#4 GSoC’18 – Repeated tasks

This week I have been working on implementing support for RepeatedTasks in SBSCL which was added in SED-ML L1V2. Briefly, RepeatedTaks is a looping construct added to SED-ML to run the same tasks multiple times. Before every iteration, there is also an option to reset model parameters or update them similar to a looping construct in any programming language.

I have only partially implemented it. There are two challenges that I need to overcome: a) Handling nested repeatedTask, and b) Merging the output of repeatedTasks.  I will be discussing possible solutions to address these issues with my mentors soon and implementing them.

An extra feature that I worked on adding to SBSCL was support for OneStep and SteadyState simulations. These elements were also added to SED-ML L1V2. Basically, an ODE simulation can be UniformTimeCourse, OneStep or SteadyState. The first type of simulation was already implemented in SBSCL while the other methods need to be incorporated. I have already added OneStep simulation since the idea is simple: only generate one simulation point after given time. The steadyState simulation is something which will be implemented in the upcoming week after discussing the potential solutions with my mentors. In layman’s terms, SteadyState simulation means simulate till a point when population stops changing.

I will keep posting updates as and when I have. Till then, have a good one!

#3 GSoC’18 – Coding begins

The coding phase for Google Summer of Code (GSoC) started on May 14th and since then I have spent day and night just reading, understanding and writing code for SBSCL.

Build process:

I talked about build process last week but this week I tried something fancy! This week, I tried building SBSCL using maven instead of m2e plugin directly from command-line. You might think that since everything works fine in eclipse, it should also be simple with mvn but that’s not the case. To cut things short, I recommend using Eclipse as the build environment for SBSCL and since the latest version comes with m2e already, the build process is a piece of cake. All you have to do is right-click > run as > maven build (or maven install).

  1. import java folder in eclipse
  2. right click on the project and Run As > maven build

If you get dependency missing errors, you need those jar files to build. Most jars files required by SBSCL are available in maven central repo except – cplexGLPKSolver, lpsolve and  SCPsolver. Note that sometimes maven might give error: unknown build environment. This might be if you are using JRE instead of JDK. You can solve this by downloading JDK or retrying to apply run as command.

Once you have all the depdency JAR files with you, they need to be added to lib/{dependency_name}. You will find empty folders inside lib folder already created for you to place the jar files.

For those of you who still want to try maven to build it, you will have to edit pom.xml file to include all the source folders to classpath and then run following command to create a standalone jar.

mvn clean package install assembly:single

After build process, the standalone jar file is created in the target folder.

Tests for SBSCL:

Moving on, I focused mainly on trying to run several TestSuites to check existing code of SBSCL. SBML community has a wonderful archive with several models which can be used to test your code. You can download a zip file from their GitHub page. There is also a BioModels database which contains models from several studies. This database is also a wonderful resource to test simulation software.  Similarly, there is an online model database for constraints-based models by BiGG and you can download a zip file containing all the models.

Extending SBSCL to support SED-ML L1V2:

After trying all the examples and testSuites, I started learning more about SED-ML Level 1 Version 2 since SBSCL needs to support repeatedTasks and Range which were added in SED-ML Level 1 Version 2. One interesting thing that I wasn’t able to find was a full testSuite of SED-ML examples similar to SBML. Anyway, I am still working on this task and will post some updates soon.


#2 GSoC’18 – Community bonding

The community bonding phase (of GSoC) is a brief period before the beginning of the actual coding phase where students get to know the organization they are selected for works. I had my first (Hangouts) meeting with my mentors Andreas Dräger, Matthias König and Nicolas Rodriguez where we discussed how NRNB works and what they expect from me as a student. It was exciting to learn about setting up the development environment for the simulation core library (SBSCL) and some other resources such as Github Projects which I will use to setup individual milestones.

Setting the development environment for SBSCL:

Download and install Eclipse IDE (latest version is Oxygen) and git. Once you have Eclipse and git on your computer, simple clone the repo using git clone <repo_name>. As per my discussion with mentors, we decided that I fork SBSCL into my Github before cloning it to be safe. This way, I can play around with the code without worrying about the master branch. Once I cloned the repo, I imported it in Eclipse. Since SBSCL uses Maven for build process, it was pretty easy to setup.

Some of you might run into the problem: Error- Unable to find cplex- and this is because SBSCL’s constraint-based model solver requires IBM’s proprietary linear programming solver library. Fortunately, IBM provides a free student license with the university email and therefore I was able to download jar file and import it as a dependency. Note that current cplex version is and not I wasn’t able to find 12.6 online so I modified the pom.xml file to expect for This worked like a charm! A great thing is that one of my GSoC tasks is to remove this dependency (by using open-source API like SCPSolver) so everyone can use linear programming feature. I will update about it once I finish implementing it.

Workflow of using the simulation core library

The library contains a folder examples which has simple codes to read, parse and simulate a systems biology model. You can write your own SBML model or download some samples from here – http://www.ebi.ac.uk/biomodels-main/. There are a lot of models there and you can simply try downloading model of the month. Once you have your model you can validate it here – http://sbml.org/validator/

Now, you know that you have a valid SBML model you can try making a new java project and try running the SimulatorExample.java file as your main file for the project. Voila! You will get output of the model as a MultiTable which can be plotted using some Java plotting library (also one of my GSoC tasks).

You can also try running CPLEX solver (if you have license) by using COBRASolverExample.java file found in the example folder.

Remember that you need to import the jar dependencies of simulation core, jlibsedml, commonMath etc. All the dependencies are written in the HelloWord code documentation page of SBSCL which can be found inside doc folder.

Wrapping up, I also found a glitch in the README.md filed which says there are multiple jar files in the dist folder. I changed it and pushed my first commit. Yay! It is in my forked Github though.

Let me know any questions or suggestions in comments 🙂

Getting started

This summer I will be working with a fantastic open-source organization National Resource for Network Biology (NRNB) thanks to Google for accepting my Google summer of code (GSoC) proposal titled “Simulating systems biology models in Java”. The official coding doesn’t begin until May 14th, however, I am currently getting familiar with the open-source practices and my build environment. I have been assigned, three wonderful mentors namely Andreas Dräger, Matthias König and Nicolas Rodriguez who will guide me throughout this process.

This blog is where I intend to share my progress. I look forward to an exciting and productive summer.

What is GSoC?

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Google Summer of Code is a global program focused on bringing more student developers into open source software development. Students work with an open source organization on a 3 month programming project during their break from school. You can know more about it by visiting http://g.co/gsoc

What is NRNB?

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The aim of the NRNB is to advance the new science of Biological Networks through analytic tools, visualizations, databases and computing resources. Biomedical research is increasingly dependent on knowledge of biological networks of multiple types and scales, including gene, protein and drug interactions, cell-cell and cell-host communication, and vast social networks. Our technologies enable researchers to assemble and analyze these networks and to use them to better understand biological systems and, in particular, how they fail in disease. You can learn more about it by visiting http://nrnb.org/