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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

Martin's posts

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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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Thoughts of our new #SED-ML #editor-to-be!
+Felix Winter stands for election, go to vote for him at
SED-ML editor vote open

Since today the vote for two new SED-ML editors is open. I only heard some days ago that I was nominated and was asked whether I would accept the nomination. Apparently I did. When I saw today the comments which were given by the nominator I realized that it could be a good idea to talk about my motivation not to decline the nomination.

My relation to SED-ML is quite young. Last May I was hired by ASD GmbH (link below) and started to work in the VPH Dare@IT project. For me this is the first project in the industry and while it is still only a part-time job it struck me how much weight is put there on the detailled documentation of the work. Having used and taught SBML and SBGN in the past I did know how to describe our models using standards, but I never really used SED-ML before. This can be attributed to two reasons: Firstly there was no real need (request from reviewers or additional value) and secondly I used mostly handwritten MATLAB code and therefore had no easy way to write SED-ML.

While the second part is still partially true, the need to create a computer-readable software-independent description of simulation experiments for documentation purposes has been added to my list of requirements lately. And having heard about SED-ML several times from +Dagmar Waltemath  I decided to have a look at the specification (L1V2 RC1 at this time) to see whether it would do the job.
Reading a spec is not always fun but I liked approach taken by SED-ML. At the same time, I felt that some of the good ideas are concealed by the somewhat cumbersome description and a few slight inconsistencies in the spec. (There is a confusing mixture of terms related to XML and terms related to UML in some sections, for example.)

When I was asked whether I want to stay on the list of nominees I started to think about what I could do to improve SED-ML and promote its use.  And I came across a few things:

While the L1V2 spec is already published, I feel like there are still a few things which could be improved in the next version. I would love to contribute there.

Software support for SED-ML is still sparse. Being in the position of working both for a company and a university, I could promote the implementation and use in different communities. I followed the discussion on SBML-discuss started by +Michael Hucka  in spring on the need to include people from outside the standardization community. This is where I see myself.

The last thing I want to mention that there are also a few tiny things in  SED-ML I believe could be changed to increase the clarity of the language. One example is the "outputStartTime" attribute of the "UniformTimeCourse" class which is not related to the simulation , but which is part of the post-processing.

All these things are not tied to a position as a SED-ML editor and I will follow these ideas independently of the result of the vote. Still, I think that they are easier to achieve if I get elected. So just in case you haven't submitted your vote yet: I would be happy to  get your support.
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