Software and Programming

Library Data Science Initiative

Workshops, programs and expertise/office hours in:

  • Finding, Managing & Sharing Data
  • Statistics, Bioinformatics and Genomics
  • Programming in R, Python and more
  • Data Visualization with Tableau

[email protected]

Secure hosting for sensitive data with web-based management and collaboration tools.

  • View, manipulate, and save data entirely in a protected environment without storing files on personal computers
  • Free access to research software applications, such as SAS, Stata, SPSS, R, TreeAge, Atlas.ti, MS Office, and Matlab - see full list
  • Collaboration tools, such as SharePoint and the UC ReX Data Explorer, facilitate the conduct of multi-site research studies
Free up to 10GB/month for UCSF PIs

MATLAB

MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment, programming language and data visualization tool. A campus-wide license is available for faculty, students and staff.

  • Matrix manipulations, plotting of functions and data, implementation of algorithms
  • Simulink and companion toolboxes for graphical multi-domain simulation and model-based design for dynamic and embedded systems
  • Training sessions, online tutorials, and videos
Free for UCSF Community

Research Software Licenses (RSL)

Offers annual licenses for research software to UCSF faculty and staff.

  • Individual licenses: SAS | SPSS | JMP | SUDAAN | NVivo | ArcGIS
  • Academic discount on Stata

Computation and Informatics Core Facilities

Find computational assets and expertise for basic, translational, clinical, and population health research. Services include:

  • Experimental design
  • Data generation, extraction and storage
  • Data analysis and interpretation

SOM Tech

Design and implementation of technical projects. Data services include:

  • Application development/programming involving data
  • Using Amazon Web Services (AWS) to host databases and applications, and for high-performance computing
  • Data security compliance

Data Systems Services

Department of Epidemiology & Biostatistics provides data collection, cleaning, and storage services to research investigators.

  • Cloud computing and server/desktop virtualization, hosted within the UCSF network and compliant with NIST-mandated security protocols
  • Customized programming and data services
  • Customized databases for outcome ascertainment studies

[email protected]

UCSF's NLP community curates knowledge as participants experiment, learn and implement NLP tools in clinical and biomedical research projects.

  • Slack channel and regular meetups
  • Recommended tools for textual analysis of clinical notes

Sample Size Calculators

Online tools for clinical researchers:

  • To determine how many subjects to include in a study
  • To answer questions related to sample size or power calculations

Table 1 SAS Macro

Download the macro and run it on your data; it summarizes continuous and categorical variables by subgroups, and generates:

  • A summary table that is useful for a simple analysis/first look at a data set
  • A final demographic descriptive table that may be used in the typical Table 1 of a clinical paper