2012 06 29 TSW NDSU
Organizers: |
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Local Point of Contact: |
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Trainers: |
Sheldon McKay, Christos Noutsos, Shannon Oliver, Jason Williams |
Date: |
12:00PM - 6:00PM on June 29, 9:30AM - 4:00PM on June 30, 2012 |
Location: |
Barry Hall, Rm 260 |
Goal
To provide an interactive, hands-on training of iPlant Tools and Services so that participants can begin to use iPlant cyberinfrastructure in their research.
Pre-Workshop Homework
1. Please test your iPlant credentials to ensure you have access. You can log-in from user.iplantcollaborative.org, click the button "iPlant Login"
- Once authenticated, click the "My Services" link
- Under "My Services" please ensure you have access to: Atmosphere, Discovery Environment, iPlant Data Store. You can also request access to other services here
- If you have account problems, please email support@iplantcollaborative.org
2. Please check your email and this wiki prior to the workshop, as this is the way we will communicate any important changes.
Workshop Notes
Here are a few important links that you may wish to refer to during and after the workshop:
Account/Password Problems
iPlant Help and Discussion Forums
General iPlant Support Issues
iPlant Privacy (And other) policies - "Your Data are Your Data"
- www.iplantcollaborative.org/privacy
- www.iplantcollaborative.org/about/data-set-hosting
- www.iplantcollaborative.org/about/general-usage-policy
Agenda
Friday June 29th
Time |
Presentation |
Audience/Prerequisites* |
Presenter |
Slides, Links |
|---|---|---|---|---|
12:00 PM - 12:30 PM |
Arrive / Sign-in / Verify iPlant Accounts |
N/A |
|
|
12:30 PM - 01:00 PM |
Welcome - Presenter/Participant Introductions |
N/A |
|
|
01:00 PM - 01:20 PM |
An Overview of the iPlant Collaborative |
All researchers |
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01:20 PM - 01:45 PM |
Overview of the iPlant Discovery Environment (DE) |
All researchers |
||
01:45 PM - 02:15 PM |
iPlant Data Store - Managing "Big Data" |
All researchers |
||
02:15 PM - 02:30 PM |
Break |
|
|
|
02:30 PM - 03:00 PM |
Building and Using Workflows Within the DE; Phylogenetics |
All researchers |
||
03:00 PM - 04:15 PM |
Using the DE to Examine Differential Expression Within an RNA-seq Dataset |
All researchers - Background in |
Indroductory_RNA-seq.ppt. |
|
04:15 PM - 4:30 PM |
Break |
|
|
|
04:30 PM - 05:00 PM |
Atmosphere - Custom Cloud Computing |
All researchers - Background in |
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05:00 PM - 06:00 PM |
Extending the DE for Your Research: Tool Integration and Customization |
Intermediate - Background in |
|
|
06:00 PM - 06:15 PM |
Collaborating with iPlant: Future Projects and Workshop Summary |
All researchers |
Saturday June 30th
Time |
Presentation |
Audience/Prerequisites* |
Presenter |
Slides/Links |
|---|---|---|---|---|
09:30 AM - 09:40 AM |
Installing Java |
All of you |
|
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09:40 AM - 11:00 AM |
Advanced CHiP-seq in the iPlant Cyberinfrastructure |
Intermediate - knowledge of |
||
11:00 AM - 11:15 AM |
Break |
|
|
|
11:15 AM - 12:00 PM |
Topics and Questions in RNA-Seq |
All researchers |
||
12:00 PM - 01:00 PM |
Lunch |
|
|
|
01:00 PM - 01:15 |
Upcoming Features in the DE |
All |
|
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01:15 PM - 01:30 PM |
Using XSEDE for Bioinformatics |
Advanced- Background |
||
01:30 PM - 02:00 PM |
Powered by iPlant - Using the iPlant API |
Intermediate/Advanced - Background |
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02:00 PM - 02:45 PM |
iCommands for data transfer |
Intermediate/Advanced Background in command line |
|
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02:45 PM - 03:45 PM |
Using Atmosphere to visualize RNA-Seq data |
Intermediate/Advanced- Background in RNA-Seq |
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03:45 PM |
Conclusion and Free Form Work |
All audiences as needed. |
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* Audience/Prerequisites - These prerequisites are meant as helpful suggestions to get the most out of each module. Everyone can attend
any/all modules and are free to follow along (or not) as their own interests and abilities dictate.
Attendee List
First |
Last |
User Acct |
|
|---|---|---|---|
Omar |
Al-Azzam |
omar.al-azzam@ndsu.edu |
X |
Aman |
Anand |
aman.anand@my.ndsu.edu |
no acct |
Deepika |
Arora |
deepika.arora@my.ndsu.edu |
X |
Filippo |
Bassi |
filippo.bassi@ndsu.edu |
X |
Ryan |
Burciaga |
ryan.burciaga@my.ndsu.edu |
X |
Anne |
Denton |
anne.denton@ndsu.edu |
X |
Sandra |
Dunckel |
sdunckel@ksu.edu |
needs Atmo |
Morgan |
Echeverry-Solarte |
morgan.echeverry-solarte@my.ndsu.edu |
X |
Ahmed |
Eldoliefy |
ahmed.el-doleify@my.ndsu.edu |
needs Atmo |
Farhad |
Ghavami |
farhad.ghavami@ndsu.edu |
needs Atmo |
David |
Horvath |
david.horvath@ars.usda.gov |
X |
Shalu |
Jain |
shalu.jain@ndsu.edu |
needs Atmo |
Renata |
Jung |
renata.jung@ndsu.edu |
needs Atmo |
Vedbar |
Khadka |
vskhadka@jacks.sdstate.edu |
needs Atmo |
Shahryar |
Kianian |
s.kianian@ndsu.edu |
needs Atmo |
Ajay |
Kumar |
ajayguptajammu@gmail.com |
needs Atmo |
Cindy |
Lawley |
clawley@Illumina.com |
X |
Yueqiang |
Leng |
yueqiang.leng@gmail.com |
X |
Guojia |
Ma |
guojia.ma@ndsu.edu |
needs Atmo |
Samira |
Mafi Moghaddam |
samira.mafi@ndsu.edu |
X |
Sujan |
Mamidi |
sujan.mamidi@gmail.com |
X |
Mona |
Mazaheri |
mona.mazaheri@ndsu.edu |
needs Atmo |
Steven |
Meinhardt |
steven.meinhardt@ndsu.edu |
X |
Monika |
Michalak de Jimenez |
monika.michalak@ndsu.edu |
no acct |
Sepehr |
Mohajeri Naraghi |
sepehr.mohajerinarag@my.ndsu.edu |
no acct |
Andres |
Noyszewsici |
anoyszew@umn.edu |
X |
Krishna |
Puri |
krishna.puri@ndsu.edu |
X |
Andres |
Salcedo |
asalcedo@ksu.edu |
X |
Raed |
Seetan |
raed.seetan@ndsu.edu |
X |
Santosh |
Sharma |
santosh.sharma@my.ndsu.edu |
X |
Gongjun |
Shi CANCELLED |
gongjun.shi@ndsu.edu |
needs Atmo |
Ricardo |
Silveira |
ricardo_biologia@hotmail.com |
needs Atmo |
Marek |
Sliwinski |
marek.k.sliwinski@uni.edu |
X |
Kristin |
Simons |
kristinsimons77@hotmail.com |
X |
Ali |
Soltani |
Ali.Soltani@my.ndsu.edu |
needs Atmo |
Qun |
Sun |
qunsun0710@gmail.com |
needs Atmo |
Prabin |
Tamang |
probin.tamang@ndsu.edu |
needs Atmo |
Vijay K |
Tiwari |
VIJTIWARI@GMAIL.COM |
needs Atmo |
Rui |
Wang |
rui.wang@ndsu.edu |
X |
Zengcui |
Zhang |
zengcui.zhang@ndsu.edu |
X |
Post-Workshop Survey
iPlant is by, for and of the community. It is extremely important for us to hear from you about what works and what doesn't in our training workshops. We'd also like to know about computational bottlenecks you've encountered in your research for which iPlant could develop community-scale solutions. We want to know how you found out about the workshop, and what you would like to see iPlant do, so please respond to the survey you will receive by email after the workshop has been completed.
Parking Information:
On-Campus Directions:
http://www.ndsu.edu/ndsu/maps/CampusMap_2pg.pdf
URLS
|
FTP Link for Demo |
|---|---|
1 |
ftp://ftp.ensembl.org/pub/release-67/fasta/canis_familiaris/dna/Canis_familiaris.BROADD2.67.dna_rm.chromosome.MT.fa.gz |
2 |
ftp://ftp.ensembl.org/pub/release-67/fasta/canis_familiaris/dna/Canis_familiaris.BROADD2.67.dna_rm.chromosome.MT.fa.gz |
3 |
ftp://ftp.ensembl.org/pub/release-67/fasta/danio_rerio/dna/Danio_rerio.Zv9.67.dna_rm.chromosome.MT.fa.gz |
4 |
ftp://ftp.ensembl.org/pub/release-67/fasta/danio_rerio/dna/Danio_rerio.Zv9.67.dna_rm.chromosome.MT.fa.gz |
5 |
ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna_rm.chromosome.MT.fa.gz |
6 |
ftp://ftp.ensembl.org/pub/release-67/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.67.dna_rm.chromosome.MT.fa.gz |
7 |
ftp://ftp.ensembl.org/pub/release-67/fasta/mus_musculus/dna/Mus_musculus.NCBIM37.67.dna_rm.chromosome.MT.fa.gz |
8 |
ftp://ftp.ensembl.org/pub/release-67/fasta/mus_musculus/dna/Mus_musculus.NCBIM37.67.dna_rm.chromosome.MT.fa.gz |
9 |
ftp://ftp.ensembl.org/pub/release-67/fasta/gallus_gallus/dna/Gallus_gallus.WASHUC2.67.dna_rm.chromosome.MT.fa.gz |
10 |
ftp://ftp.ensembl.org/pub/release-67/fasta/gallus_gallus/dna/Gallus_gallus.WASHUC2.67.dna_rm.chromosome.MT.fa.gz |
11 |
ftp://ftp.ensembl.org/pub/release-67/fasta/gorilla_gorilla/dna/Gorilla_gorilla.gorGor3.1.67.dna_rm.chromosome.MT.fa.gz |
12 |
ftp://ftp.ensembl.org/pub/release-67/fasta/gorilla_gorilla/dna/Gorilla_gorilla.gorGor3.1.67.dna_rm.chromosome.MT.fa.gz |
13 |
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/fasta/arabidopsis_lyrata/dna/Arabidopsis_lyrata.Araly1.12.dna_rm.nonchromosomal.fa.gz |
14 |
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/fasta/arabidopsis_lyrata/dna/Arabidopsis_lyrata.Araly1.12.dna_rm.nonchromosomal.fa.gz |
15 |
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.12.dna_rm.chromosome.Pt.fa.gz |
16 |
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.12.dna_rm.chromosome.Pt.fa.gz |
17 |
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/fasta/brachypodium_distachyon/dna/Brachypodium_distachyon.Brachy1.0.12.dna_rm.nonchromosomal.fa.gz |
18 |
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/fasta/brachypodium_distachyon/dna/Brachypodium_distachyon.Brachy1.0.12.dna_rm.nonchromosomal.fa.gz |
19 |
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/fasta/glycine_max/dna/Glycine_max.1.0.12.dna_rm.nonchromosomal.fa.gz |
20 |
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/fasta/glycine_max/dna/Glycine_max.1.0.12.dna_rm.nonchromosomal.fa.gz |
21 |
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/fasta/oryza_sativa/dna/Oryza_sativa.MSU6.12.dna_rm.chromosome.Pt.fa.gz |
22 |
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/fasta/oryza_sativa/dna/Oryza_sativa.MSU6.12.dna_rm.chromosome.Pt.fa.gz |
23 |
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/fasta/zea_mays/dna/Zea_mays.AGPv2.12.dna_rm.chromosome.chloroplast.fa.gz |
24 |
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/fasta/zea_mays/dna/Zea_mays.AGPv2.12.dna_rm.chromosome.chloroplast.fa.gz |
25 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Apis_mellifera/CHR_MT/ame_ref_Amel_4.5_chrMT.fa.gz |
26 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Apis_mellifera/CHR_MT/ame_ref_Amel_4.5_chrMT.fa.gz |
27 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Glycine_max/CHR_Pltd/gma_ref_V1.0_chrPltd.fa.gz |
28 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Glycine_max/CHR_Pltd/gma_ref_V1.0_chrPltd.fa.gz |
29 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_melanogaster/RELEASE_5_41/CHR_Un/NS_000188.frn |
30 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Drosophila_melanogaster/RELEASE_5_41/CHR_Un/NS_000188.frn |
31 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Chloroplasts/plastids/NC_001319.faa |
32 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Chloroplasts/plastids/NC_001319.faa |
33 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Chloroplasts/plastids/NC_000932.fna |
34 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Chloroplasts/plastids/NC_000932.fna |
35 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Chloroplasts/plastids/NC_001603.faa |
36 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Chloroplasts/plastids/NC_001603.faa |
37 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Chloroplasts/plastids/NC_001603.faa |
38 |
ftp://hgdownload.cse.ucsc.edu/goldenPath/apiMel1/database/all_est.txt.gz |
39 |
ftp://hgdownload.cse.ucsc.edu/goldenPath/apiMel1/database/all_mrna.sql |
40 |
ftp://hgdownload.cse.ucsc.edu/goldenPath/apiMel1/database/all_mrna.sql |
41 |
ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau1/database/all_mrna.sql |
42 |
ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau1/database/all_mrna.sql |