by : Kyoko Watanabe Courses, News

BioSB HotTopics: ONT Nanopore sequencing

BioSB HotTopics: ONT Nanopore sequencing

April 20, 2017, TU Delft

Nanopore sequencing has been revolutionizing the sequencing arena for the last few years. The last decade, sequencing went from highly-specialized to a commodity product that can be readily purchased from a specialty provider. ONT has taken this again a step further and is now enabling anyone to get into ‘do-it-yourself’ sequencing. Sequencing now requires no capital investment, very little in lab setup and anybody with a steady hand can start to generate data. While the technology has tremendous potential, there are still a few teething problems and sharing expert knowledge is critical to realize its full potential. Luckily, there is a comparatively large expert-user community within the Netherlands.

The goal of this meeting is to bring us together and strengthen information sharing and collaboration within the Netherlands and beyond.

Read more and register!

by : Kyoko Watanabe News

PhD retreat 2017 report

 

We had very variable days in Lunteren for PhD retreat and BioSB 2017.  YoungCB organised several events (listed below) during those days. We thank your participations and hope you all had a great time.

PhD retreat (3rd April 13:00-18:00)
This year, 32 PhD and young researches gathered from all over the Netherlands. Special thanks for Dr. Amrapali Zaveri and Dr. Erik Schultes for their keynote talks.

Pub Quiz (4th April 21:00-23:00)
We organised Pub Quiz as a social event during BioSB 2017. Congratulations for the team “The Outlijers”!! We hope you all enjoyed and please join the next BioCafe, too!!

Interactive session for master students (5th April 13:15-14:30)
Around 40 master students joined our interactive session and we discussed doing PhD in general as well as academia vs industry. We thank you all for your active participations. We are very pleased that a lot of Master students have interest in activities of YoungCB!!

by : Kyoko Watanabe Conferences, News

byteMAL 2017

byteMAL is organising an anual conference will be held in Maastricht on 23rd June, 2017!

Prof. Dr. Kevin Burrage, Prof. Dr. Michel Dumontier and Prof. Dr. Piet van der Graaf will give keynote presentations. Moreover, Prof. Dr. Martin Paul, president of Maastricht University, will give an official closing speech. Please visit the program website for information about the program details.

Deadline for registration and poster abstract submission: 1st June, 2017.
Detailed information concerning the poster submission can be found at Poster Guidelines.
Upon evaluation, six abstracts will be additionally selected for a flash talk of 7 minutes at the day of the conference. Notification of acceptance will be sent by 14th June, 2017.

 

bytemal2017

by : Kyoko Watanabe Events, News

Soft Skill Event 2017

We are pleased to announce Soft Skills Event 2017. Two speakers will train us to improve networking and presentation skills in science. Yougn researchers and (BSc, Msc and PhD) students are welcome to join!!

Date
22nd March 2017, 13:00 – 16:00

Place
Raadszaal (STR 1.301), Stratenum, Universiteitsweg 100, Utrecht

Registration
Please register from here.

Program

13:00-14:00 Magali Michaut (Senior scientist at the Netherland Cancer Institute)
Networking and collaboration in science: an interactive session
14:00-16:00 Susanne Schilderman (Trainer / city council member)
Selling your science: public speaking and presentation training
16:00- Drinks and networking

Sponsor
International Society for Computational Biology

softskill

by : Kyoko Watanabe Courses, News

BioSB course Quantitative and Predictive Modeling

Date

June 26 – 30 2017, in Wageningen,
Registration is not open!! enrollment form 

Venue

Wageningen UR, FORUM building (room C0211, practicals in room PC0629)
Route & travel information

Tutors

Jaap Molenaar (WUR), Natal van Riel (TUE), Hans Stigter (WUR), Aalt-Jan van Dijk (WUR), Fianne Sips (TUE)

Study load

3 ECTS points

Description

In this Quantitative and Predictive Modelling course the participants learn how to describe the dynamic behaviour of biological systems and to integrate experimental data. Concepts of modelling are introduced via a great variety of examples taken from diverse practices. The emphasis is on providing an introduction into modelling approaches rather than an in-depth treatment of a few techniques. So, the course provides a broad overview of Modelling in the Life Sciences and is as such useful for a broad audience. The course is a mixture of theory sessions and computer practicals. During the practicals Matlab is used. Participants not acquainted with Matlab will get an introduction. The course has to be completed with assignments in the form of practical exercises as homework afterwards.

The structure of the course is as follows:

  • Monday: refresh of Math tools (Jaap Molenaar), introduction Matlab (Hans Stigter), overview of modelling techniques (Natal van Riel)
  • Tuesday: parameter estimation (Hans Stigter), case study flowering time (Aalt-Jan van Dijk)
  • Wednesday: network inference (Jaap Molenaar, Aalt-Jan van Dijk), case study nitrate control (Hans Stigter)
  • Thursday: uncertainty analysis, sensitivity analysis, case study metabolism (Natal van Riel, Fianne Sips)
  • Friday: case study glucose and fatty acids (Fianne Sips), chemotaxis and signaling (Jaap Molenaar), assignment preparation

Programme

Location: room C0211 (theory) and room PC6.29 (practical sessions) in the Forum building

Daily programme schedule:

  • 09:00 – 12:30    Session A: theory
  • 13:30 – 15:30    Session B: practical session
  • 16:00 – 17:30    Session C: theory

Target Audience

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 the Introductory courses E-course modelling and E-course calculus, and 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.

Learning Objectives

The students will be provided with a theoretical basis, methods and computational hands-on experience on differential equation modelling, parameter estimation and uncertainty analysis.

In the course the students will learn:

  • How to set-up a dynamic model to represent biological networks using different interaction mechanisms
  • To implement, simulate and analyse dynamic network models in different software tools
  • To understand the common ground and the differences for applications in metabolic, regulatory, signalling, population and multi-scale biological processes
  • To integrate experimental data in modelling, estimate model parameters and assess the accuracy of parameter estimates and model predictions.

More information

Below please find a list with hotels in Wageningen. For more information about logistics you can contact Ms Dinie Verbeek (Wageningen UR, Biometris), tel. +31 (0)317 480798, email: dinie.verbeek@wur.nl

Hotel list:

Hof van Wageningen – Hotel & Congrescentrum
Lawickse Allee 9
6701 AN Wageningen
Tel: +31 (0) 317 490 133 | Fax: +31 (0) 317 426 243 | Email: info@hofvanwageningen.nl

Rijn IJssel Vakschool Wageningen
Hotel de Nieuwe Wereld
Marijkeweg 5
6709 PE Wageningen
Tel. +31 (0) 26-3129604 Afdeling reserveringen

Hotel Nol in ‘t Bosch
Hartenseweg 60
6704 PA Wageningen
Tel: +31 (0)317 319101 | Fax: +31 (0)317 313611 | Email: info@nolintbosch.nl

ReeHorst
Bennekomseweg 24
6717 LM EDE (Gld)
Telefoon +31 (0)318-750300

B&B in Wageningen

by : Kyoko Watanabe Career, News

Employability Outside Academia in Utrecht

The majority of PhD’s and Postdocs will pursuit a career outside academia, but making this transition can be quite a challenge. Why? Because the way PhD’s present themselves often do not correspond with what non-academic employers expect. Based on a study on this discrepancy PCDI developed the course Employability outside Academia to bridge this gap and to increase your attractiveness.

However, to make the transition,you need to find out what you want, what possibilities outside academia suit you, and what is necessary to get there. The course will help you making the transition!

The course consists of three full-day session.

Day 1 –  13 March 2017
Day 2 –  10 April 2017
Day 3 –  22 May 2017  

Attendance of all three days are strongly recommended.

Please visit the website for detail and registration from http://www.pcdi.nl/events/employability-outside-academia

by : Kyoko Watanabe Courses, News

BioSB Course Programming in Matlab

Date

13 March 2017

Location

Wageningen

Course coordinators

Hans Stigter (WUR), Celia van Gelder (BioSB, celia.van.gelder@biosb.nl)

Goal

The main goal of this course is to get acquainted with Matlab software for use within Systems Biology. After this introductory course you will have gained the basic knowledge to pursue further use via self-study of Matlab in order to apply more advanced programming techniques within Matlab in your own research. In summary, the sub-goals are:

  1. To learn the philosophy behind Matlab and its syntax
  2. To program simple Systems Biology models in Matlab (in ordinary differential equation format) and to solve these differential equations with Matlab

Course description

This is a one-day introduction to the possibilities of Matlab as a programming environment for simulation and analysis of biological models. We will start with a simple introduction of the basics of Matlab (matrices, vectors, manipulation of matrices and presentation of data). Having obtained some basic programming knowledge (writing of simple scripts and functions in Matlab), we will move on to more advanced topics. These include programming and solving ordinary differential equation models (ODEs) and the concept of “vectorized thinking” while writing Matlab-code. Finally, calibration of parameters in ODE type of models using measured data will be discussed and examples will be given. The course also includes the basics of presenting your results (graphing) in various types of plots that can easily be drawn in Matlab. Participants will, of course, get hands-on experience with Matlab and write code themselves in a practical.

Target audience

Primarily researchers from academia, but participants from the private sector are also welcome. The course focusses on the use of Matlab for building dynamic Systems Biology Models in terms of ordinary differential equations.

Course fees

The course fees for this course are:

  • Free of charge for PhD students (BioSB member *)
  • € 100 for PhD students
  • € 150 for researchers at universities or non-profit research institutes
  • €   75 for researchers at universities or non-profit research institutes (BioSB member *)
  • € 250 for researchers working in for-profit organisations (industry)

Programme

09:45 Coffee/Tea
10:00 Welcome
10:05 Introduction Matlab Basics (functions, variables, matrices, etc)
10:45 Advanced Programming (vectorised thinking, solving dynamic ordinary differential equation models in Matlab, parameter estimation for ODE-models)
12:00 Afternoon: Solving basic and advanced problems in Matlab – hands-on experience on a PC. Exercises will be provided, but you can also bring your own problems that you have encountered in your own research.
12:30 Lunch
15:00 Coffee/tea
16:30 End

 

Registration

You can now register for the course via the Enrollment form.

 

by : Kyoko Watanabe Events, News

BioSB PhD retreat 2017

DSC_0264YoungCB (ISCB Regional Student Group Netherlands) is pleased to invite you to the BioSB PhD retreat 2017 in the afternoon 3 April. The retreat will be held in Lunteren at the Congrescentrum De Werelt, preceding the BioSB conference. The retreat is sponsored by the BioSB research school. We encourage all (PhD-) students and young researchers in the fields of computational biology, bioinformatics, systems biology and related fields to attend this annual retreat to discuss your research and build a network with fellow young peers in the Netherlands.

The retreat provides you with the opportunity to present your research to fellow students and young professionals. Keynotes will be given by Dr. Amrapali Zaveri, Post-doc at Stanford University and Dr. Erik SchulDSC_0268tes, FAIR Data Scientific Project Leader at DTL. A workshop will be given by Dr. Amrapali Zaveri about how to use SPARQL Endpoints to query various biological data resources. For this workshop, you are advised to bring your laptop in order to try out the hands-on exercises. In the evening there will be a dinner in the centre of Lunteren, followed by a fun social event at the conference centre bar. The evening program provides you the opportunity to network with fellow (PhD-) students and young researchers.

Program

13:00-13:15 Registration
13:15-13:30 Welcome and introduction
13:30-14:00 Keynote: Dr. Amrapali Zaveri
“Introduction to semantic web”
14:00-14:30 PhD flash talk
TBA
14:30-14:45 – Coffee break –
14:45-16:45 Workshop byDr. Amrapali Zaveri
“How to use SPARQL Endpoints to query various biological data resources”
16:45-17:00 – Coffee break –
17:00-18:00 Keynote: Dr. Erik Schultes
“FAIR Data for scientists”
18:00-19:00 Break + walk to Lunteren center
19:00-20:30 Dinner in Lunteren center
21:00- Social activity

Submit your abstract
Interested in giving a flash presentation? Submit your abstract to rsg-netherlands@iscbsc.org.
Abstract should be 250-300 words.
Deadline to submit your abstract: 20 March 2016

Registration
Sign up for the RSG retreat via the BioSB conference registration form.

Fee:
50 Euro (without hotel room)
TBA Euro (with hotel room)

NB: You can also book a hotel room via the registration form. If you also register for the conference, please note that if you book a ‘private room’ for the PhD retreat but a ‘shared room’ for the conference, you may have to move to another room at the first day of the conference or will have to share the room the night after the PhD retreat.

Retreat coordinator: Mirella Kalafati (kalafati.mirella@gmail.com)