A knowledgebase for predictive biology

Adam is an expert in the comparative systems and synthetic biology of microbes and is dedicated to a model-driven approach to experimental science. He is a senior faculty scientist in the Environmental Genomics and Systems Biology Division at the Lawrence Berkeley National Laboratory and he is the Dean A. Richard Newton Memorial Professor of Bioengineering at the University of California, Berkeley where he has been since 1998. He is Technical Co-Manager of the ENIGMA SFA and directs the Center for Utilization of Biological Engineering in Space. He was one of six recipients of the 2013 Ernest Orlando Lawrence Award, the Department of Energy’s highest scientific honor.

Elisha M Wood-Charlson is KBase’s User Engagement Lead. She has a PhD and 10+ years of experience as a microbial ecologist focused on host-microbe-virus interactions in the marine environment. Since leaving the research bench, she has moved into the realm of scientific community engagement, with the goal of making microbiome data science more efficient through effective collaboration, building trust in online communities, and developing shared ownership throughout the scientific process.

Ellen G. Dow, Ph.D. is a member of the outreach, communications, and user development team. Inspired by involvement in science outreach throughout graduate school, she left the bench to gain experience in informal education and cultivate community engagement from the general public to science sectors. A molecular biologist by training, Ellen applies her research experience to support scientists and develop resources for the KBase community.

Gazi Mahmud is seasoned professional with two decades of extensive industry expertise, specializing in the dynamic realms of Big Data and Enterprise Architecture. His core focus lies in seamlessly integrating Data Engineering, Data Science, and modern ML/AI Engineering operations at scale, reflecting his adeptness in orchestrating cross-functional collaborations across diverse domains.

Gazi possesses hands-on experience and visionary insights in design and implementation of data-led organizational transformations, encompassing data architecture modernization, ML/AI integration, and enterprise data governance. Notably, Gazi worked across innovative technology startups and larger high tech companies delivering compelling data narratives that not only foster AI ethics but also champion model explainability within the state of the art Data Science workflow initiatives. 

Leading by example, he has navigated expansive projects aimed at crafting innovative data and AI transformation strategies for industry leaders. His expertise extends to implementing continuous delivery capabilities, underscored by meticulous observability, to ensure seamless execution of unified data and analytics platform modernization use cases.

Jason Baumohl is a software engineer and computational biologist. He has degrees in both genetics and computer science. He has worked in industry at the bench running the small QC group at a startup called Acacia, before adding the computational side of his training. He interned in bioinformatics at Zyomyx. He joined LBL in 2002 at the JGI. He later transferred to the Arkin group in 2008 to work on the MicrobesOnline and Enigma projects. In 2013 he joined the KBase team. His area of expertise are relational databases, QC, and genetics.

John-Marc Chandonia is a computational biologist at Berkeley National Lab.  He co-leads data management for the ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies) SFA, a multi-lab collaboration to study microbial ecology.  Chandonia is the creator and curator of the SCOPe (Structural Classification of Proteins — extended) database, which seeks to annotate the structural and evolutionary relationships between all proteins of known structure.  He also is a developer on the DOE Systems Biology Knowledgebase (KBase) project.  Chandonia is currently developing an efficient, scalable framework for organizing heterogeneous datasets in a way that maximizes adherence to the FAIR principles (Findability, Accessibility, Interoperability, and Reusability).

Marcin P. Joachimiak is a computational biologist and software developer, with experience across academia (U of Chicago, UCSF, UC Berkeley, LBNL) and biotech startups (Pangea Systems, DoubleTwist, FivePrime Therapeutics). He started by studying mathematics while creating a herbicide resistant wheat strain and later did his PhD at UCSF on evolutionary information in sequence families and predicting protein structure. He has developed multiple algorithms, computational pipelines, and data science applications for functional genomics of humans and microbes. Over time, he has realized that data without standardization and meaningful metadata is hampering scientific progress and he started working to solve this problem via unsupervised machine learning biclustering with high performance computing, automated labeling, and statistical enrichment analysis. At KBase he works on system design and deploying knowledge discovery algorithms based on machine learning and semantic models. Google Scholar GitHub

Roy Kamimura is the project manager for KBase- responsible for ensuring the project stays within budget and delivers on project milestones.  His work experience spans 3 biotech companies (Genencor, Codexis, Intrexon) and 2 national labs (Lawrence Livermore, Lawrence Berkeley).  His core technical competencies are in process engineering (fermentation optimization, downstream processing), data science (focus on multivariate time series, high dimensional data sets with small samples), strain engineering (bioenergetics, enzyme engineering, high throughput screening, metabolic modeling, omics analysis), biodefense, and biotech business development (agriculture, consumer, environmental, food, industrial).  His degrees are all in chemical engineering (BSChE – UC Berkeley, PhD- MIT).

Sean Jungbluth pursued a Ph.D. in Oceanography studying microbial life in the deep subseafloor. In the search for novel life in extreme environments, I used submarines and developed custom sampling equipment to extract rock-hosted fluids circulating hundreds of meters below the seafloor. Leveraging DNA sequencing techniques, self-taught coding skills, and supercomputers, I’ve forged a career making stories from DNA sequencing data and discovering novel microbial lineages. Currently, I am working at Lawrence Berkeley National Laboratory as a Data Scientist on the DOE Systems Biology Knowledge Base (KBase) project where my goals are to democratize access to bioinformatic analysis tools and support reproducible genomic science. For more information, check out my personal webpage, Github, or Google Scholar.

Chris is a scientist at Argonne National Laboratory, a fellow at the University of Chicago, and an adjunct professor at Northwestern University. He is an expert in computational biology with a focus on the prediction of phenotype from genome through the use of comparative genomics, metabolic modeling, and dynamic cellular community models. He received the Jay Bailey Young Investigator Best Paper in Metabolic Engineering Award in 2012.

Janaka N. Edirisinghe is a Computational Biologist in Data Science and Learning Division at Argonne National Laboratory (ANL). He has inter-disciplinary background in the areas of System Biology, Microbial Physiology and Molecular Genetics. He got his BSc in Computer Science, MSc in Bioinformatics and Ph.D in Microbial Physiology. He has been an integral member of the ModelSEED team at ANL headed by Chris Henry and contributed to the implementation of automated model construction pipelines of prokaryotes and Fungi. He has joined the KBase project in its beginning days and has been contributing as a scientist, educator and as a developer. His research interests are focused on bacterial and fungal modeling, community interactions, use of cheminformatics in novel pathway identification and multi-omics integration.As an educator, he has conducted numerous hands-on workshops, webinars and presented at conferences over the years in distributing and sharing the knowledge among the scientific community. He can be found in Github, Google Scholar, LinkedIn, PubFacts

José P. Faria is a Computational Biologist at Argonne’s recently formed Data Science and Learning division. He started his education as a Biologist and went on to pursue a Ph.D. in Bioengineering under the scope of the MIT Portugal Progam. He has been a member of the Henry Lab at Argonne since its inception in 2009, starting as a Visiting Fullbright Scholar to perform research for his Master’s thesis. In his young career, his research has focused on genome-scale metabolic modeling reconstruction and analysis for prokaryotes as a member of the ModelSEED team. He brought his expertise in metabolic modeling to KBase and actively engages in the development of new scientific tools for the community. In KBase he can also be found on the road as a member of the outreach team. He has lectured over 20 workshops in the last 4 years in 5 different countries. His research interests intersect the fields of Computational Biology, Bioinformatics, Metabolic Engineering and Systems Biology.

He can be found on LinkedIn, Twitter and Google Scholar

Kathleen is a postdoctoral researcher at Argonne National Lab. She uses her 10+ years of experience studying ecology and plant-microbe interactions to help make KBase workflows for amplicon sequencing data.

Tianhao Gu studies computer science and mathematics — always within close proximity to his tea. His passions are coding, designing and writing. He believes in media and technology’s ability to better the world around us. He speaks Mandarin, English, Python, and Ruby. Tianhao holds an M.S. in Computer Science from Northwestern University and a B.S. in Mathematics and Computer Science from State University of New York – Binghamton

Andrew is a Graduate Research Fellow at Argonne National Laboratory and is a PhD student of Chemical Engineering at Northwestern University. He codes simulations of genome-scale metabolic models that elucidate cellular phenotypes and the behavior of microbial communities (predominately microbiomes of the intestines and soils).

Bob has extensive experience developing computational and data management tools and systems for genetics, genomics and systems biology research with a background in bioinformatics and management including at the Baylor College of Medicine Human Genome Center as Co-Director of the Informatics Core, Operations Director of the Genome Database at Johns Hopkins University School of Medicine, and Vice President of Computing at Celltech Chiroscience, a UK biopharmaceutical company developing drugs based on gene targets. In 2008 Cottingham moved to Oak Ridge National Laboratory where he is Group Leader for Computational & Predictive Biology.

Ben Allen coordinates outreach and user development activities to build the KBase user community while engaging in scientific collaborations to advance the use of the platform. His background in biochemistry and science education helps him develop protocols and training materials that provide depth while being accessible to a wide audience. Research interests include systems biology, microbial ecology, bioremediation studies, and biology education.

Meghan Drake is a technical project manager at Oak Ridge National Laboratory, and she assists with user engagement and project planning and tracking on KBase. A member of the KBase team since 2012, Meghan looks forward to applying project controls to ensure success on KBase milestones and deliverables.

Zach Crockett is a member of the outreach, communications, and user development team. His background is in biochemistry and cellular biology. He has professional experience in medical lab science testing information management systems, creating training plans, improving processes, and developing standard operating procedures.

Dakota is an Applications Engineer for KBase. Originally from Texas, he received his PhD in mathematics from the CUNY Graduate Center for his thesis entitled “Counting Restricted Integer Partitions.” In his career as an engineer, instructor and mentor he has found that his most important contribution is often communication. He prefers Python, SQL and vim, but has a soft spot for postscript and XSLT.

Annette Greiner is a data nerd with particular interest in user interface design and visualization. She came (back) to Berkeley Lab 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. Now at NERSC, she works as a data consultant and web application developer in the Data and Analytics Services group. She created, and for many semesters led, the data visualization course in UC Berkeley’s Master’s in Information and Data Science (MIDS) program. Annette represents Berkeley Lab on the World Wide Web Consortium (W3C) Advisory Committee and has been active in W3C’s data-related working groups. A former science writer and founding member of Chicago’s Theater Oobleck, Annette also holds a B.S. in biomedical science and theater from the University of Michigan.

Lawrence Berkeley National Laboratory

Research Interests

* Computational infrastructure development for analysis of microbial community functional structure, primarily using sequencing data.

* Phylogenomic approaches for functional dissection.

* Microbial community substructure such as interaction networks of minimal viable functional cohorts.

* Principles of functional guild dynamics and the determination of whether rare species contribute to community phenotype, stability, and efficiency.

* Development of lab consortia model systems.

* Modeling of microbial community population, physiological state, and genetic adaptation in response to physical, chemical, genetic, and species perturbation.

* Manipulation of natural enzymes by structural design to engender new behaviors.

* Much of this work involves developing infrastructure to support such investigations, including the Robetta protein structure prediction server (www.robetta.org), the Genome-Linked Application for Metabolic Maps (GLAMM) metabolic network viewer (glamm.lbl.gov), the MicrobesOnline (www.microbesonline.org) and metaMicrobesOnline (meta.microbesonline.org) phylogenomic analysis platforms for microbes and microbial communities, and most recently the DOE Systems Biology Knowledgebase (kbase.us) project.

Jay R Bolton is a software engineer with strong interests in computational biology, distributed systems, graph theory, and creative coding. He joined Lawrence Berkeley National Lab after five years as the CTO of a web startup called CommitChange.

Miriam Land is a computational biologist and software developer in the Biosciences Division of Oak Ridge National Laboratory. Her experience is in developing annotation pipelines and websites for auto-annotated microbial organisms that were sequenced at the Joint Genome Institute (JGI). Currently on KBase she is the Help Desk Lead helping user tickets get triaged and processed.

Pavel Novichkov was a lead designer and developer for KBase’s prototype knowledge representation, search, and granular data management systems that still inform design decisions of today. These designs have also led to additional data systems, such the Contextual Ontology-based Repository Analysis Library (CORAL, https://doi.org/10.1093/gigascience/giac089)

Qizhi Zhang is an engineer with education background in both chemical engineering(PhD) and software engineering (MS).  During the years of working at Argonne National Laboratory, Qizhi has enjoyed opportunities of working in half a dozen of Argonne’s divisions and collaborating with researchers from many fields.  Through work, she has made friends with chemical/environmental/energy engineers,  biochemists, biophysicists, high energy physicists and computer scientists. Qizhi has worked on various data-centric projects.  She has developed software applications with SQL/NoSQL databases on the backend and desktop/web UIs on the frontend.

Shane Canon is a project engineer in the Data and Analytics Services group at NERSC at Lawrence Berkeley National Lab and is a senior member of the KBase project where he co-leads advanced development.   Shane has focused his career on enabling data-intensive applications on HPC platforms and more recently on leverage HPC and large scale computing to enable bioinformatics. Shane has held a number of positions at NERSC including leading the Technology Integration group, where he focused on the Magellan Project and other areas of strategic focus, and leading the Data Systems group which managed the global file systems and other data systems.  Shane has also served as a group leader at Oak Ridge National Laboratory, where he architected the 10 petabyte Spider filesystem. Shane holds a PhD in physics from Duke University and a BS in physics from Auburn University. 

Steve Chan is an engineer who has worked in academia (CMU, Stanford) and many tech startups during the original Dot Com boom before coming to Berkeley Lab. He’s a generalist, having worked as a backend and frontend developer, operations, cybersecurity, systems programming and E-commerce, line developer and management. At KBase he spends his time wearing management and backend/systems engineering hats.