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nrnb / GoogleSummerOfCode

Main documentation site for NRNB GSoC project ideas and resources
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Extending ModelPolisher to a universal model annotation tool #126

Closed draeger closed 5 years ago

draeger commented 5 years ago

Background

The process of building models of biological systems continues to be a demanding effort. According to Thiele and Palsson (2010) the workflow leading to a functional model comprises almost 100 steps, many of which need to be manually executed and that are often highly error-prone. Any software that automates parts of this workflow therefore greatly speeds up the model building process and simultaneously contributes to increased model accuracy. In particular, model annotation plays a central role in model reuse and makes models comprehensible to third-parties, but often does not receive the necessary attention.

Goal

In this project, a general model annotation tool should be created based on the ModelPolisher project. ModelPolisher was first created as an in-house model annotation tool for the BiGG Models Knowledgebase, but it is potentially useful to update and automatically improve any model in SBML format. To this end, its algorithm needs to be changed and the project itself needs to be updated to be compliant with software development standards. Furthermore, Neal et al. (2018) recently suggested separating models from annotation by creating a glossary file that can then be embedded within a COMBINE archive file. ModelPolisher should support this as an optional feature. Finally, ModelPolisher should be containerized to simplify the installation of its database backend.

Difficulty Level 1

The described work does neither require designing complex algorithms nor is the underlying software difficult to understand. The aspects of systems biology covered in this project remain rather technical and are therefore well suited for interested computer science students as well as enthusiasts with joy in programming, database queries, and software design.

Skills

Essential

Nice to have

Public Repository

ModelPolisher: https://github.com/draeger-lab/ModelPolisher/

Potential Mentors

Andreas Dräger (@draeger) Thomas J. Zajac (@mephenor)

Contact

Andreas Dräger

codekaust commented 5 years ago

Hi @draeger I find this issue interesting, is it open for GSOC 2019? Thank you.

draeger commented 5 years ago

Yes, it is. The best way of moving forward with your application would be to create a shared Google Document and to contact me via e-mail. I'll be happy to assist you in putting the proposal together.

fenilsuchak commented 5 years ago

Hello, @draeger I find this project interesting and aligned with my skill set. I have working knowledge of Object Oriented Programming in Java and I'm comfortable with SQL, XML. I can pick up docker, maven before/during the project. I kindly request you to please provide me with some additional material so that I can get started with the project.

draeger commented 5 years ago

@Fenil3510: Absolutely, just contact me via e-mail (see my profile) and I'll be happy to share information material with you and to help you put a competitive proposal together.

khanspers commented 5 years ago

Active GSoC 2019 project.