Non classé

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…

View original post 161 more words

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

D-BSSE in Basel meets Industry


We are very pleased to host a talk by Dr. Audrey Kauffmann, Bioinformatics group leader in oncology at Novartis.
She will be holding a talk on her experience, her work at Novartis Institutes for BioMedical Research and the field of bioinformatics/computational biology in a big pharma company. Her talk will be followed by a networking apéro, during which participants will have the opportunity to speak to her and Dr. Grainne Kerr, Bioinformatics Analyst and member of Audrey Kauffmann’s team.

More information:


1000 Beer Genomes Project on Kickstarter

Dear brewers and beer lovers,
If you want to know exactly what your beer contains, if you want to understand the diversity of frosty, foamy styles across the globe and decode the secrets hidden within, then the project BeerDeCoded will excite you. It consists of sequencing the genome of 1000 varieties of beer and comparing their biochemical parameters. The result will be made into a poster as a reward to all of our supporters.
This project brings together a multidisciplinary team of six researchers who need your help to complete the goal. The first financing campaign was launched on Kickstarter and ends on 27 June.
If you are interested, please share the following link with your social network and consider contributing your support.
Check out if your favorite beer is included in the study. The link to share is:
You may also join our analysis workshops in our laboratory at the Hackuarium (Lausanne, Switzerland: starting this summer.
Our results will be free for all to see. We believe in Open Access science and we will therefore release the results online and through a free App.


The team at BeerDeCoded
All inquires should be sent to Gianpaolo Rando (

Thanks to beer- and genome-lovers like you, in only 4 days we were 70% funded.
Thanks to the generous breweries for sending their beer! Again, the link here:

Life Science Career Day 2015: Reminder

Dear Student, PhD candidate, Postdoc or Young Scientist in Life Science,
Are you wondering how to build your career after a degree in life science or a postdoctoral experience? The Life Science Career Day aims to make you aware of numerous career options!
It is also one day full of career networking opportunities:
• 60 delegates of companies, associations and institutions
• 20 experts/trainers in career counseling and CV check
• More than 360 participants registered!
• Some places are still available for you!
Date & Venue: Saturday, May 9th 2015, University of Lausanne, Amphipôle Building, UNIL-Sorge, 1015 Dorigny
On-line Registration: Registration is OPEN & FREE (Deadline: April 9th 2015)
• Discover careers & the everyday life of professionals (3 symposia)
• Be part of a large interactive area
• Benefit of an individual CV check and career counseling services
• Boost your career and learn in several workshops (start-up, elevator pitch, competences and networking)
• Interact with scientific journalists
Our Special Guests
Benoît Dubuis
Director of the Campus Biotech Foundation, Geneva and President of the BioAlps Association
Luigi Marra
Journalist, Producer, SPECIMEN (Reports on Human Behavior), Radio Télévision Suisse, RTS
Program: Click here!
We are looking forward to meeting you there,
The Faculty of Biology and Medicine (UNIL) & BioScience Network Lausanne