the mind wobbles – Systems Biology, Bioinformatics, Ontologies, Data Integration, Workshops, News, Papers, etc.. - Systems Biology, Bioinformatics, Ontologies, Data Integration, Workshops, News, Papers, etc..
https://themindwobbles.wordpress.com/copyright/ Copyright – the mind wobbles - The Mind Wobbles Blog by Allyson Lister is licensed under a Creative Commons Attribution-Share Alike 2.0 UK: England & Wales License.
https://themindwobbles.wordpress.com/about/ About – the mind wobbles - Yes, it is a weak pun on "the mind boggles"... And also a reference/homage to the Weebles (weebles wobble but they won't fall down): the mind wobbles, but it won't fall down. You can also find me on Google+, Twitter, and SlideShare. Short Version: My name is Allyson Lister and I began working part time…
https://themindwobbles.wordpress.com/phd-thesis/ PhD Thesis – the mind wobbles - Below you can find a complete table of contents for all thesis-related posts (you can also get to the posts via the "thesis" tag I have used for each). Enjoy! Thesis Posts Abstract Additional Front Material Chapter 1: Background 1.1: Overview 1.2: What does systems biology data look like? 1.3: Modelling biological systems 1.4: Standards…
https://themindwobbles.wordpress.com/2016/09/21/the-normsys-registry-for-modeling-standards-in-systems-and-synthetic-biology/ The NormSys registry for modeling standards in systems and synthetic biology – the mind wobbles - COMBINE 2016 Martin Golebiewski http://normsys.h-its.org . NormSys covers the COMBINE standards, but they have plans to extend it to further modelling standards. Each standard has multiple versions/levels, and trying to figure out which standard you need to use can be tricky. Normsys provides a summary of each standard as well as a matrix summarizing each…
https://themindwobbles.wordpress.com/2016/09/21/sed-ml-support-in-jws-online/ SED-ML support in JWS Online – the mind wobbles - COMBINE 2016 Martin Peters In an ideal world, you should be able to reproduce any simulation published in a paper. This does happen for some models. You have a website which links the paper from JWS and data from the FAIRDOM hub. Then you can tweak the parameters of a published model and see how…
https://themindwobbles.wordpress.com/2016/09/21/the-zbit-systems-biology-software-and-web-service-collection/ The ZBIT Systems Biology Software and Web Service Collection – the mind wobbles - COMBINE 2016 Andreas Draeger In systems biology, people want to perform dynamic simulations, steady-state analyses and others. SBML is the format to use for the model, but you also need a data structure for use in the software, and as such they developed jSBML. People build models from KEGG, textbooks and more. They try to…
https://themindwobbles.wordpress.com/2016/09/21/combine-2016-day-3-signetsim-a-web-based-framework-for-designing-kinetic-models-of-molecular-signaling-networks/ COMBINE 2016 Day 3: SigNetSim, A web-based framework for designing kinetic models of molecular signaling networks – the mind wobbles - COMBINE 2016 Vincent Noel He was asked to develop a web tool which would be easy for biologists and students, but which could use a parallel simulated annealing algorithm and perform model reduction. He used Python to write the core library and the web interface, with some parts of the library in C. In…
https://themindwobbles.wordpress.com/2016/09/21/combine-2016-day-3-modelling-ageing-to-enhance-a-healthy-lifespan/ COMBINE 2016 Day 3: Modelling ageing to enhance a healthy lifespan – the mind wobbles - COMBINE 2016 Daryl Shanley Age is a major risk factor for chronic disease, and chronic diseases are the major cause of death and disability in the world, estimated at around 70% (WHO 2005). Molecular damage is the underlying factor in all of these (DNA damage (cancer), dementia and more). Ageing results from the accumulation of…
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