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
PhD student in Scientific Computing focusing on Secure Federated Machine Learning Data Science
Open PhD position in Scientific Computing Applied Cloud Computing
Two Open PhD Positions Data Science
FedQAS: Federated machine reading comprehension based on FEDn Data-Intensive Computing
Proactive Autoscaling for Edge Computing Systems with Kubernetes Applied Cloud Computing

Back in Uppsala

Posted on July 5, 2013 By admin No Comments on Back in Uppsala

After two great years as a postdoc with Linda Petzold at UCSB, I am now back in Uppsala as a senior lecturer at the division of scientific computing, department of information technology. Candidates for PhD projects, master’s thesis projects and postdoc positions are more than welcome to contact me to discuss opportunities to join the…

Read More “Back in Uppsala” »

Uncategorized

Perspective: Stochastic Algorithms for Chemical Kinetics

Posted on May 15, 2013May 15, 2013 By admin No Comments on Perspective: Stochastic Algorithms for Chemical Kinetics

In a new paper in the Journal of Chemical Physics, Dan Gillespie, myself and Linda Petzold review theory and algorithms for well-mixed and spatial mesoscopic chemical kinetics. In an associated podcast, available in the journal’s Perspectives collection, we share some of our views on the grand challenges facing us as methods developers as the field…

Read More “Perspective: Stochastic Algorithms for Chemical Kinetics” »

News, Stochastic Chemical Kinetics

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 areĀ  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

Multiscale and hybrid algorithms for stochastic chemical kinetics

Posted on April 18, 2012January 15, 2013 By admin No Comments on Multiscale and hybrid algorithms for stochastic chemical kinetics
Multiscale and hybrid algorithms for stochastic chemical kinetics

Many biochemical network models display scale separation with respect to reaction rates and/or molecular copy numbers. Depending on the type of question under study, different models are best suited to simulate the system. For some parts of the system, a macroscopic model might be appropriate. For other parts, a mesoscopic model may provide additional insight…

Read More “Multiscale and hybrid algorithms for stochastic chemical kinetics” »

Multiscale methods, Reaction Diffusion Master Equation, Stochastic Chemical Kinetics

Posts navigation

Previous 1 … 5 6

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