Software

Smart Resource Management for Data Streaming using an Online Bin-packing Strategy

December 16, 2020September 13, 2021 admin No Comments

The stream processing framework HarmonicIO is a prototype that addresses the needs for processing streams based on relatively large individual objects. In this regard, it is a specialized streaming framework well-suited for scientific workflows. Salman Toor and Oliver Stein presented this work, and our latest publication Smart Resource Management for Data Streaming using an Online…

Applied Cloud Computing, Data-Intensive Computing, HASTE, News, publication, Software

try.stochss.org: Try StochSS as a Service

June 22, 2016June 22, 2016 admin No Comments

To make it easy to try StochSS, our software for rapid model development and simulation of stochastic regulatory networks, we are now providing it as a service on http://try.stochss.org. To use it, simply follow the link to set up your account. Since this only require a modern browser and a valid email address (no software installation), we hope…

News, Software, Stochastic Chemical Kinetics, StochSS

Open Posititions: up to two PhD students

January 19, 2016March 14, 2016 admin No Comments

(Call for applications is closed. ) We are expanding the group with up to two PhD students in the areas of Applied Mathematics and Applied Cloud Computing: CIM, the Center for Interdisciplinary Mathematics are hiring students. We are, in collaboration with the Spjuth lab offering the project, Smart and Efficient Scientific Software for Exploration of Vast Amounts…

Applied Cloud Computing, Data Science, Data-Intensive Computing, Open Positions, Software, StochSS

StochSS 1.6 is now officially released!

July 6, 2015November 6, 2015 admin No Comments

New capabilities of Version 1.6 include: Spatial visualization now supports animation, wireframe rendering, and mesh slicing FlexCloud: run ‘cloud’ jobs on dedicated hardware (in addition to using EC2) Import SBML models Many bug fixes and stability enhancements Details and instructions on how to obtain the code can be found on the Download page Tutorials are…

News, PyURDME, Software, Stochastic Chemical Kinetics, StochSS

StochSS 1.4: Introducing Spatial Stochastic Modeling and Simulations

September 1, 2014September 1, 2014 admin No Comments

We are excited to announce the release of StochSS 1.4 Version 1.4 includes spatial stochastic simulation capabilities powered by PyURDME (http://www.pyurdme.org/). Details and instructions on how to obtain the code can be found on the Download page Tutorials are available on the Documentation page Linda Petzold and Chandra Krintz – University of California Santa Barbara Per Lotstedt and Andreas Hellander – Uppsala…

News, PyURDME, Reaction Diffusion Master Equation, Software, Stochastic Chemical Kinetics, StochSS

PyURDME 1.0

June 25, 2014June 25, 2014 admin No Comments

After more than a year of development, we are happy to announce the release of PyURDME 1.0.0! PyURDME is a Python module for spatial stochastic simulation model development and simulation. PyURDME is connected to URDME in that is uses a modified version of its core solver. While URDME is mainly designed as an interactive Matlab…

ECMTB 2014 and Computational Software

June 25, 2014June 25, 2014 admin No Comments

I attended this years ECMTB 2014. Apart from many interesting sessions on mathematical modeling, I attended this minisymposia on software for multicellular simulations. All the speakers had done a great job developing software for the application community, but the impression was that they managed to do this despite being productive methods researchers, not as a…

News, Software, StochSS, URDME