GSoC '21 Introduction: SBML4Humans - Interactive SBML Report for Humans

[Sankha Das]

Hello everyone!

My name is Sankha Das and I am a 2nd year Computer Science undergraduate at BITS Pilani Pilani Campus, India. I am excited to announce that I have been accepted as a Google Summer of Code student under NRNB for summer 2021.

I will be working on the project “SBML4Humans - Interactive SBML Report for Humans” and will be mentored by Dr. Matthias König and Dr. Ralf Steuer.

Systems Biology Markup Language (SBML) is a standard format for the representation and exchange of biological models between computers. The information in an SBML model file is organized as a list of components encapsulated within the model (e.g. compartments, species, parameters, reactions, etc.). My project aims to provide an interactive SBML report as a deliverable web application for easy reading and interpretation of SBML models by humans. The project encapsulates the following features:
i) interactive SBML report with navigation between SBML objects
ii) search and filter functionality
iii) web application with REST API
v) support for hierarchical model, distributions and COMBINE archives

Such an interactive report will thus significantly enhance the process of reading and exchanging SBML models.

Further details about my project can be found at the following resources:
i) Project Proposal 
ii) Project Idea: https://github.com/nrnb/GoogleSummerOfCode/issues/164 
iii) Project Repository: https://github.com/matthiaskoenig/sbmlutils 
iv) Project Blog: https://sbml4humans-gsoc-2021.blogspot.com/

Please feel free to reach out to me to know more about the project, I will be most happy to exchange ideas with the community. Looking forward to having a great summer with NRNB!

Thanks & Regards,
Sankha Das

[Andreas Dräger]

Dear Sankha Das,

Welcome to the community, and congratulations on being accepted to this competitive program! I wish you lots of fun with your summer project, which has a considerable potential to be very helpful for exploring the content of complex bio-models.

If not already considered anyway, the technique of using XSLT (https://en.wikipedia.org/wiki/XSLT) transformations could be of interest to look at, even if it is just for comparison or as a reference. There is a lot that can be done with that. Perhaps, it could save some implementation effort (just my 2 cents).

Enjoy the summer of code!

With best regards

Dr. Andreas Draeger
Assistant Professor
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University of Tübingen
Institute for Bioinformatics and Medical Informatics (IBMI)
Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens
Sand 14 · Office #C108 · 72076 Tübingen · Germany
Phone: +49-7071-29-70459 · Fax: +49-7071-29-5152
Web: http://systems-biology.info · Twitter: @dr_drae
YouTube: https://www.youtube.com/c/systemsbiology

[MUETZELFELDT Robert]

Hello Sankha, Andreas,

For reference, you might be interested in something I worked on many years ago (how many years since you last heard someone say "Web 2.0"?!).  It was called MultiGuise, and was what now would be called a single page web app.  It presented the user with a list of XML documents and a list of XSLT stylesheets, allowing the user to apply any stylesheet to any document, displaying the results in an output panel.   Both the XML documents and the XSLT stylesheets could live anywhere on the web, and were accessed via a bookmarking service, but that's not relevant to your project.  

The only available documentation is a pdf version of a presentation consisting of screenshots, archived at https://www.nature.com/articles/npre.2007.18.1.   

As it happens, one of the sample domains was SBML, and there is a brief illustration of this in the document (slides 23 and 24).   

Working with XSLT had a delicious "meta" feel about it (writing XML to transform XML documents...), and doing transformations declaratively does have a certain appeal, but it would require quite an investment on your part to get into it.

Best wishes,
Robert

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From: sbml-d...@googlegroups.com on behalf of Andreas Dräger
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Subject: Re: [sbml-discuss] GSoC '21 Introduction: SBML4Humans - Interactive SBML Report for Humans

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[Sankha Das]

Dear Dr. Andreas and Robert,

Thanks a lot for the valuable inputs, it is really very motivating to see the support and welcome being provided by the community. I'll go through the resources provided and try to incorporate valuable points to improve the project. 

Thanks & Regards,

Sankha Das

[Matthias König]

Hi all,

thanks for the great input. We looked at the XLST approach when we started but for our use case it seemed to limiting. In my opinion XLST can work great for having a static report of small models (in the range of maximal 20 species+reactions). As soon as one goes to genome-scale models and hierarchical model composition (with the comp package) XLST comes to its limits, especially in the context of usability of the report. Also things such as content MathML to presentation MathML/Latex conversion has its limitations.

As soon as we have a first prototype we would love feedback from the community.

We will send an announcement here via the channel.

Best Matthias

[Alan Garny]

Hi all,

Just in case, I thought I would mention web-xslt, which can be used to convert content MathML to presentation MathML. It has been proving quite useful for our use in OpenCOR. We had to edit it quite a bit though (see here).

Alan

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[Matthias König]

Hi Alan,

this is perfect. We looked for a clean solution for the Math rendering but the original web-xslt had too many corner cases and has not been updated for ages. We will try to use the modified OpenCOR/physiome version. I really like the Math rendering in the physiome repository and OpenCOR, so this should be very good for the report.

I assume you use MathJax for the actual rendering of the presentation MathML?

How is the support for the SBML csymbols?

Best Matthias

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Matthias König, PhD.
Junior Group Leader LiSyM - Systems Medicine of the Liver
Humboldt Universität zu Berlin, Institute of Biology, Institute for Theoretical Biology
  https://livermetabolism.com
koni...@googlemail.com

https://twitter.com/konigmatt

https://github.com/matthiaskoenig
Tel: +49 30 2093 98435

[Alan Garny]

Hi Matthias,

The XSL file I mentioned is used by OpenCOR. I am not quite sure what PMR uses when it comes to the conversion from Content to Presentation MathML, although I believe it does indeed use MathJax when it comes to the rendering.

I am definitely not a fan of MathJax (too bloated and too slow in my view and experience; at least, it used to be that way). I much prefer KaTeX, which is much smaller and quite a bit faster (see here). This is what we use to render math on the OpenCOR and libCellML websites.

Back to the XSL file used in OpenCOR: I edited the original file to account for the kind of math that we need to render in OpenCOR. So, not sure whether it would address your needs (incl. SBML csymbols). (Rendering of Presentation MathML in OpenCOR is done using Qwt and its MathML renderer in particular, which I reworked quite a bit; see here).

Alan

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Sent: 28 May 2021 8:10 PM
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[Matthias König]

Hi Alan,

KaTex looks amazing and very fast (https://katex.org/). Thanks for the input, we will definitely use this for the math rendering!

In addition to the speed there are also node packages which is amazing.

Best Matthias

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