We are a computational science and engineering group located at the Division of Scientific Computing at the Department of Information Technology, Uppsala University. With a core in computational systems biology, we pursue diverse topics ranging from particle-based simulations to modeling of multicellular systems to cloud computing and design and implementation of modern computational science and engineering software.
We participate in the wider research constellations Computational Systems Biology and Distributed Computing Applications at the department. The lab is also participating in the eSSENCE e-Science collaboration.
Current focus areas in the lab are:
- Multiscale methods for quantitative simulations of cellular pathways and cell-cell interaction
- Applied cloud computing and data-intensive computations
- CSE Software
We are looking for a talented individual to join our efforts on creating smart and scalable cloud services to support simulation-driven scientific discovery via large-scale computational experiments such as parameter sweeps. This is a classic and very important problem that we will approach in new ways, leveraging recent advances in cloud computing, data-intensive computing and machine learning. See the full advertisement here (Deadline Sept. 1):
The successful candidate will contribute to the interdisciplinary research group Distributed Computing Applications (DCA) at the Department of Information Technology, Uppsala University.
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 that this service will help experienced modelers evaluate the software, and importantly, that it will reduce the barrier for new modelers to explore the possibilities of stochastic simulations in systems biology.
Screenshot showing volume rendering of a spatial stochastic simulation of a spatial negative feedback loop modeling the Hes1 regulatory network as described further in http://rsif.royalsocietypublishing.org/content/10/80/20120988
After testing StochSS, if you think it will be useful in your research, there are multiple options for you to use it on your own resources. The simplest way to get started is to download the binary package (uses Docker).
Our trial server is deployed in the SNIC Science Cloud. If you would like to provide StochSS as a service for your reserach group or for a distributed collaboration, you can do this easily on your own servers, or in another cloud infrastructure provider such as Amazon EC2. MOLNs, another member of the StochSS-suite of tools, can help you to configure and deploy an identical setup. Please do not hesitate to reach out to us if you need help with this process.
Many of you also like the possibility to work with solvers in a programming environment. All of the tools that are powering StochSS are also available as stand alone libraries:
- PyURDME (Python API for spatial stochastic modeling and simulation )
- Gillespy (Python API for well-mixed simulations, based on StochKit2)
In addition, if you have access to cloud infrastructure, and would like to work in a pre-configured environment powered by a Jupyther Notebook frontend and interactive parallel computing, you should check out MOLNs:
- MOLNs: Cloud platform/orchestration framework for large-scale computational experiments such as ensembles and parameter sweeps, backed by Jupyther and Ipython Parallel.
We are very happy to welcome Fredrik Wrede, MSc. in Bioinformatics, to the group. Fredrik was accepted as a PhD student in CIM, the Center for Interdisciplinary Mathematics. His project will center around intelligent cloud services for processing and making sense of massive amounts of data, for example generated by large computational experiments in systems biology such as parameter sweeps. The project is an interdisciplinary collaboration with the Spjuth lab on data-intensive and translational bioinformatics.
Last week brought some great news. I am awarded the Göran Gustafsson Prize 2016 from the Gustafsson Foundation (KTH/UU). In the proposed project titled Smart Services for Scientific Discovery we will look into new and more productive ways to combine simulation software and cloud computing infrastructure to build intelligent applications for e.g. exploring an underlying model’s essential behavior.
I will be spending Feb 15-March 17 at the Isaac Newton Institute, Cambride, UK, for a program on Stochastic Dynamical Systems in Biology: Numerical Methods and Applications. Big thanks to the organizers,Radek Erban (Oxford), David Holcman (ENS – Paris), Samuel Isaacson (Boston) and Konstantinos Zygalakis (Southampton) for organizing this amazing opportunity to gather many creative people in our field at the same place!
(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:
Interested candidates are welcome to contact me for more information.
Hellander recently received the VR Young Researcher grant, for a project titled: From Single Cells to Cancer Tumors: Multiscale Simulation of Multicellular Systems. This means that we will be expanding the group with another PhD student in early 2016. Interested candidates are encouraged to contact me to discuss opportunities.
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 available on the Documentation page
Linda Petzold, Chandra Krintz, Andreas Hellander and Per Lötstedt, and the rest of the StochSS team.
We are currently hiring a PhD student to work on the project From Single Cells to Tumors – Multiscale Simulation of Stochastic (multi)cellular Systems
Deadline for application: March 15.
Instructions for how to apply can be found here:
Instructions for application.