Elisha Wood-Charlson

Elisha M Wood-Charlson

Elisha M. Wood-Charlson has a PhD in marine science and has worked in a variety of research areas including coral symbioses, marine viruses, and microbe ecology on coral reefs. For the past few years, she has been exploring the professional space around scientific community engagement. In 2017, she was selected to join the inaugural AAAS Community Engagement Fellows Program, and finally found a niche that spoke to her fundamental need to make science more efficient through improved communication and collaboration. Dr. Wood-Charlson joined KBase in September 2018 as the User Engagement Lead. A role that allows her to explore ideas on how to build virtual communities around the stages of the scientific method, while supporting a data sharing and analysis platform that is committed to open science and following the FAIR data principles (findable, accessible, interoperable, and reusable).

Dylan Chivian

Dylan Chivian

Dylan Chivian is a Research Scientist at LBL, interested in discovering the rules for assembly, stability, and dynamics of functional cohorts within microbiomes.

Keith Keller

Keith Keller

Keith Keller is a system administrator for KBase (https://kbase.us). He has been a member of the Arkin lab since 2002.

Jason Baumohl

Jason Baumohl

Jason Baumohl is a software engineer on the KBase project. He has degrees in Biology, Genetics and Computer Science. He worked for the Joint Genome Institute for 6 years in Production Informatics and often lectured for their student and community tours. After the JGI, Jason used to work on Microbes online and Enigma projects within the Arkin lab. He specializes in relational databases, Genome formats, QA/QC and python programming. His life revolves around Cathy, his wife, and Banjo, his dog, more than he would like to admit.

Akiyo Marukawa

Akiyo Marukawa

Akiyo is a former control systems engineer turned front end developer for KBase.

Annette Greiner

Annette Greiner

Annette Greiner is a data nerd with particular interest in interaction design and visualization. She joined the NERSC division upon completion of a Master’s in Information Management and Systems from UC Berkeley’s School of Information, with a focus on human-computer interaction. Before returning to school, she developed web sites for the Advanced Light Source and the DOE Joint Genome Institute. At NERSC, her duties include wrangling data and developing science gateways of all kinds. For KBase, she leads the user interface design efforts. At a broader level, she represents the Laboratory to the World Wide Web Consortium (W3C) and has served on international working groups related to publication and sharing of data. Her interests touch the UC Berkeley campus as well, where she teaches data visualization for the Master’s in Information and Data Science (MIDS) program at the School of Information. Annette also holds a B.S. in biomedical science and theater from the University of Michigan.

Marcin Joachimiak

Marcin P. Joachimiak

Marcin Joachimiak is a Staff Researcher and Software Developer in the Environmental Genomics and Systems Biology Division at Lawrence Berkeley National Lab. He studied Mathematics at University of Chicago while creating transgenic yeast strains to enable high throughput herbicide screening for wheat. In 2002 he went West and studied Biophysics at UCSF where he implemented the Evolutionary Trace method and its variants (JEvTrace), identified novel targets and inhibitors for antimalarials, and performed the first genome annotation and contributed to the first gene expression analysis of the malaria parasite. After a year at Five Prime Therapeutics, where he founded the computational infrastructure and used the Riken mouse cDNA collection to discover novel human genes, he returned to academia as a postdoc in the Brenner Group at UC Berkeley. At UCB he developed a popular visualization tool (JColorGrid), performed key sequence and phylogeny analysis for the Global Ocean Survey, and published an affinity-based model for human branch point site prediction. Since 2006 he has been a member of the Arkin Laboratory, first as part of the ENIGMA project where he developed the gene expression analysis pipeline, functional genomics analysis tools in MicrobesOnline, and a novel machine learning algorithm for multi-data type biclustering. Since 2014 he has been part of the DOE KnowledgeBase where he designs and develops applications for statistical and visualization analysis and most recently on components of the system to enable rapid data type modeling, data science and machine learning, and integration with ontologies and knowledge graphs.

Gwyneth Terry

Gwyneth Terry

Gwyneth Terry is a senior administrator supporting Adam Arkin and his laboratory at Berkeley Lab and University of California, Berkeley. She has a BSc in geology from Cal State East Bay. She assists lab personnel with the UCB and LBL bureaucracy and helps moves science forward.

William Krinsman

William Krinsman

William Krinsman is a PhD student from the Interdepartmental Group in Biostatistics at UC Berkeley working in the Arkin Laboratory at LBNL as a developer for KBase and data analyst for ENIGMA. William’s research focuses on developing novel computational methods for the statistical analysis of biological datasets. William majored in mathematics at Northwestern University, during which time William also studied at the universities TUM and LMU in the German city of Munich. Before moving to Berkeley, William was a Fulbright scholar for one year in the German capital Berlin. Afterwards, and prior to joining the Arkin Laboratory, William previously worked at LBNL’s supercomputing center NERSC and Computational Research Division (CRD), developing software to help scientists fully and easily access NERSC’s computing resources via interactive computing platforms from the open-source Jupyter project. William is fluent in German, as well as conversational in Russian and Spanish, and grew up in a household with two dogs and five cats.

Roy Kamimura

Roy Kamimura

Roy Kamimura is the project manager for KBase at Lawrence Berkeley National Laboratory (LBL). He got his BS in chemical engineering from UC Berkeley and his PhD under Gregory Stephanopoulos at MIT on applying pattern recognition techniques to fermentation data. He has worked at Genencor, Lawrence Livermore National Laboratory, Codexis, and Intrexon prior to LBL. A jack of all trades, he has experience in machine learning, strain and enzyme engineering, biochemical engineering from upstream to fermentation to downstream (using sugar, CO/CO2, and CH4 carbon sources) , high throughput screening analysis, bioenergetics, microbial physiology, biosecurity, bioforensics, and business development. His goal is to ensure that KBase achieves global domination in open source computational biology.