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NSF-funded Bioinformatics Workshop, J. Craig Venter Institute, June 16-20, 2014
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Tarball of the /export area. Download using `wget` and extract using `tar -zxvf JCVI_Workshop2014_export_area.tar.gz`http://goo.gl/ZGwkX0
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Packages to install for running workshop locallyhttps://docs.google.com/document/d/101dSrPuxeRocqSd-ZTvjKV-CZWZZMdvYGtGk4PeqXBI/edit?usp=sharing
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DayTopicPresenterLinks to Documents
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MondayTimeSelf-introductionsAll
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9.00 amOverview of Workshop; logisticsChrishttps://docs.google.com/presentation/d/1qy-YWbcb1C4ZWecCW07qrVWa_wQp_KH3gQcDUazsTwc/edit?usp=sharing
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9.10 amUnix overviewVivekhttps://drive.google.com/file/d/0Bx3KTjwwBb0rcFZXNGxrd2FINDA/edit?usp=sharing
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9.30 amHands-on: LinuxVivekhttps://docs.google.com/document/d/1IasGednFdyF2xHlPn8dwe3UGPnu4HCCkAUrqnXh027w/edit?usp=sharing
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10.30 amBreak
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10.45 amMini module 1: FASTA -> BLAST -> MSAHaibaohttps://drive.google.com/file/d/0Bx3KTjwwBb0rT3dWelU3LXdDTVU/edit?usp=sharing
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12.00 pmLunch; attendees show and tell
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1.30 pmMini module 2: FASTQ -> FASTQC -> trimmingHaibaohttps://docs.google.com/document/d/1-atbgJGImZQsq_loMBvS76FUpkkoia1QrdH-n_kUnuk/edit?usp=sharing
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2.30 pmMini module 3: GFF/BED -> BEDTOOLSVivek
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3.15 pmBreak
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3.30 pmMini module 4: SAM/BAM -> SAMTOOLSVivek
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4.30 pm Finish
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Tuesday9.00 amGenome assemblyHaibaohttps://drive.google.com/file/d/0Bx3KTjwwBb0rN0YzREpaZF94cUk/edit?usp=sharing
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10.00 amBreak
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10.15 amHands-on: Assemblers (SOAP, ALLPATHS), Validation (MUMMER)Haibaohttps://docs.google.com/document/d/1qD-rC38kqi3UlBBmjaIMw7o9RR2kyiMs84f9jToy8wg/edit?usp=sharing
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12.00 pmLunch; attendees show and tell
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1.30 pm Tour of JCVI Computational FacilitiesDarnell Edwards, Director of IT
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2.00 pmGenome annotation (structural)Chrishttps://drive.google.com/file/d/0B7Q2om33NWqmXzVKYWZPNHRaNWs/edit?usp=sharing
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2.45 pmBreak
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3.00 pmHands-on: Gene Finding, Gene EditingBenhttps://docs.google.com/document/d/1TvcONEDt1Dl5nloubzol-KdVoQF-JLXMU3izILkaFvA/edit?usp=sharing
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5.30 pmFinish
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Wednesday9.00 amFunctional annotation (HMMs, PFAM, CDD);Protein naming, paralogous families. EC. TEsBenhttps://drive.google.com/file/d/0B3JBvyedqiqZU3MyWl9yOGVhbW8/edit?usp=sharing
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9.45 amHands-on: Functional annotation Mariahttps://docs.google.com/document/d/1JryYXrSPXSjCXl3cZfJ7l7nZsqeC42VkDJT3axTfc98/edit?usp=sharing
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10.30 amBreak
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10.45 am iPlant CyberinfrastructureEric Lyonshttps://drive.google.com/file/d/0Bx3KTjwwBb0rLV9mU3VFZ2o2aUE/edit?usp=sharing
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11.30 amHands-on: iPlant servicesEric Lyonshttp://goo.gl/9p0c1r
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12.15 pmBoxed LunchesAll
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Afternoon Time-off or Work on individual projects
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Thursday9.00 amComparative GenomicsEric Lyonshttps://drive.google.com/file/d/0Bx3KTjwwBb0rbDhFczhYX09zSWc/edit?usp=sharing
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10.00 amBreak
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10.15 amComparative Genomics CoGe - hands-onEric / Haibaohttp://goo.gl/9p0c1r
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12.00 amLunch
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1.30 pmRNA-seq: "assemble-then-align"Haibaohttps://drive.google.com/file/d/0Bx3KTjwwBb0rRGVWVWVmSmc5WXc/edit?usp=sharing
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2.00 pmRNA-seq: "align-then-assemble"Vivekhttps://drive.google.com/file/d/0Bx3KTjwwBb0rUjhwamQ1UjFjeUE/edit?usp=sharing
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2.30 pmBreak
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2.45 pmHands-on: Cufflinks GG and Trinity DNVivekhttps://docs.google.com/document/d/1aZPzOQAWv1sp0Kli-J_znB9d4MHZ0yHf1YkxL5wylSs/edit?usp=sharing
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4.30 pmFinish / Happy hour
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6.00 p Group Dinner at JCVI
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Friday9.00 amGenome Browsers (GBrowse/JBrowse/IGV)Mariahttps://drive.google.com/file/d/0ByNP9PnMBJFOcDNaQUlLMU9rdDg/edit?usp=sharinghttp://medicmine.jcvi.org/medicmine/begin.do<--Intermine instance for Medicago Genome Project
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10.00 amInterMine (MedicMine, ThaleMine)Maria / Benhttp://prezi.com/72c9ajsxwr2n/intermine-a-constellation-of-data/?utm_campaign=share&utm_medium=copyhttps://apps.araport.org/thalemine<--Intermine instance for Arabidopsis Genome Projecthttp://phytozome.jgi.doe.gov/phytomine/begin.do<--Intermine interface to data from Phytozome (JGI)
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11.00 amBreak
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11.15 amHands on: InterMineBenhttps://docs.google.com/document/d/1C2vmBNeZhwwvOGuI_RD5Cy_Un1qH_mDT54b4NsHcdK4/edit?usp=sharing
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12.15 pmLunch
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1.00 pmSequencing facilty tourDana Busam
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1.15 pmSNP functional variants talkYongwookhttps://drive.google.com/file/d/0B5JJShYzH5g3MTJSLVZkN1B3Z0E/edit?usp=sharing
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1.45 pmHands on: SNP functional variantsHaibaohttps://docs.google.com/document/d/1-kJ0tgd2mmsQcULc8uuqS8vL5C5qc84gRwG3nJiHGxw/edit?usp=sharing
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3.00 pmBreak
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3.15 pmHands on: SNP functional variants cont'd
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4.00 pmRound table discussion
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4.30 pmConcluding remarks
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JCVI InstructorsGuest Instructors
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Chris Towncdtown@jcvi.orgEric Lyons, iPlant & University of Arizonaericlyons@email.arizona.edu
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Vivek Krishnakumarvkrishna@jcvi.org
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Haibao Tanghtang@jcvi.org
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Agnes Chanachan@jcvi.org
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Benjamin Rosenbrosen@jcvi.org
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Yongwook Choiychoi@jcvi.org
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Maria Kimmsarmien@jcvi.org
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Admin Assistant
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Elaine Foxefox@jcvi.org
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Public wireless network is called "internet" - open access.
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Return Flightshttps://docs.google.com/spreadsheets/d/12PNO2Q0zyCwHjCDIdEEmN9QrhkVH14GmRJHYQWVwIVM/edit?usp=sharing
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