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Main documentation site for NRNB GSoC project ideas and resources
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Generating detailed genetic logic circuit models using GeneTech #150

Closed hasanbaig closed 4 years ago

hasanbaig commented 4 years ago

Background

GeneTech (extracted from Genetic Technology mapping) is a tool which allows a user to generate genetic logic circuits only by specifying the logical function desired to be achieved in a living cell. It does not require a user (either biologist or a computer scientist) to learn any programming language. All what it requires a user to specify a desired logical function in the form of simple Boolean Algebra.

The tool first performs logic optimization, followed by synthesis and technology mapping using a library of genetic logic gates. In the end, GeneTech performs technology mapping to generate all the feasible circuits, with different genetic gates, to achieve the desired logical behavior.

GeneTech generates the circuits in the form of SBOL data, SBOL visual and Logic circuit schematic.

Though GeneTech generates the possible solutions in the form of SBOL files, the one thing where it lags is that it does not generate the corresponding stream of DNA basepairs.

Goal

Depending on the number of students work on this project, it would be required that GeneTech should be able to generate the corresponding DNA code of an entire circuit as well as each individual component of a circuit. Another aspect the student may choose to work on is the inclusion of SBOL-SBML conversion tool in GeneTech. There are also possibilities for other proposals related to GeneTech development. For more information, contact directly to the assigned mentor.

Difficulty Level 2

The project has a medium level of difficulty due to challenge of extracting DNA code of circuits' component from online repository.

Skills

Students need not have any prior experience of biology. They must have a good development skills using Python. A knowledge about SBOL, and JAVA is a plus. Students will be required to familiarize themselves with core aspects of the SBOL data specification and SBOL Visual specification.

Python (essential) Java, SBOL (nice to have)

Public Repository

GeneTech

Potential Mentors

Hasan Baig (hbaig@uchc.edu) Ritwik Aggarwal (rtwkaggarwal@gmail.com)

Contact

For more information, you may send an email to Hasan Baig

Aoun-Hussain commented 4 years ago

I am a student from Karachi, Pakistan. I have previously worked on research projects related to Wireless Communications and IoT and simulated them on Python using various libraries. I have never worked on an open source project before. This project is interesting and I would want to work on it!

hasanbaig commented 4 years ago

Thanks for your interest @Aoun-Hussain . Please share your CV. We will talk further about it.

Aoun-Hussain commented 4 years ago

Thanks for your interest @Aoun-Hussain . Please share your CV. We will talk further about it.

Sure, I have emailed you my CV @hasanbaig .

ashadhaz commented 4 years ago

Hey my name is Asad Hazariwala and I am a third year undergraduate student. I would like to contribute to this project. I have mailed you my resume.

hasanbaig commented 4 years ago

Hi Asad, Thanks for your interest. I have received it already. Please check my response and get back to me when you are done with the instructions. regards HB

ShreyanshTripathi commented 4 years ago

Hi @hasanbaig I am a third year undergraduate student. I have worked on several projects and internships and have a good experience in Python and Java. I am interested in taking this project up for GSoC. I have mailed you my CV. Please have a look and let me know of further process.

hasanbaig commented 4 years ago

Hi @hasanbaig I am a third year undergraduate student. I have worked on several projects and internships and have a good experience in Python and Java. I am interested in taking this project up for GSoC. I have mailed you my CV. Please have a look and let me know of further process.

Hi @ShreyanshTripathi I have received your email. I will check your CV and get back to you.

ms03831 commented 4 years ago

Dear @hasanbaig, I have been reading up on this project for the past 3 weeks and am interested in working on this project. I have emailed you my CV. I have about 3 years of extensive experience in Python programming as it is my language of choice. I'm also extremely comfortable with object-oriented programming and familiar with Java as well. I look forward to hearing back from you.

hasanbaig commented 4 years ago

Dear @ms03831, Thanks for reaching out to me. I have received your CV. Kindly proceed ahead with proposal preparation. We can be in touch over the email.

cjmyers commented 4 years ago

Why did you close this issue? Are you no longer planning to have anyone work on this?

On Mar 29, 2020, at 10:08 AM, Hasan Baig notifications@github.com wrote:

Closed #150 https://github.com/nrnb/GoogleSummerOfCode/issues/150.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/150#event-3176049325, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA2YH52SJKFFJNKIQJ3PW5TRJ5XAJANCNFSM4K4UBG4Q.

hasanbaig commented 4 years ago

Hi Chris, I have closed it because I have couple of students applying for this project now. I am not sure if I can take out time to review more proposals if anyone comes forward.

cjmyers commented 4 years ago

Has to be open to get a student

Chris

Sent from my iPhone

On Mar 29, 2020, at 11:39 AM, Hasan Baig notifications@github.com wrote:

 Hi Chris, I have closed it because I have couple of students applying for this project now. I am not sure if I can take out time to review more proposals if anyone comes forward.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

hasanbaig commented 4 years ago

I see. I have reopened it again.

khanspers commented 4 years ago

Active project for GSoC 2020, closing here.