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 packages provided by FastAPI (https://fastapi.tiangolo.com). Endpoints for uploading SBML files and fetching reports for example models were created and tested. 
  • Initiating frontend Vue project. The interactive report for SBML4Humans is being built with Vue.js. The Vue project was initiated as a Vue 3, typescript + scss enabled project with support for Vuex and Vue Router.
  • Components were created for the landing page and report view page. The landing page includes an about section, an SBML File Upload form and also displays a list of example models fetched from the API.
  • Features in the Report View:
    • SBML components populated in a list of SBases by parsing the JSON response report fetched from the backend.
    • SBML components are colour coded for better readability and distinguishability. 
    • Component to see meta information about an object and option to click and see its detail information on the right. 
    • Feature to filter the SBML objects based on their SBML type (e.g. Model, FunctionDefinition, Species, etc.) 
    • Feature to search objects on their meta information.
    • Math is now being rendered fast using Katex (https://katex.org/).
  • A Static switch has also been added to manually connect and disconnect from the API.
Overall, the first two weeks of the coding period have been very lively and productive. The further milestones include implementing adding inter-component navigation in the report and optimizing the search and filter algorithms. These additions will make the report even more interactive and robust.

Until next time!

Comments

Post a Comment

Popular posts from this blog

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

Image
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
Read more

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
Read more

SBML4Humans GSoC Project Preparation (Week 1 Progress Update)

Image
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
Read more