ASSETS & RESOURCES
COMPUTATION
With the advancement of new paradigms in computing designs (such as GPUs and neuromorphics), data science and artificial intelligence, the evolution of our shared high performance Research Computing Capability for advanced research remains a strategic priority at UCSF. Computing has become the third paradigm for discovery, supporting our data driven culture across all of UCSF, complementing theory and experiment. This capability is built on Wynton.
UCSF researchers today have access to a choice of computing capabilities, based on their needs and proximity to support.
Cancer Center
Computation which comes with Core services.
See website
Epidemiology & Biostatistics
Data Systems Services (DSS) serves researchers within the Dept of Epidemiology & Biostatistics with data systems, programming, network management, and a high performance compute cluster.
See website
Genetics
Computation which comes with Core services.
See website
MyResearch (Academic Research Systems)
MyResearch is a secure data hosting service for researchers, including files containing sensitive data. MyResearch also offers tools to analyze the data you store including SAS, SPSS, R, STATA, Matlab, Python, Office suite and many others.
See website
Quantitative Biology
Computation with a molecular focus, and much more.
See website
REDCap
Well-known clinical data research environment.
See website
San Francisco Coordinating Center
Range of Microsoft and open-source based technologies. Besides the listed capabilities, a SparkR cluster is targeted for late summer 2017.
See website
Biomedical Imaging Research Support: Scientific Computing Services
Hardware computing support for research, which include linux workstations, high performance computing clusters and connectivity for lab equipment as well as software support on those systems.
See website
Wynton platform and All Other
DATA & TOOLS
UCSF provides a reference to its clinical data sources, which is frequently updated. See UCSF Data Resources.
The UCSF Information Commons is an environment where a diversity of data and tools are made available to investigators for research. See details below.
For the textual analysis of clinical notes, we recommend a short list of natural language processing (NLP) tools, depending on the application.
UCSF’s Information Commons provides a shared repository data, tools and models for today’s demands of integrative research and precision medicine. It brings together the worlds of clinical, basic science and population research, at a scale that manages huge sizes of multi-factor and multi-modal data – and keeps its users compliant with regulation.
Clinical Text-Specific
- cTAKES : Apache’s clinical Text Analysis Knowledge Extraction System
Specific Tools within Clinical Text Pipeline
Eg. parsing, entity recognition, negation detection, relationships
- Columbia MedLEE
- SymText
- REX: Regenstrief Extraction
Generic Building Blocks
- Google SyntaxNet
- OpenNLP : bag of tools
- Stanford CoreNLP
- UIMA: Apache’s Unstructured Information Management
EXPERTISE
Your computation-based study probably flows in the following pattern
UCSF has several centers of expertise to serve your research needs. Many are tied to a specific biomedical process, but others are expanding into broader computational health sciences. Each of them is rapidly expanding its talent and services, so check in often – or reach out to them.
Biomedical Imaging Research Support Services
Clinical Imaging Core Services
Assistance with all aspects of your study including experiment and protocol design, imaging and data analysis, faculty/technical consultation, image processing, interpretation and transfer.
Scientific Computing Services
Hardware computing support for research, which include linux workstations, high performance computing clusters and connectivity for lab equipment as well as software support on those systems.
Pre-Clinical Imaging Core Services
Expertise, technical support, and assistance with tissue and small animal imaging studies.
Human Imaging Core Services
Assistance with investigation of human diseases and therapeutic interventions.
See website
Clinical and Translational Research
Researchers can get help with biostatistics, study design and a large variety of specialized consulting services. These consultation services are offered by UCSF’s Clinical and Translational Science Institute (CTSI).
See website
Computational Biology and Informatics (CBI) Core
The CBI provides computational biology support and computational and data infrastructure to facilitate cutting-edge cancer-related research at the UCSF Helen Diller Family Comprehensive Cancer Center (HDFCCC). Although prioritized toward members of the HDFCCC, as time permits, the Core provides support to outside investigators.
The CBI team has expertise in genetics, bioinformatics, computer science, statistics, high-performance computing, and software and database development. Work is focused on technologies such as next-generation sequencing, microarrays, and other genomic and proteomic assays. CBI activities include scientific consultation, study design, data analysis, software and database development, and grant and manuscript assistance.
See website
Epidemiology & Biostatistics Core
In addition to its collaborative role in research and the cross-campus training it provides to the basic, clinical and population sciences, the Department of Epidemiology & Biostatistics formally provides specific services in biostatistical and bioinfomatics consultations (Pletcher/McCulloch) through the Clinical and Translational Sciences Institute (CTSI) as well as support for complex, large-scale, high-volume research through its Data Systems Services (DSS) group.
See website
Gladstone Bioinformatics Core
Services, training and resources for the larger research community, spanning experimental design, statistics, omics analysis and systems biology.
See website
SOM Tech
The School of Medicine’s Technical unit (SOM Tech) creates applications, both web and mobile, for your research needs. They leverage Salesforce and Mulesoft messaging bus as their primary development platform.
See website
Sequence Analysis and Consulting Services (RBVI SACS)
With origins and strengths in genomics, this Core brings visualization, networking, computational and bioinformatic tools to the UCSF research community.
See website
