A | B | C | D | E | G | H | I | J | K | L | M | N | O | P | Q | R | S | |
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1 | NSF-funded Bioinformatics Workshop, J. Craig Venter Institute, June 16-20, 2014 | |||||||||||||||||
2 | ||||||||||||||||||
3 | Tarball of the /export area. Download using `wget` and extract using `tar -zxvf JCVI_Workshop2014_export_area.tar.gz` | http://goo.gl/ZGwkX0 | ||||||||||||||||
4 | Packages to install for running workshop locally | https://docs.google.com/document/d/101dSrPuxeRocqSd-ZTvjKV-CZWZZMdvYGtGk4PeqXBI/edit?usp=sharing | ||||||||||||||||
5 | Day | Topic | Presenter | Links to Documents | ||||||||||||||
6 | Monday | Time | Self-introductions | All | ||||||||||||||
7 | 9.00 am | Overview of Workshop; logistics | Chris | https://docs.google.com/presentation/d/1qy-YWbcb1C4ZWecCW07qrVWa_wQp_KH3gQcDUazsTwc/edit?usp=sharing | ||||||||||||||
8 | 9.10 am | Unix overview | Vivek | https://drive.google.com/file/d/0Bx3KTjwwBb0rcFZXNGxrd2FINDA/edit?usp=sharing | ||||||||||||||
9 | 9.30 am | Hands-on: Linux | Vivek | https://docs.google.com/document/d/1IasGednFdyF2xHlPn8dwe3UGPnu4HCCkAUrqnXh027w/edit?usp=sharing | ||||||||||||||
10 | 10.30 am | Break | ||||||||||||||||
11 | 10.45 am | Mini module 1: FASTA -> BLAST -> MSA | Haibao | https://drive.google.com/file/d/0Bx3KTjwwBb0rT3dWelU3LXdDTVU/edit?usp=sharing | ||||||||||||||
12 | 12.00 pm | Lunch; attendees show and tell | ||||||||||||||||
13 | 1.30 pm | Mini module 2: FASTQ -> FASTQC -> trimming | Haibao | https://docs.google.com/document/d/1-atbgJGImZQsq_loMBvS76FUpkkoia1QrdH-n_kUnuk/edit?usp=sharing | ||||||||||||||
14 | 2.30 pm | Mini module 3: GFF/BED -> BEDTOOLS | Vivek | |||||||||||||||
15 | 3.15 pm | Break | ||||||||||||||||
16 | 3.30 pm | Mini module 4: SAM/BAM -> SAMTOOLS | Vivek | |||||||||||||||
17 | 4.30 pm | Finish | ||||||||||||||||
18 | ||||||||||||||||||
19 | Tuesday | 9.00 am | Genome assembly | Haibao | https://drive.google.com/file/d/0Bx3KTjwwBb0rN0YzREpaZF94cUk/edit?usp=sharing | |||||||||||||
20 | 10.00 am | Break | ||||||||||||||||
21 | 10.15 am | Hands-on: Assemblers (SOAP, ALLPATHS), Validation (MUMMER) | Haibao | https://docs.google.com/document/d/1qD-rC38kqi3UlBBmjaIMw7o9RR2kyiMs84f9jToy8wg/edit?usp=sharing | ||||||||||||||
22 | 12.00 pm | Lunch; attendees show and tell | ||||||||||||||||
23 | 1.30 pm | Tour of JCVI Computational Facilities | Darnell Edwards, Director of IT | |||||||||||||||
24 | 2.00 pm | Genome annotation (structural) | Chris | https://drive.google.com/file/d/0B7Q2om33NWqmXzVKYWZPNHRaNWs/edit?usp=sharing | ||||||||||||||
25 | 2.45 pm | Break | ||||||||||||||||
26 | 3.00 pm | Hands-on: Gene Finding, Gene Editing | Ben | https://docs.google.com/document/d/1TvcONEDt1Dl5nloubzol-KdVoQF-JLXMU3izILkaFvA/edit?usp=sharing | ||||||||||||||
27 | 5.30 pm | Finish | ||||||||||||||||
28 | ||||||||||||||||||
29 | Wednesday | 9.00 am | Functional annotation (HMMs, PFAM, CDD);Protein naming, paralogous families. EC. TEs | Ben | https://drive.google.com/file/d/0B3JBvyedqiqZU3MyWl9yOGVhbW8/edit?usp=sharing | |||||||||||||
30 | 9.45 am | Hands-on: Functional annotation | Maria | https://docs.google.com/document/d/1JryYXrSPXSjCXl3cZfJ7l7nZsqeC42VkDJT3axTfc98/edit?usp=sharing | ||||||||||||||
31 | 10.30 am | Break | ||||||||||||||||
32 | 10.45 am | iPlant Cyberinfrastructure | Eric Lyons | https://drive.google.com/file/d/0Bx3KTjwwBb0rLV9mU3VFZ2o2aUE/edit?usp=sharing | ||||||||||||||
33 | 11.30 am | Hands-on: iPlant services | Eric Lyons | http://goo.gl/9p0c1r | ||||||||||||||
34 | 12.15 pm | Boxed Lunches | All | |||||||||||||||
35 | Afternoon | Time-off or Work on individual projects | ||||||||||||||||
36 | ||||||||||||||||||
37 | Thursday | 9.00 am | Comparative Genomics | Eric Lyons | https://drive.google.com/file/d/0Bx3KTjwwBb0rbDhFczhYX09zSWc/edit?usp=sharing | |||||||||||||
38 | 10.00 am | Break | ||||||||||||||||
39 | 10.15 am | Comparative Genomics CoGe - hands-on | Eric / Haibao | http://goo.gl/9p0c1r | ||||||||||||||
40 | 12.00 am | Lunch | ||||||||||||||||
41 | 1.30 pm | RNA-seq: "assemble-then-align" | Haibao | https://drive.google.com/file/d/0Bx3KTjwwBb0rRGVWVWVmSmc5WXc/edit?usp=sharing | ||||||||||||||
42 | 2.00 pm | RNA-seq: "align-then-assemble" | Vivek | https://drive.google.com/file/d/0Bx3KTjwwBb0rUjhwamQ1UjFjeUE/edit?usp=sharing | ||||||||||||||
43 | 2.30 pm | Break | ||||||||||||||||
44 | 2.45 pm | Hands-on: Cufflinks GG and Trinity DN | Vivek | https://docs.google.com/document/d/1aZPzOQAWv1sp0Kli-J_znB9d4MHZ0yHf1YkxL5wylSs/edit?usp=sharing | ||||||||||||||
45 | ||||||||||||||||||
46 | ||||||||||||||||||
47 | 4.30 pm | Finish / Happy hour | ||||||||||||||||
48 | 6.00 p | Group Dinner at JCVI | ||||||||||||||||
49 | ||||||||||||||||||
50 | Friday | 9.00 am | Genome Browsers (GBrowse/JBrowse/IGV) | Maria | https://drive.google.com/file/d/0ByNP9PnMBJFOcDNaQUlLMU9rdDg/edit?usp=sharing | http://medicmine.jcvi.org/medicmine/begin.do | <--Intermine instance for Medicago Genome Project | |||||||||||
51 | 10.00 am | InterMine (MedicMine, ThaleMine) | Maria / Ben | http://prezi.com/72c9ajsxwr2n/intermine-a-constellation-of-data/?utm_campaign=share&utm_medium=copy | https://apps.araport.org/thalemine | <--Intermine instance for Arabidopsis Genome Project | http://phytozome.jgi.doe.gov/phytomine/begin.do | <--Intermine interface to data from Phytozome (JGI) | ||||||||||
52 | 11.00 am | Break | ||||||||||||||||
53 | 11.15 am | Hands on: InterMine | Ben | https://docs.google.com/document/d/1C2vmBNeZhwwvOGuI_RD5Cy_Un1qH_mDT54b4NsHcdK4/edit?usp=sharing | ||||||||||||||
54 | 12.15 pm | Lunch | ||||||||||||||||
55 | 1.00 pm | Sequencing facilty tour | Dana Busam | |||||||||||||||
56 | 1.15 pm | SNP functional variants talk | Yongwook | https://drive.google.com/file/d/0B5JJShYzH5g3MTJSLVZkN1B3Z0E/edit?usp=sharing | ||||||||||||||
57 | 1.45 pm | Hands on: SNP functional variants | Haibao | https://docs.google.com/document/d/1-kJ0tgd2mmsQcULc8uuqS8vL5C5qc84gRwG3nJiHGxw/edit?usp=sharing | ||||||||||||||
58 | 3.00 pm | Break | ||||||||||||||||
59 | 3.15 pm | Hands on: SNP functional variants cont'd | ||||||||||||||||
60 | 4.00 pm | Round table discussion | ||||||||||||||||
61 | 4.30 pm | Concluding remarks | ||||||||||||||||
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65 | JCVI Instructors | Guest Instructors | ||||||||||||||||
66 | Chris Town | cdtown@jcvi.org | Eric Lyons, iPlant & University of Arizona | ericlyons@email.arizona.edu | ||||||||||||||
67 | Vivek Krishnakumar | vkrishna@jcvi.org | ||||||||||||||||
68 | Haibao Tang | htang@jcvi.org | ||||||||||||||||
69 | Agnes Chan | achan@jcvi.org | ||||||||||||||||
70 | Benjamin Rosen | brosen@jcvi.org | ||||||||||||||||
71 | Yongwook Choi | ychoi@jcvi.org | ||||||||||||||||
72 | Maria Kim | msarmien@jcvi.org | ||||||||||||||||
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74 | Admin Assistant | |||||||||||||||||
75 | Elaine Fox | efox@jcvi.org | ||||||||||||||||
76 | Public wireless network is called "internet" - open access. | |||||||||||||||||
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79 | Return Flights | https://docs.google.com/spreadsheets/d/12PNO2Q0zyCwHjCDIdEEmN9QrhkVH14GmRJHYQWVwIVM/edit?usp=sharing | ||||||||||||||||
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