[BBC] BioSB course Integrated Modeling and Optimization (preliminary announcement)

[Bosnacki, Dragan]

Dear colleagues,


Also in the new academic year the BioSB research school, Wageningen University & Reserach

and Eindhoven University of Technology will organize the course:


*Integrated Modeling and Optimization*



12-16 December 2022, Wageningen University





Computational modelling is an absolute requisite to gain understanding of

the biological mechanisms underlying patterns observed in experimental

data. However, one could say that modelling is a craftsmanship, that can

only be learned via intense exercising and ‘learning by doing’. In this

course we offer the participants the possibility to learn and exercise the

modeling process and the optimization techniques needed to fit models to

data.







In the course the students will learn:



   - to understand the common ground and the differences for applications

   of dynamic modeling in metabolic, regulatory, signaling, and multi-scale

   biological processes

   - how to set-up a dynamic model to represent biological networks using

   different interaction mechanisms

   - to implement, simulate and analyze dynamic network models

   - to understand the wide variety of problems in modelling that can be

   solved with optimization ·

   - to apply different types of numerical optimization methods: global and

   local search methods: steepest descent, Levenberg-Marquardt, genetic

   algorithms, linear programming.

   - the combination of dynamic modeling and optimization to integrate

   experimental data in modelling, estimate model parameters and design

   experiments.

   - to understand how numerical optimization (linear programming) works in

   flux balance analysis to simulate metabolic network models.





Lecturers:



·        Prof. Natal van Riel, Eindhoven University of Technology (course coordinator)

·        Dr. Aalt-Jan van Dijk, Wageningen University & Research

·        Prof. Jaap Molenaar, Wageningen University & Research

·        Dr. Hans Stigter, Wageningen University & Research

·        Dr. Robert Smith, Wageningen University & Research

·        Dr. Dragan Bosnacki, Eindhoven University of Technology





Target audience:

The course is aimed at PhD students with a background in bioinformatics, systems biology, computer science or a related field,

and life sciences. Participants from the private sector are also welcome. A working knowledge of mathematics,

especially differential equations, is recommendable, but we will distribute preparation material to be studied by students

missing the required background. Furthermore, at the start we offer a math refresher to help those participants who

are not (yet) involved in modelling on a daily basis.



More about the last year's edition:

https://www.dtls.nl/courses/integrated-modeling-and-optimization/<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dtls.nl%2Fcourses%2Fintegrated-modeling-and-optimization%2F&data=05%7C01%7C%7Cdb94a8b4fa6941832f8c08da6bf9c254%7Ccc7df24760ce4a0f9d75704cf60efc64%7C0%7C0%7C637941017718028636%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lMXj23wm05OtsLJrsGBzhsnIiOwAcawkkagtCNQdSR0%3D&reserved=0>

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Integrated modeling and optimization - Dutch Techcentre for Life Sciences<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dtls.nl%2Fcourses%2Fintegrated-modeling-and-optimization%2F&data=05%7C01%7C%7Cdb94a8b4fa6941832f8c08da6bf9c254%7Ccc7df24760ce4a0f9d75704cf60efc64%7C0%7C0%7C637941017718028636%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lMXj23wm05OtsLJrsGBzhsnIiOwAcawkkagtCNQdSR0%3D&reserved=0>
Course date 13-17 December 2021, Wageningen Location: The course will be held at: Forum Building (building nr 102), with number B0409. A Biocafe (on Thursday) will be held in “The Spot” in Building Orion (gebouw nummer 103) in the Wageningen…
www.dtls.nl<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.dtls.nl%2F&data=05%7C01%7C%7Cdb94a8b4fa6941832f8c08da6bf9c254%7Ccc7df24760ce4a0f9d75704cf60efc64%7C0%7C0%7C637941017718028636%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ul4n9%2FEPUxDdirFMnFK%2BpVxnVSfLrpToyiaWp%2FJG9cI%3D&reserved=0>

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More details about the programme and the registration will follow soon.

Please feel free to contact Dragan Bosnacki (D.Bosnacki at tue.nl) for more information.

---------------------





*About BioSB*



The Netherlands Bioinformatics and Systems Biology research school (BioSB)

is the national platform in which the Dutch community of researchers in

bioinformatics and systems biology is organized. BioSB also organizes:



   1. fundamental and advanced post-graduate courses

   <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb.nl%2Feducation%2Fcourse-portfolio%2F&data=04%7C01%7Cp.d.moerland%40amsterdamumc.nl%7Cb50e6cc624ae436c8a7608d88ff446ff%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C0%7C637417626609229476%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=2zzuqQYvfLwhU6fMZDwIKvyMwD5xlzJITlRpE4WYLzw%3D&reserved=0<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb.nl%2Feducation%2Fcourse-portfolio%2F&data=05%7C01%7C%7Cdb94a8b4fa6941832f8c08da6bf9c254%7Ccc7df24760ce4a0f9d75704cf60efc64%7C0%7C0%7C637941017718028636%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=dVkjQj1XGJZw7b4GNFAB%2Bd%2FeJjxp3TOvX%2FqsGyR%2BgQ4%3D&reserved=0>>

   2. the yearly BioSB conference

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   3. hot topics meetings

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The aim of the BioSB research school is to offer PhD students, postdocs and

senior researchers a vibrant environment for their scientific development

as well as education in bioinformatics and systems biology. In addition,

BioSB acts as a parent organization for YoungCB

<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.youngcb.nl%2F&data=04%7C01%7Cp.d.moerland%40amsterdamumc.nl%7Cb50e6cc624ae436c8a7608d88ff446ff%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C0%7C637417626609239472%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=s0JGs6hegGU%2BskTBgKnAYY6fz5U%2B8cSifF9QF0IbILo%3D&reserved=0<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.youngcb.nl%2F&data=05%7C01%7C%7Cdb94a8b4fa6941832f8c08da6bf9c254%7Ccc7df24760ce4a0f9d75704cf60efc64%7C0%7C0%7C637941017718028636%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xUUf%2BnrnFmY8xc4XaDOhArNQbwIjd4g6u64x28aKVBM%3D&reserved=0>>,

the official Regional Student Group (RSG) of the International Society of

Computational Biology (ISCB).

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