# Extended Development of the CIPRES Science Gateway, a Resource for Biological Research.

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2020 · $464,476

## Abstract

Project Summary/Abstract. Understanding the evolutionary history of living organisms is of central importance
to every field of biological and biomedical research. Evolutionary information is critical to the discovery process
across all biological scales, from proteins to populations. The CIPRES Science Gateway (CIPRES) is a global
resource that speeds up inference of evolutionary history from DNA sequence data. CIPRES provides public
access to community phylogenetics software run on high performance computing (HPC) resources at no cost to
the user. CIPRES allows investigators to access all the capabilities of phylogenetics software efficiently though
a browser interface, without having to install the codes, learn the details of schedulers, and construct command
lines. CIPRES is the sole public resource for many of these codes, completes analyses 5-30 fold faster than a
typical laptop computer, allows users to run many analyses simultaneously, and provides indefinite storage of
the results. At present, approximately 2,000 users per month submit 20,000 jobs through CIPRES; they have
produced more than 3,000 peer reviewed publications in subject areas relevant to NIH priorities, from
enzymology to epidemiology. CIPRES has provided support for research ranging from HIV virus transmission to
the discovery of an entire new branch in the tree of life. All of these discoveries happen more quickly because
CIPRES provides easy access to HPC resources. The project proposed here will improve the software used to
create CIPRES, making it more effective and easier to access. It will provide an environment that allows
researchers to easily collaborate, share data selectively, and make their results publicly available. It will expose
access to CIPRES services through other important software environments, including Galaxy and Geneious.
The project will add a number of user-requested features so work is more efficient, including restarting jobs that
have terminated prematurely, transferring large files, and input file validation with automatic configuration of jobs
for optimal execution. The project will provide access to many new community codes that have been requested,
and those that appear during the project lifetime. Improvements to the interface will make it faster, more intuitive,
and useable on smart phones and tablets. The project will also give users “cloud-bursting” capabilities. Users
will be able to submit jobs to a commercial cloud provider on a fee-for-service basis or via NIH commons account
when their job is too large for the standard CIPRES community resources. This capability means CIPRES can
be scaled and sustained indefinitely for a user population of any size. These improvements (both in capabilities
and compute capacity) are expected to greatly expand the number of users who incorporate CIPRES into their
day-to-day workflow. The improvements made here will be available to the global research community through
release of the underlying soft...

## Key facts

- **NIH application ID:** 9824534
- **Project number:** 5R01GM126463-03
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** MARK A MILLER
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $464,476
- **Award type:** 5
- **Project period:** 2017-12-15 → 2021-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9824534

## Citation

> US National Institutes of Health, RePORTER application 9824534, Extended Development of the CIPRES Science Gateway, a Resource for Biological Research. (5R01GM126463-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9824534. Licensed CC0.

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