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Native Python support for the Synthetic Biology Open Language (SBOL) #129

Closed jamesamcl closed 4 years ago

jamesamcl commented 5 years ago

Background

The Synthetic Biology Open Language (SBOL) is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. To achieve this goal, it is necessary for existing and new software to support SBOL as a data format, which is accomplished using programmatic libraries. There exist up to date libraries for SBOL written in Java, C++, and JavaScript, but not in Python. While the existing SBOL C++ library can be used from Python, the library itself is intractable to Python developers which makes integration of SBOL into the wider Python ecosystem (e.g. biopython) problematic. As Python is a highly popular language for software development in the life sciences, it would be highly beneficial for SBOL if it had a native implementation in Python.

Goal

A proof of concept implementation for a Python SBOL library has already been developed by members of the SBOL community, but it does not support the latest version of the SBOL standard, does not implement any validation rules, and has no testing or documentation. The ultimate goal of this project would be to develop this library into a fully fledged SBOL 2.2.1 implementation in line with the other SBOL libraries. This would be accomplished by first implementing the remaining classes from the SBOL specification and support for remote repositories such as SynBioHub. A second stretch goal would then be to create documentation, examples, and integration with the SBOL Test Suite as used by other libraries.

Difficulty Level 2

This project has a medium level of difficulty due to the complexity of the SBOL specification.

Skills

No prior knowledge of biology is necessary. Proficiency in Python programming is required.

Public Repository

http://github.com/udp/pysbolgraph

Potential Mentors

Chris Myers, University of Utah, US (myers@ece.utah.edu) James McLaughlin, Newcastle University, UK (j.a.mclaughlin@newcastle.ac.uk)

Contact

For more information, please comment on this issue or contact James McLaughlin.

jamesamcl commented 5 years ago

@VIGS25 Sorry for the late reply - glad to hear you're interested in the project. I've had some interest from others via email too, so I'm going to open some issues on the repo later to give some indication as to what needs working on. 👍

FabricioLayedra commented 5 years ago

@udp I am interested in working on this project. I worked on parsing FASTA data in a project for a hackathon before and I am proficient in Python for data Analytics.

My background is Computing Science with a minor in Big Data Analytics. I sent you an email.

cjmyers commented 5 years ago

@FabricioLayedra glad to hear of your interest. Please use this tracker to communicate with James and I as you take a closer look.

hdsingh commented 5 years ago

Hi, I am second year under-graduate pursuing Bachelor of Technology (Computer Science) in India.

I would love contributing to Pysbolgraph for GSOC. I have looked at the resources mentioned above. This is is the task list I have prepared to get started:

I would be sharing my progress here.

Thanks!!

cjmyers commented 5 years ago

Sounds good. Look forward to hearing your progress and any questions you might have.

On Mar 18, 2019, at 5:23 AM, Harman Deep Singh notifications@github.com wrote:

Hi, I am second year under-graduate pursuing Bachelor of Technology (Computer Science) in India.

I would love contributing to Pysbolgraph for GSOC. I have looked at the resources mentioned above. This is is the task list I have prepared to get started:

Understand SBOL-data-model-2 http://sbolstandard.org/wp-content/uploads/2016/06/SBOL-data-model-2.2.1.pdf. Started Get overview of pySBOL https://pysbol2.readthedocs.io/en/latest/index.html Solve issues related to udp/pysbolgraph https://github.com/udp/pysbolgraph I would be sharing my progress here.

Thanks!!

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/129#issuecomment-473871432, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWD93GHhZkHd053RD7E00e2mZ-w7RRCks5vX3dOgaJpZM4Z5hun.

yash170106065 commented 4 years ago

can i work on this??

khanspers commented 4 years ago

Hi. Please contact the potential mentors directly (contact info above). If there is interest, this could be run as an NRNB Academy project.

cjmyers commented 4 years ago

This has been supported outside of GSoC.