science support: software and database resources for … · science support: software and database...
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Science Support: Software and Database Resources for Research
Maze Ndonwi
Science Support: Software and Database Resources for Research
Marcy Vana, PhD [email protected] Maze Ndonwi, PhD [email protected]
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 • 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
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 [email protected] Marcy Vana, PhD [email protected]
Senior Support Scientists
Bernard Becker Medical Library http://becker.wustl.edu/services/science-support