by : Annika Jacobsen Events, News

BioSB PhD retreat 2015

The RSG retreat 2015 preceding the Netherlands Bioinformatics and Systems Biology (BioSB) Conference 2015 was hosted in Lunteren, Netherlands, on 19 May, gathering 24 (PhD-) students and young professionals in bioinformatics and systems biology from all over the Netherlands.

Program overview
Sjoerd Huisman – Welcome and introduction to YoungCB
Flash presentations
Niclas Nordholt – “The growth-rate dependence of a gene regulatory function in Bacillus subtilis”
Tim Offermans – “The Structural Role of a-bulges in G Protein-Coupled Receptors”
Tom van den Bergh – “Protein superfamily data integration”
Sarah Stolle – “Metabolic network robustness during ageing”
Mohammed El-Kebir – “Unmixing a tumor”
Lieneke Kusters – “Privacy-preserving model for DNA sequences”
Celia van Gelder – BioSB Update
Bas E. Dutilh – “Metagenomics: a motivating career move”
Flash presentations
Damarius Fleming – “Genomic diversity and markers of tolerance in livestock”
Anne-Claire Martines – “The effects of high-fat diet and fasting on MCAD KO mice”
Jochem Evers – “Automated improvement of ZnCys4 complexes”
Terry Hwa – “Driven by function: a personal journey from physics to biology”
Dinner and social activities

Sjoerd Huisman gave the welcome speech with a short introduction on the activities organised by RSG Netherlands. This also included presenting our new local name “Young Computational Biologists (YoungCB) Netherlands” and welcoming all young bioinformaticians and systems biologist to join our community.

Celia van Gelder gave an update on the Netherlands Bioinformatics and Systems Biology (BioSB) Research School and their upcoming courses. Also she talked about ECCB16, which will be held in Den Haag, Netherlands, encouraging us to take part in the ESCS16.

Bas E. Dutilh, Assistant Professor at Theoretical Biology and Bioinformatics, Utrecht University, gave the first career talk “Metagenomics: a motivating career move”.

Again this year, we gave the participants the opportunity to do a 5 min flash presentation of their research.  9 of the participants took this opportunity and we got very good feedback on this. It is an easy, fast way to introduce to your peers what you are working on and also led to scientific discussions later on. It was very clear to see the diversity in the field, which of course reflects the recent merging of the bioinformatics and systems biology communities in the Netherlands.

Terry Hwa, PI at Laboratory for Quantitative Microbiology, U.C. San Diego, gave the second career talk “Driven by function: a personal journey from physics to biology”.

The evening program consisted of a dinner at the local pizza restaurant, social activities and drinks, where we continued with discussions and networking.

During the BioSB conference the RSG Netherlands board was in charge of the poster committee. In addition RSG Netherlands also held a BOF session to encourage even more people to join the network of young bioinformaticians and systems biologists. This was a very successful meeting were we got one new board member with a systems biology background.

by : Julian de Ruiter Courses

BioSB Course: Quantitative and Predictive Modelling

On June 22-26 2015, BioSB organises the first edition of the course Quantitative and Predictive Modelling. The main theme of the Quantitative and Predictive Modelling course is how to describe the dynamic behaviour of biological systems and integrate experimental data. Concepts of modelling are introduced via a great variety of examples taken from diverse practices. The emphasis is on providing an overview of modelling approaches rather than an in-depth treatment of a few techniques. After classification of biological systems (metabolic, regulatory, signalling, population, multi-scale, statistical models), the concepts of top-down versus bottom-up modelling will be introduced, with emphasis on bottom-up approaches. Parameter estimation is an important modelling tool and will receive adequate attention. In the course Matlab will be used as software tool for the practicals. Participants not familiar with Matlab will get a short introduction.

This course is primarily targeted at academic researchers such as PhD students and Postdocs in Life Sciences, Bioinformatics, Systems Biology or Biomedical Engineering. Participants from private sector are also welcome. Participants are expected to have some experience in modelling with differential equations or to have followed Introductory courses from the BiosB Course Portfolio, e.g. E-course modelling , E-course calculus, Discovering Systems Biology Principles or Applications for Systems Biology and Bioinformatics in the Medical Sciences. The course will start with a session to refresh the basic elements of modelling with differential equations.

This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology.

More information about BioSB can be found at www.biosb.nl.

Date 22-26 June, 2015
Location Wageningen
Course Coordinators Jaap Molenaar (WUR), Natal van Riel (TUE)
Website Website link
Registration Website link

 

by : Julian de Ruiter Courses

BioSB Course: Advanced de novo assembly and resolving complex genomic regions

This course is targeted at PhD students and Postdocs in Life Sciences or Bioinformatics with basic knowledge of next-generation sequencing (NGS) technology and data analysis. This course covers topics on what every biologist should know about de novo assembly and study design, overview of available technologies and sampling strategies, methodologies and framework for de novo assembly (haploid and polyploid genomes), gap closure, quality assessment and functional annotation. In addition, we will showcase recent achievements, novel discoveries and current limitations in resolving complex genomes. The practical sessions are designed in such a way to promote lively discussions on how to design your study, the best practices, dos and don’ts, and provide you with an outlook on how to move from sequencing data to high-quality assembly and meaningful biological interpretation. After following this course, participants will gain insights on how to design a genome assembly study and will have an overview of challenges and various techniques to choose the most fitting strategy in order to produce a high-quality genome assembly.

This course is primarily targeted at academic researchers such as PhD students and Postdocs in Life Sciences or Bioinformatics with experience in genomics or NGS data analysis. However, participants from private sector are also welcome. Participants are expected to have experience in NGS data analysis or to have followed the NGS data analysis course.

This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology.

More information about BioSB can be found at www.biosb.nl.

Date 1-3 June, 2015
Location Leiden
Course Coordinators Yahya Anvar (LUMC), Johan den Dunnen (LUMC)
Website Website link
Registration Website link

 

by : Julian de Ruiter Conferences

BioSB 2015

BioSB 2015

Bioinformatics & Systems Biology conference

The BioSB 2015 conference combines the annual Netherlands Bioinformatics Conference (NBIC) and the annual Systems Biology Symposium (SB@NL). Because of the great success of the NBIC conference format in the past, this years’ BioSB conference will be organised in the familiar style: a 2-day conference at Congrescentrum De Werelt in Lunteren.

Conference details

Date: May 20 – 21, 2015 (May 19: Satellite meetings/workshops)
Venue: Congrescentrum De Werelt, Lunteren
Website: http://www.aanmelder.nl/biosb2015
Registration page: http://www.aanmelder.nl/biosb2015/subscribe

Science & applications

BioSB 2015 discusses the latest developments in bioinformatics, systems and computational biology and interrelated disciplines, and their wide-ranging applications in life sciences & health, agriculture, food & nutrition and industrial biotechnology. BioSB 2015 offers a cross-disciplinary scientific program of (poster) presentations, application demonstrations, satellite meetings and workshops.

Registration

You can register for the BioSB 2015 conference via the registration page. Here you will also find information about the registration fees and categories, hotel rooms and the payment and cancellation policy.
Registration deadline: May 11, 2015

BioSB Young Investigator Award 2015

We received a number of nominations for the BioSB Young Investigator Award 2015. The Young Investigator Award commission will select a winner who will give his/her honorary lecture on May 20, 17.30 h after receiving the award.

by : Julian de Ruiter Events, News

NKI Company Visit

On the 21st of April, we visited the NKI (Netherlands Cancer Institute) in Amsterdam to learn more about the institute and its research. The organized program (shown below), promised a nice overview of the different aspects of cancer research performed at the institute by giving an introduction to fundamental, translational and clinical research topics. All with (where possible) an added focus on computational aspects of course, as computational work is becoming more and more important with the growing datasets in cancer research.

Program overview
Julian de Ruiter – Introduction and history of the NKI
Magali Michaut: Computational Cancer Biology
Lab tour + hands on
Jos Jonkers: Identification of cancer drivers and therapy resistance mechanisms in mouse models of human breast cancer
Huib Huurderman: ‘Basics of radiology’ – talk + tour
Wilbert Zwart: Personalized prostate and breast cancer: where biologists and bioinformaticians meet
Closing borrel

The day was kicked off by Julian de Ruiter with a short introduction and a brief historical overview of the NKI, which reached all the way back to 1913 with the founding of the institute. Magali Michaut then proceeded with an overview of the research being performed in the Computational Cancer Biology group, which is run by Lodewyk Wessels and is the only purely computational group at the NKI. After some heated questioning, the group then proceeded downstairs for a guided tour of one of the labs, which also offered the opportunity for some hands-on work for those who were interested.

After a short break, Jos Jonkers gave a talk about his work on identifying cancer drivers and therapy resistance mechanisms in mouse models of human breast cancer. Jos gave a nice overview of the different questions people in his lab are pursuing, and explained why he thinks that his engineered models are a crucial aspect of this research. After Jos, Huib Huurderman gave everyone a short introduction into the different modalities of radiology being used at the NKI to treat and diagnose patients in the clinic. Huib then took us along into the hospital and gave us a tour of the radiology department, where we even got to see a live scan in progress!

Last but not least, Wilbert Zwart gave a talk about his research on personalized prostate and breast cancer. He gave a nice overview of some different ongoing projects in his lab, highlighting the crucial role that his two computational researchers have in these projects. As such, he gave a few striking examples of how computational and wetlab people can work together intimately to gain novel insights into the biology underlying these cancers and how these insights may be applied to provide personalized treatment to cancer patients.

After a long afternoon of talks, the program ended with a well-deserved borrel during which lab members from the different research groups joined for some networking and to answer any remaining questions. Overall, I think we had a very successful company visit, judging from the number of participants and the reactions we received. Definitely something to repeat in the future!

by : Annika Jacobsen Events, News

BioCafé Amsterdam

Young Computational Biologists organised a successful BioCafé on 23 March 2015 in Amsterdam in collaboration with the BioSB research school course “Pattern Recognition”.

During the BioCafé we had a Bio-Pantomime in a relaxed atmosphere with drinks and snacks and networked with (PhD-) students and young researchers in bioinformatics and systems biology.