JSBML - the Java™ library for working with systems biology models in SBML format

[draeger]

Background

The file format SBML constitutes the de facto standard exchange format for computational models in computational systems biology. It has been established nearly two decades ago and quickly gained popularity. Nowadays, many scientific journals require models in that format to be uploaded as supplementary information of publications about computer models in systems biology. However, SBML has not been developed to be manually written. Instead, these files should be created and manipulated using algorithms and specialized software.

The JSBML project's aim is to provide an SBML parser and library that maps all SBML elements to a flexible and extended type hierarchy. Currently, JSBML supports all constructs for SBML up to the latest Level 3 Version 2 specification, including an API to add support for SBML Level 3 extension packages for advanced modeling techniques.

The documentation of the JSBML project is currently distributed across a few resources, including a website, a users' guide in PDF format, a GitHub page, and an entry in Wikipedia. In addition, JavaDoc is used to explain the detailed functions of the source code directly. For users, it is currently difficult to get started with the library. We have observed that while the users' guide provides the most comprehensive overview of the project, most new users do not entirely read it up front, but use a combination of Google and resources such as StackOverflow to answer specific questions.

Goal

We are therefore considering creating a cookbook-like resource in addition to improving the users' guide. We also plan to have more cross-links between different locations of documentation available, so that users may more quickly find information. We also need to avoid that users of JSBML are mistakenly directed to solutions based on the Java API wrapper of the complementary C/C++ library libSBML. In some cases, libSBML can be used to solve problems in Java, but it is not recommendable because of the compromised platform independence this native library introduces.

We need to identify common use cases of JSBML and to provide questions and answers, code examples, and an easy to query documentation. We need linking between currently distributed information.

Technical Skills

It would be an advantage to be familiar with Java and JavaDoc, Markdown, LaTeX, and Wikipedia.

Link

• Website: http://sbml.org/Software/JSBML/
• Project's GitHub page: https://github.com/sbmlteam/jsbml/
• Users' Guide: https://github.com/sbmlteam/jsbml/raw/master/doc/user_guide/User_Guide.pdf

Potential Mentors

@draeger
@niko-rodrigue

Contact

[email protected]

[prathamesh-pvs]

sir, in am interested in this project . I have started reading user guide . Please can you assign me some task that will be useful .

[draeger]

Dear Prathamesh, thanks for your interest in the JSBML project. The best would be to discuss next steps via e-mail using the SBML Team mailing list SBML.

[haardikdharma10]

Hey @draeger, I am interested to work on this project for GSOD 2020. Also, I have mailed you regarding the same. I look forward to receiving a positive response from your side:)

[haardikdharma10]

Greetings,

Hello @niko-rodrigue, I already had a word with @draeger and also have sent him the project proposal for this project. He did find the proposal helpful. I have also shared the google docs link with Andreas and you on your email: [email protected]. I came to know from Andreas that you're the main contact for this project. Kindly review the proposal at your convenient time. Hope to hear from you soon:)

Regards,
Haardik

[niko-rodrigue]

Thanks, [email protected] is not valid since 6 months, @draeger could you put jsbml-team for the contact as I asked ? It will always be valid and reach people.

[haardikdharma10]

Hey @niko-rodrigue, I've revised the proposal as per the changes you and @draeger suggested and also have mailed you regarding the same. Please review the proposal at your convenient time so that we can proceed further. Thank you.

Regards,
Haardik.