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try.stochss.org: Try StochSS as a Service

Posted on June 22, 2016June 22, 2016 By admin No Comments on try.stochss.org: Try StochSS as a Service

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…

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News, Software, Stochastic Chemical Kinetics, StochSS

Fredrik Wrede joins the group

Posted on May 13, 2016May 13, 2016 By admin No Comments on Fredrik Wrede joins the group

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…

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Applied Cloud Computing, Data-Intensive Computing, News, StochSS

Göran Gustafsson prize

Posted on March 14, 2016 By admin No Comments on Göran Gustafsson prize

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…

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Applied Cloud Computing, Data Science, Data-Intensive Computing, News

At Isaac Newton Institute

Posted on February 15, 2016February 15, 2016 By admin No Comments on At Isaac Newton Institute

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…

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Isaac Newton Institute, Multiscale methods, Stochastic Chemical Kinetics

Open Posititions: up to two PhD students

Posted on January 19, 2016March 14, 2016 By admin No Comments on Open Posititions: up to two PhD students

(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…

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

VR Young Researcher Grant

Posted on November 15, 2015November 18, 2015 By admin No Comments on VR Young Researcher Grant

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.

News

StochSS 1.6 is now officially released!

Posted on July 6, 2015November 6, 2015 By admin No Comments on StochSS 1.6 is now officially released!

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…

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News, PyURDME, Software, Stochastic Chemical Kinetics, StochSS

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…

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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

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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

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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

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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!

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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

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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.

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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/

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