Science Support: Software and Database Resources for Research

Maze Ndonwi

Science Support: Software and Database Resources for Research

Marcy Vana, PhD vanam@wustl.edu Maze Ndonwi, PhD ndonwimaze@wustl.edu

Senior Support Scientists

Bernard Becker Medical Library http://becker.wustl.edu/services/science-support

Science Support: Software and Database Resources for Research

https://becker.wustl.edu/services/science-support

Science Support: Software and Database Resources for Research

• Sources of Research Software at WUSTL

• Training resources associated with Research software

Sources of Research Software at WUSTL

• Becker Library Research Pod (and beyond) - FREE • Becker Library’s software licensing program - $

• Software licensing from WUSTL Software Licensing - $

• Other groups on campus – Free or $

BECKER LIBRARY RESEARCH POD • https://becker.wustl.edu/services/research-pod

• Cluster of iMacs and PCs equipped with a collection

of research software • Computers freely available to WUSM community

• Show ID at Information Services Desk to get

username and password

BECKER LIBRARY RESEARCH POD

BECKER LIBRARY RESEARCH POD • Adobe Creative Suite, EndNote, Microsoft Office

• GraphPad Prism, JMP Pro, SAS (PCs), SPSS

• Mathematica

• MATLAB

• PyMOL

BECKER LIBRARY RESEARCH POD

http://becker.wustl.edu/services/research-pod

Click on a software title for more information

BEYOND THE RESEARCH POD Install on your own computer

• ChemOffice – provided by Olin Library https://becker.wustl.edu/services/software/chembiooffice

• JMP Genomics – provided by the Division of Statistical Genomics

https://becker.wustl.edu/services/software/jmp-genomics

• FlowJo – available for purchasing at a reduced cost through a site license managed by the FACS core in the Department of Pathology and Immunology

http://pathology.wustl.edu/research/cores/facs/

BEYOND THE RESEARCH POD

• NovoAlign - provided by the Genome Technology Center (GTAC)

NovoAlign is installed on the Center for High Performance Computing Cluster and the Center for Genome Sciences and Systems Biology Cluster.

BEYOND THE RESEARCH POD Web-based and limited to the WUSTL network

• Cambridge Structural Database – provided by Becker

Library and Olin Library https://becker.wustl.edu/services/software/ccdc-cambridge-structural-database

• Reaxys - provided by Becker Library and Olin Library

https://becker.wustl.edu/services/software/reaxys

BEYOND THE RESEARCH POD • Web-based and limited to the WUSTL network • Kyoto Encyclopedia of Genes and Genomes (KEGG) –

site license and local mirror provided and managed by the Center for Genome Sciences & Systems Biology, the McDonnell Genome Institute, and Becker Library

https://kegg.wustl.edu/

BEYOND THE RESEARCH POD • Web-based and limited to the WUSTL network • Main KEGG site in Japan is free to browse, but

WUSTL mirror provides a faster and more reliable connection for downloading large amounts of KEGG data

BEYOND THE RESEARCH POD

https://kegg.wustl.edu/

BEYOND THE RESEARCH POD • Web-based and limited to the WUSTL network

• Galaxy – local WUSTL instance provided by the Center

for High Performance Computing (CHPC) and Becker Library

http://galaxy.chpc.wustl.edu/

BEYOND THE RESEARCH POD • Galaxy – public and private forms

• Central public platform is called “Main”

https://usegalaxy.org/

BEYOND THE RESEARCH POD • Galaxy – Open Source, web-based analysis platform

for data intensive biomedical research

• No programming experience required, enables researchers without programming experience to run jobs on large datasets

(RNA-Seq, ChIP-Seq, variant calling, etc.)

BEYOND THE RESEARCH POD • In addition to being a web platform, Galaxy is also

open source software

• Many additional public and private instances have been created, some with a specific focus (for example, instances focused on ChIP-Seq data analysis tools), some more general like Main, some restricted to specific university campuses (like WUSTL)

BEYOND THE RESEARCH POD • Public instances of Galaxy are great, especially Main

(lots of space for registered users!), but local instances can be useful as well

• Any given Galaxy instance may not have all of the tools you need (Galaxy Tool Shed)

• A local instance can be customized over time based on feedback from the community of users

BEYOND THE RESEARCH POD • WUSTL Galaxy instance continues to get customized

over time based on feedback from WUSTL users – implementing tools WUSTL users want/need

• WUSTL Galaxy mailing list – use list to post questions, suggest enhancements (tools you’d like to see added), and/or report problems

http://management.wustl.edu/mailman/listinfo/galaxy

BEYOND THE RESEARCH POD • Web-based and limited to the WUSTL network

• WUSTL Galaxy – jobs run on the CHPC cluster

• Each registered user gets 50GB of temporary storage • Data is not backed up and gets deleted after 90 days

to make sure space is available for as many users as possible

http://galaxy.chpc.wustl.edu/

BEYOND THE RESEARCH POD

BECKER SOFTWARE LICENSING • Site/group licenses managed by Becker Library to

provide labs with popular software at a reduced price

https://becker.wustl.edu/services/science-support

• Software titles are chosen by researchers on campus

BECKER SOFTWARE LICENSING • We are always willing to investigate interest in

additional tools – send us your suggestions

• Investigations may be associated with onsite software demo/training and a university-wide free trial for a period of time

• Current investigation - Human gene mutation database

BECKER SOFTWARE LICENSING • Lasergene Core Suite, SnapGene

• GraphPad Prism

• Ingenuity Pathway Analysis (IPA), MetaCore

• Partek Genomics Suite, Partek Flow (newest

addition), Spotfire with OmicsOffice

• PyMOL

WUSTL SOFTWARE LICENSING • http://sl.wustl.edu/ • Group/site licenses for many tools of broader

interest across WUSTL schools (Adobe Creative Suite, EndNote, JMP/JMP Pro, Mathematica, MATLAB, SAS, SPSS)

TRAINING RESOURCES • Onsite software training – Additional educational

benefits associated with some WUSTL site licenses

FYI 2016 trainings: Partek Flow, MetaCore, PyMOL and IPA workshops (and HGMD demo /training coming up next month)

• Sign up for training notifications:

https://becker.wustl.edu/services/science-support

TRAINING RESOURCES

https://becker.wustl.edu/services/science-support

TRAINING RESOURCES • Training materials available from “Help menu” within

software, on vendor website, on vendor YouTube site, on tool Wiki, on discussion forum, etc.

• Becker Library software pages link out to various vendor training resources

• Washington University SAS Users group (we are always exploring ways to help).

• Free e-learning courses – JMP/JMP Pro, SAS

TRAINING RESOURCES

https://becker.wustl.edu/services/software/sas

GENOMIC MEDICINE SEMINAR SERIES 28-week seminar series covering a variety of topics associated with genomics in medicine and research https://becker.wustl.edu/services/bioinformatics/genomic-medicine-series Digital Commons collection devoted to seminar series lecture materials – screencasts, audio recordings, slides

GENOMIC MEDICINE SEMINAR SERIES Collaboration between Departments of Genetics, Medicine, Pathology & Immunology, Pediatrics, and Becker Library Sponsored by the Institute of Clinical and Translational Sciences (ICTS) – class taken for 1- credit in fall and spring. Our role – lead the running of the seminar series and serve as instructors/course directors for the fall and spring courses

EDUCATION AND TRAINING Future offerings: • Genomics and the Era and Personalized seminar

series • Basic computing classes to be offered in

collaboration with CHPC : basic Unix, cluster computing etc.

• Human gene mutation database demo/training coming up on June 9th.

Science Support • Let us know if you can’t find training resources, we

can help • Let us know if you have suggestions for additional

pieces of software you’d like to see a group or site license for or on the Research Pod

Science Support: Software and Database Resources for Research

Maze Ndonwi, PhD ndonwimaze@wustl.edu Marcy Vana, PhD vanam@wustl.edu

Senior Support Scientists

Bernard Becker Medical Library http://becker.wustl.edu/services/science-support