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Add SBOL Import and Export Capabilities to the Synthetic Biology Tool TinkerCell #72

Closed hsauro closed 4 years ago

hsauro commented 7 years ago

Background

TinkerCell is a widely used open source network design and simulation application tool for synthetic biology (tinkercell.com). The software allows synthetic biologists to design new synthetic circuits and simulate them. TinkerCell is written in C++ and runs on Windows, Mac and Linux. It uses Qt as the GUI framework.

The synthetic biology open language (SBOL: sbolstandard.org) is an international standard for exchanging synthetic biology designs. Many software tools and data repositories now support SBOL which allows designs to be easily downloaded from the internet and loaded into a variety of tools. Currently TinkerCell only has very limited support for SBOL.

Goal

The goal of this project is to enhance TinkerCell so that is can read and write standard SBOL Version 2 and access circuits from well known repositories such as JBEI in the US and the SBOL Stack in the UK. SBOL is supported by the libSBOL library (https://github.com/SynBioDex/libSBOL) and the work would require this library to be intergrated into TinkerCell.

If successful a research paper would be written and submitted for publication.

Skills Required:

Cross-platform development in C++ using CMake. Familiarity with Qt and an interest in synthetic biology would be beneficial.

Public Repository

https://github.com/dchandran/tinkercell

Potential Mentors

Herbert M Sauro Kyle Medley Kiri Choi Bryan Bartley

Main Contact

Herbert M Sauro

References

TinkerCell: modular CAD tool for synthetic biology Deepak Chandran, Frank T Bergmann and Herbert M Sauro Journal of Biological Engineering 2009, 3:19

lajulienn commented 7 years ago

Hello! I got really interested about this project! The issue is suitable for me because I have quite good skills in programming on C/C++ (now I'm a second-year student of MIPT, department of Innovation and High Technology) and also I have recently realised that I'm excited about bioinformatics. Furthermore, I'm ready to study everything which is required from me to know (there's enough time for that now). So could you please tell me what should I know about synthetic biology for participating? Can you recommend some literature? And one more thing: may I have after that some small (or not small) task for you to evaluate my skills?

hsauro commented 7 years ago

Thanks for getting in touch, c++ knowledge is a must, the rest such as QT and sbol can probably be picked up on as needed. As for reading, the sbol docs at sbolstandard.org will be important, and reading about qt will be important. Basic knowledge of molecular biology is also obviously important. You don't have to know much about synthetic biology, basic molecular biology knowledge is more important. Getting to know the tinkercell sourcecode is probably the biggest hurdle.

lajulienn commented 7 years ago

Thank you very much! I'll immediately start studying all mentioned above.

SamuelSauce commented 6 years ago

Hello! I am posting this comment in regards to my interest in the project. I'm actually a student here at the University of Utah and have been in touch with Chris Myers, as my good friend worked on a GSoC project for him last summer. I have managed to get a hold of, Engineering Genetic Circuits, by Chris Myers, which should give me the necessary knowledge of molecular biology. Additionally I would like say that I am proficient in C++/Qt, as my software practice class required a few projects designed through Qt. Besides downloading TinkerCell, and getting familiar with the source code, as well as reading through some molecular biology, if there is anything you would recommend to strengthen my proposal that would be excellent feedback.

hsauro commented 4 years ago

Yes it is, but it’s a complex problem to resolve.

H

On Sun, Oct 20, 2019 at 9:39 PM Vignesh Ram Somnath < notifications@github.com> wrote:

Hi @hsauro https://github.com/hsauro, is this still an open problem?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/72?email_source=notifications&email_token=AAIBSDTZX3N4O3LEVI7J4DLQPUXBBA5CNFSM4C4OZMQKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBZA5DQ#issuecomment-544345742, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIBSDUFKHL4AWXMUVO6FZTQPUXBBANCNFSM4C4OZMQA .

-- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org hsauro@uw.edu Books: http://books.analogmachine.org/