Release of Tellurium 2.0
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Jk Medley
Oct 12, 2017, 3:08:51 PM10/12/17
to sbml-discuss
Dear SBML Community,
We are pleased to announce the release of version 2.0 of Tellurium. This version contains major improvements to SED-ML and COMBINE archive handling. Kudos go to Matthias König for leading this effort. Also new in this version is a Notebook environment similar to Jupyter which supports specialized notebook cells for human-readable representations of SBML models and COMBINE archives (including syntax highlighting). Our goal is to make it easy to work with systems biology community standards by offering the same level of tool support as a regular programming language, and the Notebook viewer brings us closer to this goal.
Installation:
Installation instructions can be found here.
Distribution:
This version is distributed in three formats: The Notebook app, PyPI, and the Spyder IDE used in Tellurium 1.0. The reason for this is that we want to appeal to users across the spectrum, from developers to modelers, and there really is not a one-size-fits-all approach. Tellurium supports Python 2.7, 3.4, 3.5, and 3.6 for 64-bit Mac, Linux, and Windows operating systems.
Additional tips:
For testing COMBINE archive import, I recommend trying the example archives from the SED-ML Web Tools. JWS Online archives also appear to work, although our testing has not been exhaustive. We recently became aware of the new BioModels COMBINE archives. These cannot be imported yet because they are SBML-only but we plan on implementing support as soon as possible. Please let us know if you have trouble during installation or need help.
Regards,
Kyle Medley
We are pleased to announce the release of version 2.0 of Tellurium. This version contains major improvements to SED-ML and COMBINE archive handling. Kudos go to Matthias König for leading this effort. Also new in this version is a Notebook environment similar to Jupyter which supports specialized notebook cells for human-readable representations of SBML models and COMBINE archives (including syntax highlighting). Our goal is to make it easy to work with systems biology community standards by offering the same level of tool support as a regular programming language, and the Notebook viewer brings us closer to this goal.
Installation:
Installation instructions can be found here.
Distribution:
This version is distributed in three formats: The Notebook app, PyPI, and the Spyder IDE used in Tellurium 1.0. The reason for this is that we want to appeal to users across the spectrum, from developers to modelers, and there really is not a one-size-fits-all approach. Tellurium supports Python 2.7, 3.4, 3.5, and 3.6 for 64-bit Mac, Linux, and Windows operating systems.
Additional tips:
For testing COMBINE archive import, I recommend trying the example archives from the SED-ML Web Tools. JWS Online archives also appear to work, although our testing has not been exhaustive. We recently became aware of the new BioModels COMBINE archives. These cannot be imported yet because they are SBML-only but we plan on implementing support as soon as possible. Please let us know if you have trouble during installation or need help.
Regards,
Kyle Medley
Matthias König
Oct 13, 2017, 3:33:51 AM10/13/17
to sbml-d...@googlegroups.com
Additional Info
For testing the COMBINE archive and SED-ML support all SED-ML specification examples are available for download as COMBINE archives with reference results from
https://sed-ml.github.io/examples.html
For testing the COMBINE archive and SED-ML support all SED-ML specification examples are available for download as COMBINE archives with reference results from
https://sed-ml.github.io/examples.html
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Dr. Matthias König
Junior Group Leader LiSyM - Systems Medicine of the Liver
Humboldt-University Berlin, Institute of Biology, Institute for Theoretical Biology
https://www.livermetabolism.com
koni...@googlemail.com
Tel: +49 30 20938450
Tel: +49 176 81168480
Junior Group Leader LiSyM - Systems Medicine of the Liver
Humboldt-University Berlin, Institute of Biology, Institute for Theoretical Biology
https://www.livermetabolism.comkoni...@googlemail.com
Tel: +49 30 20938450
Tel: +49 176 81168480
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