Informatics

Informatics

From site-licensed software for basic research to massively-parallel computing power to handling clinical research data.

Shared Facilities:

Computational Service and Bioinformatics Facility (CSBF)

• Description — Computer resources for biomedical research at Stanford. Membership access to computer hardware; Mac, PC, and UNIX software; consulting; and workshops.
• Available Software — https://cmgm3.stanford.edu/computing/setup/keyserver/software_list.html
• Location — Beckman Center B062D
• Questions — Contact Lee Kozar  , (650) 725-4483
• Website — http://cmgm.stanford.edu

Data Coordinating Center (DCC)

• Description — The Data Coordinating Center (DCC) provides services to members of the School of Medicine related to managing data of ongoing or new research projects. We specialize in the planning, development, management, and secure implementation of systems to achieve project goals in a technologically modern environment. In particular, we have expertise in integrating advanced statistical and bioinformatics tools in a technologically modern environment.
• Questions — Contact Bonnie Chung  , (650) 723-5301
• Website — http://med.stanford.edu/dcc/

Parallel Computing

• Description — The Bio-X Parallel Computing Cluster is currently closed to new users. Somewhat more modest parallel computing resources are available for free (for Stanford users) on the “barley” cluster.
• Website — http://stanford.edu/group/farmshare

Stanford Center for Clinical Informatics

• Description — The Stanford Center for Clinical Informatics is a resource center for researchers’ data needs. In addition to being the official conduit of clinical data for research purposes, we offer expert advice on best practices in data management, hands-on assistance with our recommended data management framework REDCap, a suite of self-service tools for cohort identification and chart review, and a variety of other software and clinical research data related services, including real time clinical research alerting and HIPAA compliance advice and guidance. For informatics help with your clinical research, schedule a free consultation at https://clinicalinformatics.stanford.edu/
• Location — X200 Medical School Office Building
• Questions — Contact Us  , (650) 724-6920
• Website — https://clinicalinformatics.stanford.edu/
• Selected References

  Predictors of survival after surgical treatment of spinal metastasis. Arrigo RT, Kalanithi P, Cheng I, Alamin T, Carragee EJ, Mindea SA, Park J, Boakye M. Neurosurgery. 2011; 68 (3): 674-81; discussion 681. PubMedID: 21311295.

  STRIDE--An integrated standards-based translational research informatics platform. Lowe HJ, Ferris TA, Hernandez PM, Weber SC. AMIA Annu Symp Proc. 2009: 2009 391-5. PubMedID: 20351886.

  Detecting Drug Interactions From Adverse-Event Reports: Interaction Between Paroxetine and Pravastatin Increases Blood Glucose Levels. Tatonetti NP, Denny JC, Murphy SN, Fernald GH, Krishnan G, Castro V, Yue P, Tsau PS, Kohane I, Roden DM, Altman RB. Clin Pharmacol Ther. 2011 Jul;90(1):133-42. doi: 10.1038/clpt.2011.83. Epub 2011 May 25. PubMedID: 21613990.

HANA Immersive Visualization Environment (HIVE)

• Description — The HIVE is a scientific visualization wall that is 10 feet tall and 24 feet wide with 13440X5400 resolution.
• Location — Huang Building, Suite B050
• Questions — Contact Brian Tempero  , (650) 724-8122
• Website — http://hive.stanford.edu

Genetics Bioinformatics Service Center

• Description — Stanford Genetics Bioinformatics Service Center was set up in summer of 2013 to provide for the growing needs of Big Data genetics research at Stanford. GBSC provides best-in-class computational infrastructure for ultra high throughput high performance workload for genomics and related research. The current infrastructure has over 1000 cores, 2 petabytes of storage and offers over 50 software tools, several of which are commercially licensed. This infrastructure serves over 300 researchers and covers a wide range of research including non-mammalian and microbial genomes, basic science research like ENCODE, human variant analysis, cancer research and personalized medicine, integrative omics profiling, evolutional biology and population genetics. GBSC team comprise of BS/MS/PhDs in variety of computational fields including Computer Science, BioMedical Engineering, Computational Physics and Bioinformatics and represent over 50 years of professional experience in solving complex scientific and software problems. The team brings a suite of expertise in Next Generation Sequencing bioinformatics data analysis and software development. The team has successfully delivered on a variety of projects including large scale sequencing center data analysis, laboratory management systems, and development of cutting edge variant and cancer genomics analysis pipelines.
• Location — The computational cluster: Forsythe Hall Data Center, 275 Panama Street, Stanford, CA. Bioinformatics team: SoM Technology and Innovation Park, 3165 Porter Drive, Palo Alto, CA.
• Questions — Contact Somalee Datta  , (650) 725-9710
• Website — http://gbsc.stanford.edu/
• Selected References

  Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes; Rui Chen*, George I. Mias*, Jennifer Li-Pook-Than*, Lihua Jiang*, Hugo Y.K. Lam, Rong Chen, Elana Miriami, Konrad J. Karczewski, Manoj Hariharan, Frederick E. Dewey, Yong Cheng, Michael J. Clark, Hogune Im, Lukas Habegger, Suganthi Balasubramanian, Maeve O’Huallachain, Joel T. Dudley, Sara Hillenmeyer, Rajini Haraksingh, Donald Sharon, Ghia Euskirchen, Phil Lacroute, Keith Bettinger, Alan P. Boyle, Maya Kasowski, Fabian Grubert, Scott Seki, Marco Garcia, Michelle Whirl-Carrillo, Mercedes Gallardo, Maria A. Blasco, Peter L. Greenberg, Phyllis Snyder, Teri E. Klein, Russ B. Altman, Atul Butte, Euan A. Ashley, Mark Gerstein, Kari C. Nadeau, Hua Tang, and Michael Snyder; Cell. 2012 Mar 16; 148:1293-1307. PMCID: PMC3341616.

  ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Landt SG*, Marinov GK*, Kundaje A*, Kheradpour P*, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M; Genome Res. 2012 Sep;22(9):1813-31. PMCID: PMC3431496