Re: [sbml-interoperability] JSBML Installation

[Andreas Dräger]

Am 21.07.2017 um 04:35 schrieb Deepa <deepama...@gmail.com>:

Hello Everyone,

I am facing an issue with the installation of JSBML. I have downloaded the JSBML 1.2 with dependencies  from sourceforge.
The classpath and path for JRE have been set up.When I click on the jar file it doesn't get executed for some reason.
Am I missing something?

Thanks a lot for your time .

PS:Other packages like KEGGTranslator and SBMLSqueezer work fine.

Deepa

Dear Deepa,

JSBML is not intended to be a stand-alone tool that you could execute by clicking on a JAR file. Tools such as KEGGtranslator and SBMLsqueezer include JSBML as their internal library for parsing, manipulating, and writing SBML language elements. In order to work with JSBML directly, you will need to implement some Java program (or use any other language that creates and understands Java Byte Code or that can access this Byte code).

What you can do here is to follow the instructions in the Users' Guide (http://sbml.org/Software/JSBML/docs) or look up the API documentation and write your own program that reads SBML files and strips out the information you need.

(Please note, I am transferring this conversation to the more specific list jsbml-development where all future discussion about this topic should take place, so please remove sbml-inter...@googlegroups.com when answering to this e-mail.)

I hope this helps!

With best regards

Dr. Andreas Draeger
Principal Investigator
---
University of Tübingen
Center for Bioinformatics Tübingen (ZBIT)
Applied Bioinformatics Group
Sand 14 · Office #C320 · 72076 Tübingen · Germany
Phone: +49-7071-29-70459 · Fax: +49-7071-29-5152
Web: http://draeger-lab.org · Twitter: @dr_drae
YouTube: https://www.youtube.com/channel/UCp7fWtXGFOIjV35u7ONiVbg

[Nicolas Rodriguez]

On 21/07/17 07:50, Andreas Dräger wrote:

Am 21.07.2017 um 04:35 schrieb Deepa <deepama...@gmail.com>:

Hello Everyone,

I am facing an issue with the installation of JSBML. I have downloaded the JSBML 1.2 with dependencies  from sourceforge.
The classpath and path for JRE have been set up.When I click on the jar file it doesn't get executed for some reason.
Am I missing something?

Thanks a lot for your time .

PS:Other packages like KEGGTranslator and SBMLSqueezer work fine.

Deepa

Dear Deepa,

JSBML is not intended to be a stand-alone tool that you could execute by clicking on a JAR file. Tools such as KEGGtranslator and SBMLsqueezer include JSBML as their internal library for parsing, manipulating, and writing SBML language elements. In order to work with JSBML directly, you will need to implement some Java program (or use any other language that creates and understands Java Byte Code or that can access this Byte code).

What you can do here is to follow the instructions in the Users' Guide (http://sbml.org/Software/JSBML/docs) or look up the API documentation and write your own program that reads SBML files and strips out the information you need.

(Please note, I am transferring this conversation to the more specific list jsbml-development where all future discussion about this topic should take place, so please remove sbml-inter...@googlegroups.com when answering to this e-mail.)

Also, I will send to Deepa and the list an eclipse project ready to be used and that contain several examples files that are using jsbml to do some complex real life examples. like creating a submodel given a set of kegg ids but I need a bit of time and I hope to send it around on Monday or Tuesday.

cheers,
Nico

[Nicolas Rodriguez]

Hi Deepa,

You can find a ready to use eclipse project at https://github.com/sbmlteam/jsbml/raw/master/doc/tutorials/JSBML-Tutorial.zip.

Once you unzip it, you will have further instructions in a document on how to install the project into eclipse. If you are not familiar with coding in java, you should probably start by following the tutorial before going further. As Andreas mentioned, you will need to write code in order to use JSBML.
I have added a more complex example in 'JSBML-Tutorial-HandsOn/src/org/sbml/jsbml/examples/SubModelExample.java', it will show you how to read annotations from a text file and filter an sbml file using those annotations to create a submodel (you need to have java 1.8 for this example).

cheers,
Nico