We are right in the middle of the 5th year of SEMS funding, meaning that the project will come to an end soon – we’re closing down on the 28th of February, 2017.

However – all our code is (or will be) available openly on github, bitbucket… And we are looking forward to what the future will bring :-)

We provide all code on github. The outcomes of the meetings, a discussion on the suitability of standards for whole cell modells, and our experiences with organising hands-on educational events are described in our new paper entitled: “Toward community standards and software for whole-cell modeling” in the journal IEEE Transactions on Biomedical Engineering.

Paper abstract:
“Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells.
Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in SBML.
Results: Our analysis revealed several challenges to representing WC models using the current standards.
Conclusion: We, therefore, propose several new WC modeling standards, software, and databases.
Significance: We anticipate that these new standards and software will enable more comprehensive models.”

Open access paper

SEMS memeber Vasundra Touré is currently responsible for the project. Symbol of the month for January is the SBGN compartment.

We also encouraged people to try out our own model management solutions, particularly BiVeS, MaSyMoS, M2CAT and CAT.

The slides for the introductory talk are available on slideshare.

The hands-on session focuses on the SEEK database management system hosted on the fairdomhub.

Fun.

During the COMBINE tutorial on modeling and simulation tools and standards, we’ll be giving a talk about the COMBINE Archive and the COMBINE Archive Web Tools. The talk will be followed by a hands-on session in the afternoon.

Date: 25th November, 2015.

We’ll also show four posters at the main conference:

1. Ron Henkel et al: Common Pattern in Computational Model Reaction Networks (P107)
2. Martin Scharm et al: Diving into open Model Repositories: Investigating the Evolution of Computational Models (P128)
3. Dagmar Waltemath and Olaf Wolkenhauer: Issues with and achievements of the reproducibility movement in systems biology (P175)
4. Vasundra Touré et al: STON, SBGN to Neo4j: Representation of Systems Biology pathways as graph-oriented models (P176)

Vasundra is currently on a research stay at Monash University where she works with Prof. Falk Schreiber and Dr. Tobias Czauderna.

SEMS annotation retreat

Besides all the social and group building activities, we evaluate and discuss possibilities to provide metadata for computational models and COMBINE Archives. The idea is to harmonise current approaches to metadata annotation in SBML, CellML, COMBINE Archive, etc.

We will be able to fully fund about 10 students from the original team. It will be good to see people again and have another two days of modeling, hacking, discussing and fun :-)

The workshop brings together scientists who wish to learn about open science, open data, and how to make their research results reproducible.

In the mornings, invited key note speakers will talk about programs and initiatives such as F1000, OpenAire, or the COMBINE initiative. The afternoons are reserved for guided hands-on sessions. So please do not forget to bring your data and models!

Registration to the workshop is free. Please register until 1st of July to be part of three days of discussion and exploration.