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GSoC 2021 : SBML4Humans - Interactive SBML Report for Humans - Final Report

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Overview Over the past 10 weeks, me and my mentors, Dr. Matthias König and Dr. Ralf Steuer have been working on the project “SBML4Humans - Interactive SBML Report for Humans” under Google Summer of Code 2021. The project is headed by the organization National Resource for Network Biology (NRNB). As the programme comes to an end this week, the project is also nearing its successful completion. The final product created out of this project is an interactive web application that generates human-readable, customizable reports for biological models written in SBML, now available at https://sbml4humans.de .  The web application was developed using the Vue.js framework and uses the sbmlutils package written in Python as a backend. An API instance created using the FastAPI package provides endpoints to make requests to the sbmlutil s package from the SBML4Humans application. The basic workflow of the application is as follows: An SBML file is uploaded to the client web application and is
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Coding Period : Week 1 and 2 Progress

The community bonding period at NRNB was a great experience for me, I was thrilled to be in such a wonderful and supportive community with people from all over the world, looking forward to connect with each other. We had a live interaction session within NRNB's GSoC community on 7th June to introduce ourselves, where we got to know more about the people in the organization and their interests. The Coding Period officially kicked-off on 7th June as well. I have been enjoying working a lot over the last two weeks over the project and interacting with my mentors. We have made significant progress in developing the backend API and frontend web application of SBML4Humans. Following is a summary of the major features added till now. Refactoring of the sbmlutils package to make the generated model report JSON serializable. Many components such as unit definitions, rules and math components were cleaned and refined. Setting up the sbmlutils API. A robust API was set up using tools and pac
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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.
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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
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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
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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
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