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GSOC 2020 PROJECT

Spreadsheet Plug-in for SynBioHub

Synthetic Biology is a discipline that connects many disciplines and heterogeneous researchers. To be useful as a tool, a platform such as SynBioHub...

Contributor
Isabel Marleen
Mentors
Christopher Myers, JVM, jakebeal
Organization
National Resource for Network Biology (NRNB)Science and medicine
Program
GSoC 2020Completed

About this project

Description from the program archive

<p>Synthetic Biology is a discipline that connects many disciplines and heterogeneous researchers. To be useful as a tool, a platform such as SynBioHub should reflect this diversity. SynBioHub is a repository of genetic components and designs and can represent a powerful way to share and curate synthetic biology projects. To do so, it should invite and fulfill the needs of bioinformaticians and mathematicians while at the same time bridging the gap to wet lab experimentalists. One of these differences is the common preference of wet lab biologists to use spreadsheets, which as of now cannot be used as input for SynBioHub. This can be changed by creating a plugin, which accepts a spreadsheet as input and converts it into SBOL which can be processed by SynBioHub. This could simplify the process of data curation for publication by bridging the gap between those that perform the experiments and those that write about them from the very beginning.</p>

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  1. Implementation of SBML-JSON converter and SBML-JSON scheme

    HemantMentored by Matthias König, Lucian Smith, Andreas Dräger +1

  2. Development of a system that generates spatial SBML models using deep learning

    Medha BhattacharyaMentored by Kaito Ii, Akira Funahashi, tokkuman

  3. Developing a tool for implementing clustering algorithms to Cytoscape app ClusterMaker2

    Maija UtriainenMentored by Dexter Pratt, John "Scooter" Morris, ALEXANDER PICO

  4. LACE-View : A Visualizer for Longitudinal Clonal Trees

    Bhavesh NarraMentored by Marco Antoniotti, Daniele, Alex Graudenzi

  5. Improving compmodelmatch.org

    Sahil JhaMentored by Danny Fryer, Michael Blinov

  6. Implement a comment/discussion system in GraphSpace

    Yash Agarwal_Mentored by Daniyal Jahan, Aditya Bharadwaj, T. M. Murali

  7. Enhancing PathwayMapper in cBioPortal and PathwayMapper editor

    Merve KılıçarslanMentored by Ugur Dogrusoz, ALEXANDER PICO, Onur Sumer +1

  8. Redevelop Model Bricks code base architecture

    Saksham RaghuvanshiMentored by Ann Cowan, Frank Morgan, Michael Blinov +1

  9. Simulation of systems biology models in Java: support for new features

    Hemil PanchiwalaMentored by Shalin Shah, Matthias König, Mykola Zakharchuk +1

  10. Integrating RRPlugins with libRoadRunner

    Debashish RoyMentored by Kiri Choi, Herbert Sauro

  11. Integration of sequence visualization into SynBioHub

    Linhao MengMentored by Geoff Baldwin, Christopher Myers

Data: Google Summer of Code public archive. This project in the official archive