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GSOC 2020 PROJECT

Integration of sequence visualization into SynBioHub

As a design repository for Synthetic Biology, SynBioHub facilitates the sharing and searching for information, combining data from a variety of...

Contributor
Linhao Meng
Mentors
Geoff Baldwin, Christopher Myers
Organization
National Resource for Network Biology (NRNB)Science and medicine
Program
GSoC 2020Completed

About this project

Description from the program archive

<p>As a design repository for Synthetic Biology, SynBioHub facilitates the sharing and searching for information, combining data from a variety of sources. SynBioHub uses the Synthetic Biology Open Language (SBOL) an open source data standard that enables an information rich encoding of genetic information. To enable greater utility of the SynBioHub platform, it is necessary to extend its capability in a manner that will enhance its usability to genetic wet-lab workers, creating a better synergy between the digital and physical workflows. When creating or using genetic designs in the laboratory, experimentalists frequently want to interrogate the information for specific DNA ‘parts’ prior to using them. The annotation of a DNA sequence will define which strings of the DNA nucleotide sequence encode specific function. Being able to visualize the correlation of sequence to function is critical for experimentalists. Currently SynBioHub lacks a visualization tool that would enable this visualization. Addressing this will greatly enhance the usability of the platform by experimentalists and this will facilitate the integration of digital and physical workflows.</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

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

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  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. Spreadsheet Plug-in for SynBioHub

    Isabel MarleenMentored by Christopher Myers, JVM, jakebeal

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