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Commencing SBML4Humans: Getting Accepted into GSoC 2021 and the Road Ahead

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There come some special days in a person's life which they remember lifelong. For me, one such day would be Monday, 17th May 2021, when I got accepted into Google Summer of Code 2021 under National Resource for Network Biology! It is a most extraordinary feeling to see the hardwork of the past few months finally paying off and to get accepted under such a wonderful organization. I will now be officially working on the project "SBML4Humans - Interactive SBML Report for Humans" over the summer and will try to achieve the planned out milestones with full enthusiasm. The link to my project description can be found  here .  As a start to this journey, I had a video conference with my project mentor Dr. Matthias  König  last week. It felt really good to receive his best compliments on me getting accepted for GSoC and to listen to his motivational words.   We had a good discussion on the road ahead in the project and chalked out some project milestones according to the proposal.

SBML4Humans GSoC Project Preparation - Week 3-5 Progress Update

  Over the past 2-3 weeks, I have gained hands-on experience in working on the sbmlutils project ( https://github.com/matthiaskoenig/sbmlutils/ ) in preparation for the GSoC project. Most of the work was on fixing issues in the repository via pull requests and working on the reviews given for each pull request. Working on issues helped me gain a better understanding of the repository and especially the reports module which is responsible for the generation of SBML reports in HTML format. It also gave me good knowledge about the code of conduct for working on the codebase, enhanced my open source workflow knowledge and regular reviews on my work. My mentor Dr. Matthias König provided code reviews and suggestions which helped me to improve and fix the solution and code.  I have solved around 11 issues till now, which are a collection of small and medium-sized issues. Following is a brief description about the pull request for each issue in chronological order: #181 doc: fixed the link to

SBML4Humans GSoC Project Preparation (Week 2 Progress Update)

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This project focuses on developing an interactive report interface for presenting SBML model information. This requires a strong base in understanding the current state of the SBML report and the code that helps in generating the reports. This week’s exercises were centred around understanding the reports module and tests.  The second week of preparation taught me many new things related to SBML report generation and rendering of the report. I learnt about reading (parsing) SBML model documents, creating structured and formatted document trees from the parsed models, and presenting them in pretty-printed and HTML formats. During this period, I have studied the following resources: Overview and test examples of the SBML report generation process from the documentation ( https://sbmlutils.readthedocs.io/en/latest/notebooks/sbml_report.html ) Code of the reports module from the repository ( https://github.com/matthiaskoenig/sbmlutils/tree/develop/src/sbmlutils/report ) Code of related mod

SBML4Humans GSoC Project Preparation (Week 1 Progress Update)

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The Systems Biology Markup Language (SBML) is a standard language to represent biological models in a computer readable and exchangeable format. The goal of this project is to create a human-readable, reactive and navigable web-based interface for easy visualization of these SBML models. More information about the project can be found on the Github issue ( https://github.com/nrnb/GoogleSummerOfCode/issues/164 ). I am preparing myself for this project and am being mentored by Dr. Matthias König . The first week of learning taught me some great things, some new and some known (e.g. the SBML 3 structure, history, abstract and core ideas). I have gone through the following resources have reached a good understanding of the core ideas: The SBML Homepage ( http://sbml.org/Main_Page ) The SBML 3 abstract and overview in the following publication https://www.embopress.org/doi/full/10.15252/msb.20199110 Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gill