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Dagmar Waltemath
but the visions that I see believe in me [weakerthans]
but the visions that I see believe in me [weakerthans]
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Funded PhD project with me on optimising experiments for developing models of ion channel kinetics is available to start September 2017:

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SEMS highlights in 2016 (sorted by month in the year, JAN-DEC ;-)):

(1) My visit to the group of +Claudine Chaouiya (http://compbio.igc.gulbenkian.pt/nmd/node/26), trying to make SED-ML work out for logical models. Very nice & friendly group, and Lisbon is a very nice city as well! The coffee is remarkable - and it can be enjoyed outside in the sun, in February! https://figshare.com/articles/Proposal_for_SED_ML_extension_to_cover_models_in_SBML_Qual_format/2075143 (No coffee pic, but the SED-ML proposal!)

(2) We (that is +Martin Scharm, +Pedro Mendes, +Olaf Wolkenhauer) made an ontology of types of differences between model versions: COMODI http://comodi.sems.uni-rostock.de/latest/ https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0080-2 It lets us characterise the changes identified by BiVeS, which is great, because

(3) within SEMS, we had a couple of hackthon-like meetings to get together a website that knows all BioModels (SBML) and all CellML models from PMR2 in all publicly available versions, and generates some figures on the changes occurring. We called it MOST (Model statistics, the name was set when we thought we were doing statistics ;-)). A prototype runs here: http://most.sems.uni-rostock.de/ (work with +Martin Scharm, +Martin Peters, +Vasundra Toure, Andrea Bagnacani, and Tom Gebhardt)

(4) The SED-ML Web Tools are finally published (took a few years to write the manuscript)! I was happy to join the friendly paper writing team, with +Frank Bergmann, +David Nickerson and +Martin Scharm. Paper accepted with BIOINFORMATICS, so far, read the preprint @ +PeerJ https://peerj.com/preprints/2515/

(5) The year ended with the RSG congress in Luxembourg (http://rsg-luxembourg.iscbsc.org/?q=node/37).- and I not only enjoyed the pub! But also the active meeting (lots of questions), nice discussions and career opportunities with startup companies :-) I would like to mention my co-talk with +Anna Zhukova on standards and model reusability: http://www.slideshare.net/anna_zhukova/a-modeling-workflow-in-systems-biology-an-overview and www.slideshare.net/dagwa/model-management-for-systems-biology-projects Thanks, Anna!

That's it for 2016 - let's see what 2017 brings :) Happy New Science Year.


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Dear colleagues and fans of SBGN!

After the positive experiences with the whole-cell educational event last year, we want to turn this into a tradition.

This year, co-located with COMBINE 2016 in Newcastle (http://co.mbine.org/events/COMBINE_2016), we are organizing a workshop on the Systems Biology Graphical Notation (SBGN).

If you want to know more about standard for network visualization, how to draw proper SBGN maps or how to generate SBGN maps from your own network, this workshop is for you!

Introductory talks on SBGN and software tools that offer SBGN support will be given in the morning. The afternoon will be dedicated to hackathon sessions in which you will learn to generate SBGN maps. We will also have a competition for the best SBGN map!

Come and join us in Newcastle, the 24th of September 2016.
You can register for free at: http://bit.do/SBGN2016Reg
The number of participants is limited to 25 persons (first come first served).

More information is available on https://www.sbi.uni-rostock.de/research/events/sbgn2016/

We are looking forward to seeing you there!

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Dear colleagues,
please spread the word about this great opportunity to do research in multi-scale modeling of neuronal signaling pathways.
Looking for talented PhD student in computational neurobiology to work on modelling of signalling pathways in neurodevelopmental disorders. Please spred the word! http://tinyurl.com/hcgn9sq

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SWAT4LS 2016: dates and location
The 2016 edition of SWT4LS will be held in Amsterdam. The conference will take place on the 6th and 7th od December, while the 5th and 8th of December will be reserved for tutorials and hackathon. We will soon communicate submission deadlines and the program.

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HARMONY 2016 is rapidly approaching: June 7-11 in Auckland, New
Zealand, http://www.co.mbine.org/events/HARMONY_2016.

To help with planning, it would be great if everyone planning on
attending could register by this Friday, May 27. That will help us get
some preliminary numbers settled for the catering, meeting room
allocations, etc.

Registration information is available at:
http://www.co.mbine.org/events/HARMONY_2016#Registration.


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We are running a de.nbi workshop in May on the occasion of the 10th
anniversary of SABIO-RK (http://sabiork.h-its.org/).

The workshop also provides introductions to COPASI (http://copasi.org/) and to SEEK, a data- and model management system for life sciences
(http://seek4science.org/).

Registration is open until 9th of May:
http://www.h-its.org/en/research/sdbv/kinetics-on-the-move 
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