Center funded by NIBIB

July 1st, 2018|

We are excited to announce that the NIBIB has committed to fund the center through 2023 to develop technologies for scalable and reproducible modeling, provide free services to the community, advocate for reproducible modeling, and [...]

Karr Lab launched new version of to foster whole-cell modeling

July 1st, 2018|

The new website features an overview of the goals, challenges, plans, and methods of whole-cell modeling, as well as links to whole-cell models and whole-cell modeling tools, training materials, events, and research groups.

Jonathan Karr contributed to a panel discussion on standards for GP-Write

May 2nd, 2018|

Jonathan Karr contributed a perspective on modeling and simulating to the standards panel at the 2018 GP-Write meeting.

Karr Lab joined the GP-Write Standards Working Group

March 16th, 2018|

The Karr Lab joined the GP-Write Standards Working Group and helped write a white paper on the standard protocols and formats that are needed for genome design and writing.

Karr Lab published a perspective on emerging goals and methods for whole-cell modeling

December 21st, 2017|

The Karr Lab published a perspective on how researchers are beginning to leverage recent progress in measurement technology, bioinformatics, data sharing, rule-based modeling, and multi-algorithmic simulation to build the first whole-cell models.

Karr Lab published a blueprint for human whole-cell modeling

November 9th, 2017|

The Karr Lab proposed a plan for a project, termed the Human Whole-Cell Modeling Project, to achieve human whole-cell models. The foundations of the plan include technology development, standards development, and interdisciplinary collaboration.

Karr Lab published a survey on the goals and bottlenecks of biomodeling

November 9th, 2017|

To develop a plan for achieving human whole-cell models, the Karr Lab analyzed the existing models of individual cellular pathways, surveyed the biomodeling community, and reflected on theirr experience developing whole-cell models of bacteria.

Early version of kinetic_datanator data aggregation software released

August 24th, 2017|

Prof. Karr has his team have released an early version of their kinetic_datanator software tool for finding experimental data for building and calibrating dynamical models of cellular biochemistry. kinetic_datanator helps users find data such as  metabolite, RNA, and [...]

SemGen version 4.0 released

August 24th, 2017|

We released a new version (4.0) of the SemGen platform that includes a new user interface and new model merging capabilities.

Tellurium version 1.3.7 released

August 24th, 2017|

Prof. Sauro released an updated version (1.3.7) of the Tellurium modeling and reproducibility platform.

libRoadRunner version 1.4.18 released

August 24th, 2017|

Prof. Sauro released an updated version (1.4.18) of the libRoadRunner high-performance simulation engine.

“Systems Biology: Introduction to Pathway Modeling” updated

August 24th, 2017|

Prof. Sauro has released an updated version of his textbook "Systems Biology: Introduction to Pathway Modeling"