Skip to content

Integrative Scalable Computing Laboratory

A research group at the Department of Information Technology, Uppsala Universtity.

  • Home
  • Projects
  • People
  • Publications
  • Teaching
  • Software
  • Recruitment
  • About us
  • Toggle search form

Mesoscopic-microscopic hybrid algorithm with automatic partitioning

Posted on September 11, 2017September 11, 2017 By Stefan Hellander No Comments on Mesoscopic-microscopic hybrid algorithm with automatic partitioning
Mesoscopic-microscopic hybrid algorithm with automatic partitioning

We have developed a multiscale method coupling the mesoscopic and microscopic scales. On the mesoscopic scale, systems are modeled as discrete jump processes on a structured or unstructured grid, while on the microscopic scale, molecules are modeled by hard spheres diffusing in continuous space. Microscopic simulations are accurate but computationally expensive. In this paper we…

Read More “Mesoscopic-microscopic hybrid algorithm with automatic partitioning” »

Multiscale methods, News, publication, Reaction Diffusion Master Equation

Open PhD position

Posted on February 5, 2015February 5, 2015 By admin No Comments on Open PhD position

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.

Multiscale methods, News, PyURDME, Reaction Diffusion Master Equation

StochSS 1.4: Introducing Spatial Stochastic Modeling and Simulations

Posted on September 1, 2014September 1, 2014 By admin No Comments on StochSS 1.4: Introducing Spatial Stochastic Modeling and Simulations

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…

Read More “StochSS 1.4: Introducing Spatial Stochastic Modeling and Simulations” »

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

Open PhD student position

Posted on June 25, 2014June 25, 2014 By admin No Comments on Open PhD student position

We have an opening for a PhD student in computational systems biology. Interested candidates are encouraged to contact me for more details. Apply to the position here.

Multiscale methods, News, Reaction Diffusion Master Equation

PyURDME 1.0

Posted on June 25, 2014June 25, 2014 By admin No Comments on PyURDME 1.0

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…

Read More “PyURDME 1.0” »

News, PyURDME, Reaction Diffusion Master Equation, Software, StochSS, URDME

PhD and Postdoc positions

Posted on January 17, 2014 By admin No Comments on PhD and Postdoc positions

The Center for Applied Mathematics (CIM) in Uppsala are looking for up to 3 PhD students in applied mathematics. Within this call there is an opportunity to joint the group working on the project From cell-cell interactions to embryo development: Multiscale models and simulation in systems biology. This project is a collaboration with Carolina Wählby….

Read More “PhD and Postdoc positions” »

Hes1, Multiscale methods, News, Reaction Diffusion Master Equation, Stochastic Chemical Kinetics, StochSS, URDME

Spatial Stochastic Simulation of the Hes1 gene regulatory network

Posted on January 23, 2013 By admin No Comments on Spatial Stochastic Simulation of the Hes1 gene regulatory network

Individual mouse embryonic stem cells have been found to exhibit highly variable differentiation responses under the same environmental conditions. Recent experimatal evidence suggest that the noisy cyclic expression of Hes1 and its downstream genes are  responsible for this, but the mechanism underlying this variability in expression is not well understood. Together with Mark Chaplain’s group,…

Read More “Spatial Stochastic Simulation of the Hes1 gene regulatory network” »

Hes1, News, Reaction Diffusion Master Equation

URDME 1.2 Released

Posted on December 18, 2012December 18, 2012 By admin No Comments on URDME 1.2 Released

We are happy to announce the release of URDME 1.2. New features include support for Comsol 4.1, 4.2 and 4.3. We have also added the ability to compile the solvers independently of Matlab libraries. This will greatly simplify deployment of URDME jobs by StochSS down the line. To get URDME 1.2: www.urdme.org Or visit us…

Read More “URDME 1.2 Released” »

Reaction Diffusion Master Equation, URDME

URDME paper in BMC Systems Biology

Posted on August 16, 2012August 17, 2012 By admin No Comments on URDME paper in BMC Systems Biology

Ever since the first version of URDME, a software framework based on our theoretical work on RDME simulations on unstructured meshes, was made public in 2008, we have wanted to write up a journal publication that describes the software. For variuos reasons we have not gotten around to it, until now. The paper, published in…

Read More “URDME paper in BMC Systems Biology” »

Reaction Diffusion Master Equation, URDME

On the reaction-diffusion master equation in the microscopic limit

Posted on August 16, 2012January 25, 2016 By admin No Comments on On the reaction-diffusion master equation in the microscopic limit

The RDME will break down in the limit of vanishing voxel sizes, in the sense that contributions from bimolecular reactions will be lost. The problem sets on earlier (for larger voxels), the more diffusion limited the reaction is. This is a problem that has attracted a lot of interest since it was pointed out by…

Read More “On the reaction-diffusion master equation in the microscopic limit” »

publication, Reaction Diffusion Master Equation

Posts navigation

1 2 Next

Data-and simulation-driven life science. Much of our work in eScience and applied ML has applications in life science, and in Systems Biology in particular. We aim to enable data-and simulation-driven scientific discovery.

HASTE - a cloud native framework for intelligent processing of image streams: http://haste.research.it.uu.se/

Follow us on twitter

Andreas HellanderFollow

Andreas Hellander
A_HellanderAndreas Hellander@A_Hellander·
11 May

Are you using StochSS? Please help us gather insights into what is working well and what can be improved by filling in this short survey https://forms.gle/mEqfASuUd3MDWuPS9

@LindaPetzold @briandrawert @mhucka

Reply on Twitter 1524477596930654214Retweet on Twitter 15244775969306542141Like on Twitter 15244775969306542141Twitter 1524477596930654214
A_HellanderAndreas Hellander@A_Hellander·
9 May

Apply to this PhD student position in the eSSENCE and SciLifeLab graduate school in data-intensive science!

This project is the intersection of cybersecurity and big data with main supervisor @sztoor.
https://www.uu.se/en/about-uu/join-us/details/?positionId=501061

Reply on Twitter 1523559501965987841Retweet on Twitter 1523559501965987841Like on Twitter 15235595019659878411Twitter 1523559501965987841
A_HellanderAndreas Hellander@A_Hellander·
28 Apr

PhD position in the eSSENCE/@scilifelab graduate school in data-intensive science with @cnettel: https://uu.se/en/about-uu/join-us/details/?positionId=501716 Apply and be part of a new interdiciplinary research effort @UU_University!

Reply on Twitter 1519564476856557568Retweet on Twitter 15195644768565575686Like on Twitter 151956447685655756810Twitter 1519564476856557568
A_HellanderAndreas Hellander@A_Hellander·
23 Apr

If you are a current user of StochSS please let us know your thoughts by filling out this brief user survey: https://forms.gle/3r836iph8gqFEpZX7

#systemsbiology #stochss @LindaPetzold @briandrawert @prashant_rsingh

Reply on Twitter 1517753867403993089Retweet on Twitter 15177538674039930892Like on Twitter 15177538674039930891Twitter 1517753867403993089
Retweet on TwitterAndreas Hellander Retweeted
AssistSweASSIST Sweden@AssistSwe·
14 Apr

Soon the partners in the ASSIST project will attend a workshop on federated learning arranged by Scaleout. Partners from different countries (Sweden, Belgium, Netherlands, Turkey) will contribute with nodes that train a segmentation network.

Reply on Twitter 1514516928823447553Retweet on Twitter 15145169288234475532Like on Twitter 15145169288234475531Twitter 1514516928823447553
Load More...

Decentralized AI, Federated Learning. One focus area of the group is development of methods and software to address decentralized and privacy-preserving AI. We are core contributors to the FEDn open source framework for scalable federated machine learning:

https://github.com/scaleoutsystems/fedn
Introduction to Federated Learning by Andreas Hellander
Join the discussion on Decentralized AI:

Scaleout Systems is a spin-out from ISCL on a mission to enable decentralized AI and federated learning to production.

https://www.scaleoutsystems.com/

Copyright © 2022 Integrative Scalable Computing Laboratory.

Powered by PressBook Blog WordPress theme