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Martin Scharm
phd-student, sys-admin, linux-guy, zsh-lover, net-fan
phd-student, sys-admin, linux-guy, zsh-lover, net-fan


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just submitted a proposal for :)
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The equivalent of Fat is Fiction!
The equivalent of Sugar is Approbation!
The equivalent of Protein is Truth!

read more:
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Job post: Scientific Programmer to continue the development of the existing SBGN-ED software, Germany
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The WHO recommends to not have more than 6 tea spoons of sugar a day! That's not very much, as much of the sugar is hidden in our food:

| For example, 1 tablespoon of ketchup contains around 4 grams
| (around 1 teaspoon) of free sugars. A single can of sugar-sweetened
| soda contains up to 40 grams (around 10 teaspoons) of free sugars.
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We are seeking motivated people to join our team at the University of Rostock!

Full-Time | do a PhD | travelling
SEMS is hiring!

We are looking for a scientific developer to join our team at Rostock University. The post is for three years, full time.

Major tasks:
• promotion and further development of COMBINE standards
• developing support for SEMS tools in the data management system SEEK4SCIENE

Desired qualifications:
• Java programming, library development
• interest in COMBINE standards and community work (SBML, SED-ML, SBGN)
• knowledge of graph databases
• knowledge of XML
• communicative person

As part of the position, you can take the opportunity to work on a SEMS-related PhD project. Possible topics include, but are not limited to:
• information retrieval: Ranked model retrieval
• graph databases: integrated storage of heterogeneous, linked data
• model comparison based on semantic annotations, bio-ontologies
• provenance of simulation studies

Please note that you will be employed through the HITS gGmbH, but your work location is Rostock.

Please apply until April 3rd, 2015.
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New SBML survey/SBML Software Guide form!
For many years, the SBML Team has used a survey system for gathering data about SBML-compatible software tools to put into the #SBML  Software Guide.  We have recently completely replaced the survey system.  The most important new change is that it finally allows authors to edit existing data, instead of requiring people to fill out the survey from scratch every time.  We also changed the questions in an effort to make them more clear and more precise.

Our ultimate goal is to replace the existing "matrix" on with a better interface; that part is not yet available, but the data-gathering survey form is, and we would like to start gathering data from people.

So, if you have developed software that works with SBML, please visit

If you have an existing entry and you provided an email address in the old Surveymonkey-based system, then it should be possible for the system to prepopulate the new form using your old entry's data (so that you don't have to fill out the form from scratch).  If you cannot remember the email address you used previously (or if we created the entry for you), then you can contact us ( and we'll send you a URL for editing the data.  And if you have new software to add, there's a link for filling out a fresh copy of the survey form.

Please let us know of any issues, suggestions, or questions.
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It feels slightly awkward to have a #SEMS meeting on a Sunday night. We are the only people in the University building.

On the other hand, it is also Monday morning right now, and the start of this year's CellML Workshop. "Traditionally" opened by a remote talk from Rostock.

And suddenly it feels almost normal to be here :)
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