore.do?structureId=1L1M The biochemical basis of a particular motif]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/GibbsSampling.pdf Gibbs Sampling]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/AlignAce.pdf AlignAce]

'''Mar 7, 2017 - Genomes II'''<br>
* Homework #3 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM March 22'''.
* We're finishing up the slides from Mar. 2, then on to motif-finding. Note: we'll increasingly be discussing primary papers in the lectures.  Here are a few classics and reviews that will come up after Spring Break if you want to start looking ahead.<br>
* [http://www.marcottelab.org/users/BCH364C_394P_2017/ESTs.pdf Gene expression by ESTs]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/SAGE.pdf Gene expression by SAGE]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Affy2.pdf Affy microarrays 1] & [http://www.marcottelab.org/users/BIO337_2014/Affy1.pdf Affy microarrays 2]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/DeRisi.pdf cDNA microarrays]
* [http://en.wikipedia.org/wiki/RNA-Seq RNA-Seq]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/eisen.pdf Clustering by gene expression]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Spellman.pdf Cell cycle data]
-->
'''Mar 2, 2017 - Genome Assembly'''
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_GenomeAssembly_Spring2017.pdf Today's slides]
* A gentle reminder that Problem Set 2 is '''due by 11:59PM March 6'''<br>
* [http://www.marcottelab.org/users/BCH364C_394P_2017/DeBruijnPrimer.pdf DeBruijn Primer] and [http://www.marcottelab.org/users/BCH364C_394P_2017/DeBruijnSupplement.pdf Supplement]
* Here are a few explanations of using the BWT for indexing: [http://blog.avadis-ngs.com/2012/04/elegant-exact-string-match-using-bwt-2/ 1] [http://www.di.unipi.it/~ferragin/Libraries/fmindexV2/index.html 2]
* Here are some [http://www.marcottelab.org/images/5/5a/Annotated_peptides.txt example yeast protein sequences], annotated with their transmembrane and soluble regions (according to UniProt).

'''Feb 28, 2017 - Next-generation Sequencing (NGS)'''
* Guest speaker: [https://www.linkedin.com/in/scott-hunicke-smith-6081767 Dr. Scott Hunicke-Smith], former director of the [https://wikis.utexas.edu/display/GSAF/Home+Page Genome Sequencing and Analysis Facility], and current VP, Molecular R&D at [http://www.sonichealthcareusa.com/ Sonic Reference Laboratory].
* [http://www.youtube.com/watch?v=77r5p8IBwJk Illumina/Solexa Sequencing (Youtube Video)]
* [http://www.youtube.com/watch?v=45vNetkGspo Genome Analyzer (Youtube Video)]

'''Feb 23, 2017 - Gene finding II'''
* We're finishing up the slides from Feb. 21, then moving on into [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_GenomeAssembly_Spring2017.pdf Genome Assembly]

'''Feb 21, 2017 - Gene finding'''
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-GeneFinding-Spring2017.pdf Today's slides]
* [http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A61755389-61788517&hgsid=477602291_ccTRfcOcZIQHnMkBKGzbQLBRc6HL The UCSC genome browser]
Problem Set 2, due before midnight Mar. 6, 2017:<br>
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_ProblemSet2_Spring2017.pdf '''Problem Set 2'''].  
* You'll need these 3 files: [http://www.marcottelab.org/users/BCH364C_394P_2017/state_sequences State sequences], [http://www.marcottelab.org/users/BCH364C_394P_2017/soluble_sequences Soluble sequences], [http://www.marcottelab.org/users/BCH364C_394P_2017/transmembrane_sequences Transmembrane sequences]
Reading:<br>
* [http://www.marcottelab.org/users/BCH364C_394P_2017/EukGeneAnnotation.pdf Eukaryotic gene finding], [http://www.marcottelab.org/users/BCH364C_394P_2017/GeneMark.hmm.pdf GeneMark.hmm], and [http://www.marcottelab.org/users/BCH364C_394P_2017/BurgeKarlin-main.pdf GENSCAN]

'''Feb 16, 2017 - HMMs II'''
* We're finishing up the slides from Feb. 18. 
* News of the day: [https://www.washingtonpost.com/news/speaking-of-science/wp/2017/02/15/broad-institute-scientist-prevails-in-epic-patent-fight-over-crispr/?utm_term=.ab548bb221c4 CRISPR patent! #1] [http://www.sciencemag.org/news/2017/02/how-battle-lines-over-crispr-were-drawn #2], [http://www.nature.com/news/broad-institute-wins-bitter-battle-over-crispr-patents-1.21502 and #3]. I recommend reading the [http://www.marcottelab.org/users/BCH364C_394P_2017/Broad-Cal-Decision-on-Motions.pdf actual decision].

'''Feb 14, 2017 - Hidden Markov Models'''
* Don't forget: Homework #2 (worth 10% of your final course grade) is due on Rosalind '''by 11:59PM February 20'''.
* Linking out to [http://www.uniprot.org/ UniProt], discussed last time
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-HMMs-Spring2017.pdf Today's slides]<br>
Reading:<br>
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-HMMs.pdf HMM primer] and [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-Bayes.pdf Bayesian statistics primer #1], [http://www.marcottelab.org/users/BCH364C_394P_2017/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?])

'''Feb 9, 2017 - Biological databases'''
* Just a note that we'll be seeing ever more statistics as go on. Here's a [http://www.marcottelab.org/users/BCH364C_394P_2017/StatisticsPrimer.pdf good primer] from [http://www.bio.utexas.edu/research/meyers/LaurenM/index.html Prof. Lauren Myers] to refresh/explain basic concepts.
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-BiologicalDatabases-Spring2017.pdf Today's slides]<br>

'''Feb 7, 2017 - BLAST'''
* News of the day: [https://www.genomicsengland.co.uk/the-100000-genomes-project-by-numbers/ The UK 100K genomes project is up to 19,072 human genomes sequenced!]  Such data are extremely valuable for learning about human variation and gene function. For example, [http://www.marcottelab.org/users/BCH364C_394P_2017/Study-2017-Nature.pdf exome sequences of >4,000 families] are revealing [http://www.marcottelab.org/users/BCH364C_394P_2017/DDD-Figure2.jpg critical genes for developmental disorders].
* Homework #2 (worth 10% of your final course grade) has been assigned on Rosalind and is '''due by 11:59PM February 20'''.
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-BLAST-Spring2017.pdf Our slides today] are modified from a paper on [http://dx.doi.org/10.1371/journal.pbio.1001014 Teaching BLAST] by Cheryl Kerfeld & Kathleen Scott.
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BLAST.pdf The original BLAST paper]
* [http://www.marcottelab.org/paper-pdfs/jmb-lgl.pdf The protein homology graph paper]. Just for fun, here's a link to a [http://www.moma.org/interactives/exhibitions/2008/elasticmind/#/211/ stylized version] we exhibited in the engaging [http://www.moma.org/interactives/exhibitions/2008/elasticmind/ Design and the Elastic Mind] show at New York's Museum of Modern Art. 

'''Feb 2, 2017 - 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/BCH364C_394P_2017/BioinformaticsClass_sp2017.pdf Today's slides]<br>

'''Jan 31, 2017 - Sequence Alignment II'''
* News of the day: [https://www.nytimes.com/2017/01/26/science/chimera-stemcells-organs.html?_r=0 pig-human chimeras not science fiction?]
* We're finishing up the slides from Jan. 26. 
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-DynamicProgramming.pdf Dynamic programming primer]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/GALPAS.xls An example of dynamic programming using Excel], created by [http://www.thepmcf.ca/News-Media/Blog/The-PMCF-Blog/January-2014/Meet-Michael-Hoffman Michael Hoffman] (a former 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]

'''Jan 26, 2017 - Sequence Alignment I'''
* [https://www.eurekalert.org/pub_releases/2017-01/sumc-rmp012517.php news of the day--growing a mouse pancreas in a rat!]  [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature21070.html This] is the follow-up to [http://www.sciencedirect.com/science/article/pii/S0092867410008433 one of my favorite studies from the last few years], growing a rat pancreas in a mouse!
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-Spring2017-SequenceAlignmentI.pdf Today's slides]<br>
Problem Set I, due before midnight Feb. 6, 2017:<br>
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_ProblemSet1_Spring2017.pdf Problem Set 1]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/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: a few of you have pointed out that 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/BCH364C_394P_2017/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/BCH364C_394P_2017/MysteryGene1.txt MysteryGene1], [http://www.marcottelab.org/users/BCH364C_394P_2017/MysteryGene2.txt MysteryGene2], [http://www.marcottelab.org/users/BCH364C_394P_2017/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.
* For those of you who could use more tips on programming, there's a peer-led open coding hour happening on Wednesdays 4-5pm in MBB 2.232 (2nd floor lounge). It's a very informal setting where you can ask questions of more experienced programmers.
Reading:<br>
* [http://www.marcottelab.org/users/BCH364C_394P_2017/NBTPrimer-BLOSUM.pdf BLOSUM primer]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BLOSUM_paper.pdf The original BLOSUM paper] (hot off the presses from 1992!)
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BLOSUM62Miscalculations.pdf BLOSUM miscalculations improve performance]
* There is a good discussion of the alignment algorithms and different scoring schemes [http://www.bioinformaticsonline.org/ch/ch03/supp-all.html here]

'''Jan 24, 2017 - Rosalind help & programming Q/A'''
* [http://www.bbc.co.uk/news/science-environment-25576718 One of my favorite news items of the last few last years: China cloning on an 'industrial scale'.] Favorite quote: "If it tastes good you should sequence it..."  BGI is one of the biggest (the biggest?) genome sequencing centers in the world and employs >2,000 bioinformatics researchers.<br>
* [http://www.scipy-lectures.org/packages/statistics/index.html Statistics in Python]
* We'll be finishing Python slides from last time.

'''Jan 19, 2017 - Intro to Python'''
* News of the day/Science in action:  There's a huge ongoing debate raging about the development of CRISPR genome editing technology, stemming in part from an [https://www.washingtonpost.com/news/wonk/wp/2016/01/13/control-of-crispr-biotechs-most-promising-breakthrough-is-up-for-grabs/ ongoing patent contest] over who made key innovations in characterizing, engineering, and applying CRISPR. You can read some of the debate [http://www.the-scientist.com/?articles.view/articleNo/45072/title/Who-Owns-CRISPR--Cont-d/ here], [http://www.the-scientist.com/?articles.view/articleNo/45119/title/-Heroes-of-CRISPR--Disputed/ here], and [http://genotopia.scienceblog.com/579/landergate-a-link-list/ here], among many other sites.  There's a good chance we'll hear the major CRISPR patents decided this semester.
* REMINDER:  My email inbox is always fairly backlogged (e.g., my median time between non-spam emails yesterday was 11 minutes), so please copy the TA on any emails to me to make sure they get taken care of.
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-PythonPrimer-Spring2017.pdf Today's slides]<br>
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_Lecture2-Python_primer-Spring2017.pdf Python primer]
* [http://www.marcottelab.org/users/BCH364C_394P_2017/Ecoli_genome.txt E. coli genome]
* [http://astrofrog.github.io/blog/2015/05/09/2015-survey-results/ Python 2 vs 3?]. For compatibility with Rosalind and other materials, we'll use version 2.7. 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].

'''Jan 17, 2017 - Introduction'''
* [http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P-IntroAndRosalind-Spring2017.pdf Today's slides]<br>
* Some warm-up videos to get you started on Python: [http://www.codecademy.com/tracks/python Code Academy's Python coding for beginners]<br>
* We'll be conducting homework using the online environment [http://rosalind.info/faq/ Rosalind].  Go ahead and register on the site, and enroll specifically for BCH364C/BCH394P using [http://rosalind.info/classes/enroll/b22533ccd7/ ''this link''].  Homework #1 (worth 10% of your final course grade) has already been assigned on Rosalind and is '''due by 11:59PM January 26'''.
* A useful online resource if you get bogged down: [http://pythonforbiologists.com/index.php/introduction-to-python-for-biologists/ Python for Biologists]. (& just a heads-up that some of their instructions for running code relate to a command line environment that's a bit different from the default one you install following the Rosalind instructions.  It won't affect the programs, just the way they are run or how you specific where files are located.) '''However, if you've never programmed before, definitely check this out!!!'''<br>
* An oldie (by recent bioinformatics standards) but goodie:  [http://www.marcottelab.org/users/BCH364C_394P_2017/ComputersMarsOrganismsVenus.pdf Computers are from Mars, Organisms are from Venus]

== Syllabus & course outline ==

[http://www.marcottelab.org/users/BCH364C_394P_2017/BCH364C-394P_2017_syllabus.pdf Course syllabus]

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

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

''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.''<br>

Most of the lectures will be from research articles and slides posted online, with some material from the...<br>
'''Optional text (for sequence analysis):''' [http://www.amazon.com/exec/obidos/ASIN/0521629713/qid=999041246/sr=1-1/ref=sc_b_1/002-0505297-3336044 ''Biological sequence analysis''], by R. Durbin, S. Eddy, A. Krogh, G. Mitchison (Cambridge University Press),

For biologists rusty on their stats, [http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025/ref=sr_1_1?s=books&ie=UTF8&qid=1295395775&sr=1-1 ''The Cartoon Guide to Statistics''] (Gonick/Smith) is very good. A reasonable online resource for beginners is [http://www.refsmmat.com/statistics/index.html Statistics Done Wrong].<br>

Some online references:<br>
[http://lectures.molgen.mpg.de/ An online bioinformatics course]<br> 	
Assorted bioinformatics resources on the web: [http://zlab.bu.edu/zlab/links.shtml Assorted links]<br>
Online probability texts: [http://omega.albany.edu:8008/JaynesBook.html #1], [http://www-users.york.ac.uk/~mb55/pubs/pbstnote.htm #2], [http://www.dartmouth.edu/~chance/teaching_aids/books_articles/probability_book/pdf.html #3]<br>

'''No exams will be given.  Grades will be based on online homework (counting 30% of the grade), 3 problem sets (given every 2-3 weeks and counting 15% each towards the final grade) and an independent course project (25% of final grade).'''  The course project will consist of a research project on a bioinformatics topic chosen by the student (with approval by the instructor) containing an element of independent computational biology research (e.g. calculation, programming, database analysis, etc.). This will be turned in as a link to a web page. '''The final project is due by midnight, April 27, 2017.  The last two classes will be spent presenting your projects to each other. (The presentation will account for 5% of the project.)'''<br>

Online homework will be assigned and evaluated using the free bioinformatics web resource [http://rosalind.info/faq/ Rosalind].<br>

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.<br>

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

Students are welcome to discuss ideas and problems with each other, but '''all programs, Rosalind homework, and written solutions should be performed independently'''. Students are expected to follow the UT honor code. Cheating, plagiarism, copying, & reuse of prior homework or programs from CourseHero, Github, or other sources are all strictly forbidden and constitute breaches of academic integrity ([http://deanofstudents.utexas.edu/sjs/acint_student.php UT academic integrity policy]) and cause for dismissal with a failing grade.

'''The final project web site is due by midnight April 27, 2017.'''

* How to make a web site for the final project 
** Google Site: https://support.google.com/sites/answer/153197?hl=en

* [http://abstrusegoose.com/strips/ars_longa_vita_brevis.PNG Why we don't teach C++]