Bioinformatics in the pub – Sept/2017


Dear all,

Please join us for bioinformatics in the pub, a friendly gathering around food and drinks of PhD students, Post-Docs and young bioinformaticians, Wednesday 20.09.17 7pm at Les Brasseurs.

Registration is non-mandatory but appreciated for booking tables:

Please help us spread the word to other bioinformaticiasn in Lausanne.


On Behalf of the International Society for Computational Biology  Regional Student Group of Switzerland (ISCB-RSG-Switzerland)

Elsa Guillot


Bioinformatics in the pub

iscbrsgswiss_bioinfopubDear all,

The ISCB-RSG is an association supporting students and young researcher in computational biology and bioinformatics. We aim at connecting bioinformaticians from different places around Switzerland.

Please join us a for the first bioinformatics in the pub, a friendly gathering around food and drinks of PhD students, Post-Docs and young bioinformaticians, Thursday 29.06.17 at 7pm at Brasserie du Chateau.

Registration is non-mandatory but appreciated for booking tables:

To be informed about future similar events please join our mailing list by replying to this message or follow us on twitter @rsg_switzerland
Best regards,

On Behalf of the International Society for Computational Biology Regional Student Group of Switzerland.

Elsa Guillot

Company visit at Syngenta

Dear fellow post-docs and PhD students,
The BioScience Network Lausanne and the SV postdoc association are organizing a company visit at Syngenta on the 7th of October (Friday) 2016 in Basel. The aim of this visit is to promote interactions among researchers in industry and PhD students and postdocs from EPFL and UNIL.
In attachment you will find the final schedule for the visit!! 
!! Registration deadline is in 1 week. Do not miss this great opportunity !!
Since the Syngenta company is not well connected with public transportations, a bus will be provide and the cost is 60 CHF per person. The registration is now open and the deadline is the 27th of September 201612:00.   Places are limited to 20 participants,  so register early! The organising committee will select participants based on their CV and a small paragraph about their motivation. The results of the selection will be communicated by September 30th, 2016. 
To register, please send an email to with your CV and your motivation paragraph
For the payment:
  • Transfer 60 CHF to the official BSNL bank account:
    IBAN: CH50 0900 0000 8946 8243 2
    PostFinance AG BERN
    BSNL- BioScience Network Lausanne
    P.a. EPFL AA DAF
    Station 1
    CH-1015 Lausanne
    Make sure to include the following line as the reason for payment: “Syngenta visit”
  • Send an email to with the proof of payment.
    Include “YourName Syngenta visit” in the subject line
Screen Shot 2016-09-23 at 13.33.10.png
! Registration opens now and closes on the 27th of September 2016 at noon!
In case you have any questions, don’t hesitate to contact us.
Martina, on behalf of the BioScience Network Lausanne (BSNL) and the SV postdoc association
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MedLem Meeting “INFLAMMATION in the era of BIG DATA” the 17th of November 2016 in Geneva-Centre Louis Jeantet.

The Faculty of Biology and Medicine  of LAUSANNE 

and the Faculty of Medicine of Geneva

 are very pleased to present the 1stMedLem Meeting 

that will held on Thursday, the 17th of November 2016

 in Geneva-Centre Louis Jeantet. 

The 2016 theme is

« INFLAMMATION in the era of BIG DATA »

Invited Speakers :

  • Prof. Francine Behar-Cohen (Hôpital opthtalmique Jules-Gonin)
  • Dr. Lydie Lane (Swiss Institute of Bioinformatics)
  • Dr. Luc Stoppini (Hepia//HES-SO and Swiss Centre for Applied Human Toxicology)

Deadline Abstract: 30.09.2016

(More info at

The MedLem meeting will be a fantastic opportunity to discover the breadth of research around Lake Geneva            

 We encourage you to participate!

Scientific & organizing committee:

  • Olivier Gaide (Department of Dermatology and Venereology, Lausanne University Hospital) contact
  • Maxime Pellegrin (Division of Angiology, Lausanne University Hospital) contact
  • Aurélien Thomas (Unit of Toxicology, CURML, Lausanne University Hospital, Geneva University Hospital) contact
  • Natacha Turck (Department of Human Protein Sciences, University Medical Center-Geneva) contact



Science Hackathon at UniverCité

Friday 25th, Saturday 26th and Sunday 27th of November, Hackuarium with Inartis Foundation and THE Port association organise a Science Hackathon at UniverCité!
So if you have a science project, a problem or some skills you want to share with a team of 25-30 other bright minds, sign-up HERE before September 30th!
It will be 3 days of intense brainstorming, prototyping and problem solving.
Everyone welcome! And please, spread the word!

IBM Research – María Rodríguez Martínez – 7th of September


Dear all,

The ISCB regional student group for Computational Biology in Switzerland is very pleased to host the talk “Systems approaches to unravel molecular mechanisms of cancer ” by

María Rodríguez Martínez, Technical Leader of Systems Biology at IBM, Zurich Research Lab, on Wednesday the 7th of September 2016 at 18:00 at UZH, Irchel campus, Y03-G91.

Abstract: Despite their great promise, high-throughput technologies in cancer research have often failed to translate into major therapeutic advances in the clinic. One challenge lies in the difficulty of transforming next generation molecular data into mathematical disease models that can make actionable clinical statements. A second challenge arises from the high level of intra-tumor heterogeneity exhibited by most human cancers. To address these challenges new methodologies that can reconstruct the map of genomic alterations and understand its influence on phenotype need to be developed. In this talk I will give an overview of current projects at the Systems Biology group in IBM Research, Zurich, that illustrate systems medicine approaches to understand cancer complexity and that can bridge the chasm between basic research and clinical applications.

The talk will be followed by an apéro, during which participants will have the opportunity to continue discussions with María Rodríguez Martínez.

We are looking forward to seeing you at the event!

The RSG Switzerland Team


Novartis – Industry Talk for ISCB-RSG Zürich


There will be a talk this Thursday the 21st of April for those in the Computational Biology, Systems Biology, and Bioinformatics related fields to discuss opportunities of doing related work in industry.

Time: 17:30

Location: University of Zurich, Irchel Campus room Y03-G91

Additional details: please see attached flyer.

The invited speaker is Dr. Audrey Kauffmann PhD, a bioinformatics group leader at Novartis.

Audrey along with one of her colleagues, Gráinne Kerr, will be present following the talk for an apéro to have discussionwith attendees regarding their career path.


Medical Data Access event report

BSNL and the RSG-Switzerland co-organized in the biohacker space Hackuarium an open discussion about the risks, challenges and opportunities of medical data sharing.
Approximately 50 people attended the round table to discuss about different aspects related to Medical data access. And we were honoured to host as invited speakers:
– Jacques Beckman (Head of Clinical Bioinformatics, SIB),
– Christine Currat (Executive director of the Swiss biobanking platform),
– Manolis Dermitzakis (Professor of Genetics at the Department of Genetic Medicine, UNIGE) and
– Jeanne-Pascale Simon (Lawyer at the Unit of Legal Affairs, CHUV).
At the beginning, Jacques and Manolis told us about their view of this complex question, and exposed some of the current limitations and the link with their own research. They envisioned the situation that we will face in the future as patients, scientist or citizen.
Then, Jeanne-Pascale and Christine described the current status of the law  and how hospitals and more…

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ilastik workshop

20th of Novembre 2015 at EPFL

What is ilastik?

“ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode. Using it requires no experience in image processing.”

Workshop outline

The workshop will begin with an introduction and a walk through of the different workflows that ilastik offers, and everyone is welcome to attend.
For the following “show and tell” as well as the “hands-on” sessions, we kindly ask you to register for one of the 20 available seats. This group size should allow all participants to receive the required amount of support.

Also, we invite the participants to bring their own data during the “hands-on” session,  so they can explore solving their own problem using ilastik, while being supported by the ilastik team.

The workshop will be given by Fred Hamprecht, Anna Kreshuk, Janez Ales, and Carsten Haubold.

Workshop schedule

09:00 – 10:40  –  SV 1717A       

Introduction to Ilastik and its workflows  – Open to everyone

11:00 – 12:00  –  AAC 132  AAC 106

Show and Tell – Participants only

12:00 – 13:00  

Lunch break

13:00 – 15:00  –  AAC 132  AAC 106

Hands-On session – Participants only


The registration page can be found here.

What should I bring?

  • A laptop
  • A mouse with a mouse wheel
  • My data


We would like to thank our sponsors, the Life Science Faculty and the Swiss Institute of Bioinformatics, without which this workshop would not have been possible.


epfl                   sib_logo_trans_background_high




Medical data access: challenges, opportunities and risks

The Bioscience Network Lausanne (BSNL) and the regional section group of the International Society of Computational Biology (ISCB RSG Switzerland) are glad to announce the round table about medical data access.

Indeed, new practices and technologies such as digital medical records and high-throughput sequencing open new ways for medical doctors and scientists to investigate human biology and diseases. However, this new model raises many fundamental questions. We would like to discuss them in our round table to make clear what are the opportunities that exist now and how can the medical data be handled in a way that the rights of patients are preserved.

During the round table we will go through the following questions:
– What can personalized medicine offer?
– What ethics problematic are at stake with personal medical data and how can the law protect patients?
– What is the current state of the infrastructure for these data and the existing tools for researchers?
– How to manage these data and ensure confidentiality, but to allow access to researchers?
– How much investment is needed today to support this data tsunami?
– What is the need in medical data literacy for its potential users?
– How many trained people do we need in the area?
– Can citizens take part in this revolution by doing citizen science/biohacking/DIYbio?

We are honored to discuss these topics with four important actors in the field that confirmed their participation:

Jacques Beckmann (Head of Clinical Bioinformatics, SIB)
Christine Currat (Executive director of the Swiss biobanking platform)
Manolis Dermitzakis (Professor of Genetics at the Department of Genetic Medicine, UNIGE)
Jeanne-Pascale Simon (Lawyer at the Unit of Legal Affairs, CHUV)

Come and join us in the discussion next Thursday, 5th November at 19:00, at UniverCité (Chemin du Closel 5, Renens)

Looking forward to meeting you there,

Leonor Rib & Jonathan Sobel