Who are the brains behind Clotho?
Clotho is an interdisciplinary research effort currently run primarily by researchers at Boston University and UC Berkeley. Members of the Clotho team are faculty members, post doctoral researchers, graduate students, and undergraduate students. This page provides more information on those currently involved as well as alumni of the project.
Project Leaders
Douglas Densmore
Doug was the original creator of Clotho when he was a UC Chancellor’s post doctoral fellow at UC Berkeley. He also served as the research advisor for the 2008 and 2009 Clotho iGEM teams. He is now the Richard and Minda Reidy Family Career Development Assistant Professor at Boston University in the Department of Electrical and Computer Engineering. He is the leader of the Center for Integrating Design Automation Research (CIDAR) and a member of the Center for Advanced Biotechnology (CAB). His interests span both traditional electronic design automation as well as the emerging field of bio-design automation.
J. Christopher Anderson
Chris is an Assistant Professor at UC Berkeley in the Department of Bioengineering at UC Berkeley and LBNL, and a principal investigator of the Synthetic Biology Engineering Research Center. With broad research interests in applications and foundational technologies for synthetic biology, the Anderson lab works on both wetlab and computational projects. Chris has been the faculty advisor for the Berkeley iGEM program for the past 5 years including Clotho’s winning 2008 and 2009 teams. Chris became an active programmer and project manager for Clotho beginning in 2010.
Current Team
Bing Xia
Bing was an Applied Math, Molecular Biology, and Computer Science triple major at UC Berkeley. He was on the 2008 Berkeley Wet Lab iGEM team and he thoroughly enjoyed the experience. In 2009 Bing switched from pipetman to PCs joining the Clotho development team and then continued his participation in the project in 2010. Bing masterminded the inner workings of Clotho’s core including the Datum layer, plugin environment, Hibernate connections, and algorithm framework. His research interests mainly lie in the area of computational biology, although he isn't sure what subarea he's most interested in. He hopes to pursue graduate studies in the future. In his few hours of spare time, Bing enjoys running, taekwondo, classical piano, and origami.
Ben Bubenheim
Ben double majored in Computer Science and Molecular Biology at UC Berkeley and has a special interest in computational biology and genetic engineering. He joined the Clotho development team for Berkeley 2010 iGEM where he spearheaded the development of Clotho’s biosafety management and sequence analysis apps. In the future he hopes to go on to graduate school in the field of computational biology, and to continue to find and research ways that computational techniques can aid in biological research. Outside of academics, Ben enjoys intramural softball and soccer, as well as running and snowboarding.
Josh Kittleson
Josh is a graduate student in the Anderson lab getting his PhD in Bioengineering from UC Berkeley. Having completed undergraduate degrees in Biochemistry and Computer Engineering at the University of Arizona, he turned to Synthetic Biology to mate his interests in engineering and biology. Though Josh’s current work is dominated with a passion for developing experimental tools for biologists and pursuing novel applications of microorganisms, he’s been involved in the Clotho project since 2008. Josh's primary role has been to create and maintain databases for the core development team. In addition to providing database support, Josh serves as an advisor to the project, guiding many aspects of the Clotho API and data model.
Swapnil Bhatia
Swapnil Bhatia is a postdoctoral research associate at Boston University working with Douglas Densmore in the Center for Integrating Design Automation Research (CIDAR). Swapnil received his B. Engg. in Computer Engineering from Bombay University. His PhD is from the University of New Hampshire where he worked on access, sensor, and storage networks. He held a postdoctoral position at Palo Alto Research Center (formerly known as Xerox PARC) in the Proteomics group. He currently is developing Apps for Clotho which will allow it to interface with other design environments and languages to raise the level of abstraction at which users create designs.
Current Collaborators
Michal Galdzicki
Michal is a PhD Candidate in Biomedical and Health Informatics at the University of Washington. In his dissertation research, he aims to encourage the re-use of standard biological components through the application of Semantic Web standards for the representation of knowledge in synthetic biology. In collaboration with Dr. Cesar Rordiguez of the BIOFAB, he leads the effort to develop the Synthetic Biology Open Language (SBOL), an effort to form a consensus for the electronic exchange of data in synthetic biology. Michal is advised by Dr. John Gennari and works as part of Dr. Hebert Sauro’s Synthetic Biology Group at the Department of Bioengineering. Michal received his BS in Biology from the University of Maryland in 2002 and a MS in Bioinformatics from Boston University in 2005.
Timothy Ham
Tim is the creator and the software architect of the Joint BioEnergy Institute Registry of Biological Parts (JBEIR). After finishing his PhD at UC Berkeley designing and constructing heritable genetic memory circuits, he became passionate about building software that work seamlessly together to enable biologists to create new and useful biological functions. As part of the Synthetic Biology Department at JBEI, Tim is working to bring harmony to the synthetic biology software world by developing widely used, quality open source software.
Carlos Olguin
Carlos is the Head of the Nanotechnology Group at Autodesk Research. As a collaborator of the Clotho effort, he guides the development of communication resources for the Clotho project and user testing of the tools. In his role within Autodesk Research, Carlos leads a new initiative to understand and exploit the intersection of synthetic biology and (bio)nanotechnology with 3D visualization, simulation, and design. He obtained a Master of Science in Information Networking from Carnegie Mellon.
Cesar Rodriquez
Cesar is the software lead at the BIOFAB. The software team is developing Clotho BIOFAB Edition which is a version of Clotho customized to the needs of the BIOFAB. They are also developing "electronic datasheets" which provide CAD tools a web-based application interface for retrieving design information and performance data for BIOFAB parts.
Marc Juul
Marc is part of the BIOFAB (www.biofab.org) software team, and is developing algorithms that combine multiple existing sequence-based expression level predictors with the goal of increased forward design capability. These algorithms will be able to integrate into Clotho as Apps. Marc is a graduate student from the Technical University of Denmark currently working on his master's thesis.
Alumni
Lesia Bilitchenko
Joanna Chen
Adam Liu
Richard Mar
Thien Nguyen
Nina Revko
Matthew Johnson
Nade Sritanyaratana
