Institute for Biodiversity Science & Sustainability
Research institute located within the California Academy of Sciences
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Beetles in the collection at the IBSS.
The Institute for Biodiversity Science and Sustainability (IBSS) is a part of the California Academy of Sciences. The Cal Academy is a museum and research organization in San Francisco's Golden Gate Park. The organization runs programs for science education, outreach, and advocacy. Founded in 1852, the Academy employs 700 people and focuses primarily on natural sciences. With met with Joe Russack, a computer scientist who supports genomic research in ISBB.

Because Joe worked within the research arm at the Cal Academy, we learned about the software that was used to enable and empower research at the Academy. This post doesn't cover the software that the Academy uses to manage the museum floor, from things like membership to ticketing to operations.

600+
employees
164
years in operation
1.2M+
annual visitors
Software used
Illumina
Genomic sequencing
Illumina makes a suite of products for genome sequencing. Usually, ISBB researchers send samples to Illumina for sequencing, and then use the data returned to power their research.
Trimmomatic
Genomic analysis
Russack said that genomic researchers are constantly developing and trying out new software to improve the quality of sequencing. New techniques are published daily, and most are open-source. Trimmomatic, for example, analyzes the quality of the genome and trims it into segments.
Velvet
Genomic analysis
Velvet and other similar tools like Abyss help with assembly, the process that reconstructs genetic sequences from unordered tagged sections. Russack said that assembly software is constantly evolving.
Globus
Large file transfer
Globus is a platform that supports file transfer for large files. It’s specialized for researchers transferring, publishing, and sharing genomic data with peers.
Ansible
Remote configuration
Joe uses Ansible to help researchers set up computational systems and jobs. For starting computational systems, Ansible makes for a predictable and replicable environment, which enables researchers to get started faster.
Commentary
The Cal Academy is a huge organization made of many different arms. We focused solely on the research arm, where many industry tools were needed to make sure that data was processed correctly, efficiently, and quickly. The group also had any ongoing digitization efforts, to allow their collections to be more accessible to everyone.