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nrnb / GoogleSummerOfCode

Main documentation site for NRNB GSoC project ideas and resources
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Develop a web service which provides simulation / steady state analysis / parameter estimation with SBML models #82

Closed funasoul closed 7 years ago

funasoul commented 7 years ago

Background

Currently, there are over 280 software packages which support SBML. While there are enormous numbers of software packages to support mathematical modeling, simulation and analysis tools for research related to systems biology, it is still quite hard for a software tool to solve all required tasks on a single application so that users have to install several different software packages and configure them to work on their platform. This process is not a hard task for computer scientists, but sometimes it is a big hurdle for biologists, who are not familiar with tweaking computers and operating systems. Systems biology operates at the interface of mathematics, computer science, and biology, so that developing a software tool which has a user-friendly UI, is easy to install and easy to manipulate is still an important task in this field.

This summer, we would like to mentor a student in developing a web service with Graphical User Interface (GUI) which provides ODE (Ordinary Differential Equation) simulation, steady state analysis, and parameter estimation which are commonly used in this field. To make an install procedure as easy as possible, we decided to provide this service as a web service so that users do not have to install any software tool on their computers.

Goal

The project could be split down into following 4 tasks.

Following simulator / analysis tools will be used to run simulations etc.

Student requirements

Students should be familiar with the Java™ and JavaScript programming. Better to have an experience in numerical calculation, but not required.

Potential Mentors

PratyushTalreja commented 7 years ago

Hi

I am pursuing Masters from Indian Institute of Technology Bombay. I had completed Bachelors in Information Technology. I am having a work experience of 1 year working with Cognizant Technology Solutions in Java domain. I am having hands on experience working with JavaScript during my work experience and previous year Google Summer of Code project. Also, I am having experience working with Web Services because of my course projects.

I am very much interested in working for this project. Can you guide me with the further steps.

Thank you.

funasoul commented 7 years ago

Hi,

Thank you for your interest in our project. At first, if you have not yet tried Docker, then please have a try and launch a web server (nginx, apache httpd, etc) on a virtual machine. It will make you easy to try and test your web service. Next step is to look into APIs. If you are familiar with Java, then I prefer you to look into Simulation Core Library which is a pure Java library for simulating SBML models. Also, understanding SBML (not completely, but the concept of SBML and its example models) will be a help. For example, the specification of SBML Level 3 Version 1 Core will be a good starting point.

Hope this helps.

PratyushTalreja commented 7 years ago

Thank you @funasoul for the detailed information. I have started working on the tasks and will keep you posted in case of any difficulty with any task.

draeger commented 7 years ago

Dear @PratyushTalreja, if needed contact me via e-mail and I will provide you with a few examples for excellent student proposals from earlier years that you can use to shape your proposal.

PratyushTalreja commented 7 years ago

Thanks @draeger . I have sent you a mail.

TakahiroYamada commented 7 years ago

Hi, I am Doctor student from next year from Keio University, Japan. I mainly researched biological phenomenon using the methodology of systems biology in Bachelor and Master course. I have experience of ODE simulation and steady state analysis using COPASI with my coworker and I understood detail algorithm of these method. I have knowledge of Java language and have experience of implementing Runge-Kutta simulator. I'm very interested in this project. I'm not familiar with JavaScript now but I'm willing to learn and apply for this project.

Thank you.

draeger commented 7 years ago

@TakahiroYamada: do you have an e-mail address to contact you? You can also directly contact the mentors listed above via e-mail and we will assist you putting your proposal together.

TakahiroYamada commented 7 years ago

Thanks @draeger. I have an e-mail address. I will send you my proposal via e-mail after writing.

draeger commented 7 years ago

@TakahiroYamada: sounds good, thanks.

niko-rodrigue commented 7 years ago

Might be nice to have a look as well, time permitting, at tools like https://pdp10.github.io/sbpipe/ who already do a lot works for complex parameter estimation tasks.

niko-rodrigue commented 7 years ago

Also something that modelers struggle a lot to do in standard tools is bifurcation analysis.

khanspers commented 7 years ago

GSoC 2017 selected project