<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span id="docs-internal-guid-f8cc2bee-7450-959f-1235-6e698d23b88a" class=""><h1 dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;background-color:#ffffff;" class=""><span style="font-size: 10pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">BioSB course: Optimisation techniques in Bioinformatics and Systems Biology</span></h1><p dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;" class=""><span style="font-size: 9pt; font-family: Arial; font-weight: 700; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Course coordinators:</span><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""> </span><span style="font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Jaap Kaandorp (UvA), Jaap Molenaar (WU), Hans Stigter (WU), Cajo ter Braak (WU)</span></p><p dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;" class=""><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Date: </span><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""><span class="Apple-tab-span" style="white-space:pre;"> </span></span><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""><span class="Apple-tab-span" style="white-space:pre;"> </span></span><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">12-16 February 2018</span><span style="font-size: 9pt; font-family: Arial; font-weight: 700; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""><br class="kix-line-break"></span><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Location: </span><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""><span class="Apple-tab-span" style="white-space:pre;"> </span></span><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Wageningen</span><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""><br class="kix-line-break"></span><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Website </span><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""><span class="Apple-tab-span" style="white-space:pre;"> </span></span><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""><span class="Apple-tab-span" style="white-space:pre;"> </span></span><a href="http://biosb.nl/education/course-portfolio-2/optimisation-techniques-in-bioinformatics-and-systems-biology/" style="text-decoration:none;" class=""><span style="font-size: 9pt; font-family: Arial; color: rgb(17, 85, 204); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">link</span><span style="font-size: 9pt; font-family: Arial; color: rgb(0, 0, 0); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""><br class="kix-line-break"></span></a><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Registration </span><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""><span class="Apple-tab-span" style="white-space:pre;"> </span></span><a href="http://biosb.nl/education/course-portfolio-2/optimisation-techniques-in-bioinformatics-and-systems-biology/enrollment-optimisation-techniques-2018/" style="text-decoration:none;" class=""><span style="font-size: 9pt; font-family: Arial; color: rgb(17, 85, 204); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">link</span></a></p><p dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;" class=""><span style="font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-weight: 700; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Course description</span></p><p dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;" class=""><span style="font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Many problems in bioinformatics and systems biology require at a certain moment application of some optimisation technique. When facing optimisation problems, many researchers suffice with applying a simple algorithm in Excel, coming to the conclusion that it does not work properly or runs into convergence problems. It is not necessary to stick to that stage, since optimisation is a rapidly expanding field of research, that generates more and more efficient, successful, and easy-to-use algorithms.</span></p><p dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;background-color:#ffffff;" class=""><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">This course is intended to provide you with the main ideas underlying optimisation, and to get you acquainted with the optimisation techniques that are nowadays available and widely used. In addition, a great variety of examples of optimisation problems in life sciences will be presented and discussed.</span></p><p dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;background-color:#ffffff;" class=""><span style="font-size: 9pt; font-family: Arial; font-weight: 700; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Course programme</span></p><p dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;background-color:#ffffff;" class=""><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">The course has the following structure:</span></p><ul style="margin-top:0pt;margin-bottom:0pt;" class=""><li dir="ltr" style="list-style-type: disc; font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre;" class=""><p dir="ltr" style="line-height: 1.2; margin-top: 10pt; margin-bottom: 0pt;" class=""><span style="font-size: 9pt; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Day 1: Math refresher and univariate optimisation (Jaap Molenaar+ Hans Stigter)</span></p></li><li dir="ltr" style="list-style-type: disc; font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.2; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 9pt; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Dag 2: Local multivariate optimisation (Jaap Molenaar + Hans Stigter)</span></div></li><li dir="ltr" style="list-style-type: disc; font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.2; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 9pt; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Dag 3: Global stochastic optimisation (simulated annealing, evolutionary algorithms) (Jaap Kaandorp)</span></div></li><li dir="ltr" style="list-style-type: disc; font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre;" class=""><div style="line-height: 1.2; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 9pt; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Dag 4: Parameter estimation, systems control and optimisation (Hans Stigter + Jaap Molenaar)</span></div></li><li dir="ltr" style="list-style-type: disc; font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre;" class=""><p dir="ltr" style="line-height:1.2;margin-top:0pt;margin-bottom:10pt;" class=""><span style="font-size: 9pt; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Dag 5: MCMC techniques (Cajo ter Braak)</span></p></li></ul><p dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;background-color:#ffffff;" class=""><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">The first day is devoted to study simple problems that allow the use of algorithms that are intuitively clear. On day 2, we extend to problems that are bit more complicated. On day 3, we introduce techniques that are based on stochastic searching, while day 4 is spent on the frequently met problem of finding values for the parameters in a model, given a dataset. This challenging problem requires a bit more sophisticated optimisation tools. You will learn about uncertainty and identifiability of the parameters. In addition, you will get some experience with using appropriate parameter estimation tools. On the last day, the state-of-the-art will be presented, since then the popular and powerful Markov Chain Monte Carlo (MCMC) technique will be dealt with. This method is based on a Bayesian approach. So, you will learn about prior distribution, posterior distribution, likelihood, and how in MCMC likelihood and prior distribution are combined to arrive at a posterior distribution.</span></p><h3 dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;background-color:#ffffff;" class=""><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Target audience</span></h3><p dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;background-color:#ffffff;" class=""><span style="font-size: 9pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">We assume that the participants have some basic knowledge of modelling in the life sciences. However, it is not necessary to be an expert in mathematics, since the course starts with a session to refresh the mathematical background needed for optimisation.</span></p><p dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;" class=""><span style="font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-weight: 700; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">BioSB research school</span></p><p dir="ltr" style="line-height:1.2;margin-top:10pt;margin-bottom:10pt;" class=""><span style="font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">This course is part of the</span><a href="http://biosb.nl/education/course-portfolio-2/" style="text-decoration:none;" class=""><span style="font-size: 9pt; font-family: Arial; color: rgb(128, 0, 128); background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class=""> Education Programme of BioSB</span></a><span style="font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology.</span></p><span style="font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">More information about BioSB can be found at </span><a href="http://www.biosb.nl/" style="text-decoration:none;" class=""><span style="font-size: 9pt; font-family: Arial; color: rgb(128, 0, 128); background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">www.biosb.nl</span></a><span style="font-size: 9pt; font-family: Arial; background-color: rgb(255, 255, 255); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">.</span></span><br class=""><div class="">
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class=""><div><div style="font-size: small; font-variant-ligatures: normal; font-family: Calibri, sans-serif; word-wrap: break-word;" class=""><font face="Arial Unicode MS" color="#484848" class=""><div class=""><span style="font-size: 12px;" class=""><b class=""><br class="Apple-interchange-newline">Femke Francissen</b></span></div><div style="font-size: 14px;" class=""><span style="font-size: 12px;" class="">Community manager</span></div><div style="font-size: 14px;" class=""><span style="font-size: 12px;" class="">BioSB Research School</span></div></font></div></div></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class=""><br class="webkit-block-placeholder"></div><br class="Apple-interchange-newline"><span><img apple-inline="yes" id="3335B641-9780-4A23-B69F-D5797C10BF57" src="cid:7AF4BDB8-DB76-4EC7-BE44-DB9092A11E6C@home" class=""></span>
</div>
<br class=""></body></html>