The Systems Bioinformatics section of the VU University in Amsterdam (NL) is offering a 3-year position for a

PhD student to study How a single cell integrates multiple signals via one of its G-protein coupled receptors

We are looking for a master student with a degree in systems biology, biophysics, or molecular biology who is highly motivated to pursue a PhD study. You should be highly interested in combining state-of-the-art fluorescence microscopy with theoretical methods to understand how single human cells integrate signals via one of its G-protein coupled receptors (GPCRs) and its downstream signalling network. You will be working with FRET-sensors, which monitor the activation of particular G-proteins upon GPCR activation, and fluorescent reporters of downstream signalling activity. Theoretical methods from systems biology and biophysics shall be used for data analysis, mechanistic understanding and predictive modelling.

This project is part of the European Marie Curie ITN project “CaSR Biomedicine”. It combines the expertise of about 10 EU-research labs that aim to understand the role of the calcium sensing receptor, a GPCR, from protein to patient level. This vacancy is at the section Systems Bioinformatics (www.teusinklab.nl, VU University, Amsterdam, The Netherlands) and the Molecular Cytology lab (www.molecularcytology.nl, University of Amsterdam, The Netherlands). Students are only eligible if at the time of the selection by the host university, the candidate has not resided or carried out their main activity (work, studies, etc) in the Netherlands for more than 12 months in the 3 years immediately prior to the starting date.

Please send your CV (including your grade list) and the contact information of two  previous supervisors to Prof Dr Frank J Bruggeman (f.j.bruggeman@vu.nl).

For additional information see:
http://www.meduniwien.ac.at/hp/ipa/forschung/forschungsgruppen/kallay-enikoe-tumour-pathology/projects/recruitment/

Modelling standards and systems biology, you hear a lot of talk about both these topics. But what would it mean if modellers and software engineers actually started using them. In the latest special issue of ERCIM news dealing with “Big Data” Brett and Bas take a look at an idealized day in the life of a computational systems biologist.

A new book on Systems Medicine has recently been published and includes a contribution on Modeling and Simulation Tools: From Systems Biology to Systems Medicine co-authored by ex-VU colleagues Martijn Mone, Maciej Swat and Brett Olivier.

We explore how software and standards need to evolve when considering Systems Medicine as compared to Systems Biology and Systems Pharmacology, PubMed: PMID:26677194.

Dan Fraenkel and Jens Nielsen recently undertook an in-depth review and extended analysis of our Science paper (van Heerden et al., 2014), and we are excited to see that their story has been published!

Fraenkel and Nielsen, 2016. Trehalose-6-phosphate synthase and stabilization of yeast glycolysis

Constraint-based modelling is a popular methodology used in systems biology whose stock in trade is the genome-scale model. However an ongoing problem in this field is that no formal standard exists for encoding such models. Brett Olivier together with Frank Bergmann have led the development of an extension to the Systems Biology Markup Language (SBML), a widely used format for encoding and exchanging mathematical models, that for the first time allows these models to be encoded and annotated in a standard way.

Version 1 of this extension, the SBML Level 3 Flux Balance Constraints (FBC) package has now been published.
BG Olivier, FT Bergmann, (2015) The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints, Journal of integrative bioinformatics 12 (2), 269

As part of the BioSB Research School, which brings together bioinformaticians and systems biologists, we organised an introductory systems-biology course. In this course, we focussed on the basics of mathematical modelling of molecular circuits and the emergent properties of those circuits, such as their (in)stability, robustness and (in)sensitivity properties. We will organise a similar course next year; so keep an eye on the BioSB website to stay informed, or register for their mailing list.

Dr. Sam Seaver is bioinformatician at Argonne National Laboratory known from e.g. modelSEED and works on (automation of) metabolic reconstructions. He discussed with lab members and presented a seminar. Sam was on a tour through Europe  and we were privileged enough to be on his tour list!