Tvb

Release on Pypi

The Datatypes got few new methods.

Jira tasks on this version:

* [TVB-2986] - Import data Lesion2TVB
* [TVB-2122] - Parallelize test suite run
* [TVB-2219] - Project monitor incorrectly pads gain matrix
* [TVB-2634] - Ordering of cortical and subcortical gain rows not respected
* [TVB-2799] - History shape mismatch surface simulation
* [TVB-2902] - Region mapping viewer displays empty navigator windows
* [TVB-2962] - neotraits test fails after numpy upgrade
* [TVB-2990] - default cortex
* [TVB-2991] - Connectivity needs to be transposed for allen_creator.py adaptor and related notebook
* [TVB-3007] - User tab from footer not active on user page
* [TVB-2981] - Review range parameters
* [TVB-2982] - Work on D6.4 report
* [TVB-2983] - VRE integration
* [TVB-2988] - Add comments and review code about Keycloak and OpenShift
* [TVB-2989] - Support context path
* [TVB-2996] - Reporting Period 2
* [TVB-3008] - Prepare, test and do release 2.5
* [TVB-2977] - Some simulation related params should be displayed as symbols in Web GUI
* [TVB-3006] - Integrate Sonar with tvb code

2.4.1TVB_Distribution
Fix Jupyter kernel for Windows/Linux distributions.

Bug
* [[TVB-2984](https://req.thevirtualbrain.org/browse/TVB-2984)] - Jupyther kernel not starting from tvb Dockerfiles

* [TVB-2979] - Replace infinite values with float max in Matrix Viewer

Improvement
* [TVB-2916] - Remove dependency with typing package for python>3.5
* [TVB-2932] - Refactor storage encryption to support multi-pod deploy
* [TVB-2933] - More functionality from exporters could move to tvb-storage
* [TVB-2934] - Review HPC encryption exposed in the StorageInterface
* [TVB-2945] - Keep configuration of monitors throughout simulator page
* [TVB-2947] - Disable editing of monitored variables at simulation branch
* [TVB-2948] - Hide the Tumor Dataset importer from importers list
* [TVB-2964] - Provide option to generate TS file through the console interface

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A,
van der Vlag M, Diaz-Pier S, Peyser A, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A,
Akintoye S, Stahl C, Deco G, McIntosh, Hilgetag C, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie J, Amunts K,
Mersmann J, Jirsa V, Ritter P. https://arxiv.org/abs/2102.05888
Brain simulation as a Service: The Virtual Brain on the European Research Platform EBRAINS.

Improvement
* [TVB-2883] - Branch button should be active only if simulation is finished
* [TVB-2908] - Ensure all operations of PSE are cancelled
* [TVB-2923] - Optimise operations page



Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A,
van der Vlag M, Diaz-Pier S, Peyser A, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A,
Akintoye S, Stahl C, Deco G, McIntosh, Hilgetag C, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie J, Amunts K,
Mersmann J, Jirsa V, Ritter P. https://arxiv.org/abs/2102.05888
Brain simulation as a Service: The Virtual Brain on the European Research Platform EBRAINS.

2.2.2TVB_Distribution
Release notes
* Fix migration of H5 files to work in case truncated files are present

Bug
* [TVB-2925] - Solve truncated H5 files migration related bugs

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A,
van der Vlag M, Diaz-Pier S, Peyser A, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A,
Akintoye S, Stahl C, Deco G, McIntosh, Hilgetag C, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie J, Amunts K,
Mersmann J, Jirsa V, Ritter P. https://arxiv.org/abs/2102.05888
Brain simulation as a Service: The Virtual Brain on the European Research Platform EBRAINS.

2.2.1TVB_Distribution
Release notes
* Fix second startup with SQLite after migrating data from 1.5.8
* Fix second startup with PostgreSQL with clean storage

Bug
* [TVB-2917] - TVB with Postgres startup fails at the second attempt
* [TVB-2921] - TVB with Sqlite and migration does not start at second attempt

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A,
van der Vlag M, Diaz-Pier S, Peyser A, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A,
Akintoye S, Stahl C, Deco G, McIntosh, Hilgetag C, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie J, Amunts K,
Mersmann J, Jirsa V, Ritter P. https://arxiv.org/abs/2102.05888
Brain simulation as a Service: The Virtual Brain on the European Research Platform EBRAINS.

2.2TVB_Distribution
Release Notes
* Make code compatible with Python 3
* Neotraits (splitting the aspects of: datatypes, storage, indexing, web forms)
* Add a REST API
* Support authentication in web with a Keycloak server
* Added encryption mechanism for the TVB storage
* Added encryption mechanism for uploaded data
* Support an HPC backend to run heavy simulations with secured data
* Change the Simulator configuration page towards a wizard structure
* The command API has been improved and can be used individually from the web GUI now
* Use Jinja instead of Genshi for tvb web GUI
* CFF importer was removed
* New export button on datatypes to allow exporting a datatype together with its references.
* Data migration from version 1.5.8 is supported. For data generated with older versions, users should first install 1.5.8 to update their data, and then install 2.2

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A,
van der Vlag M, Diaz-Pier S, Peyser A, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A,
Akintoye S, Stahl C, Deco G, McIntosh, Hilgetag C, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie J, Amunts K,
Mersmann J, Jirsa V, Ritter P. https://arxiv.org/abs/2102.05888
Brain simulation as a Service: The Virtual Brain on the European Research Platform EBRAINS.

* [TVB-2906] - Prepare video of TVB on JupyterHub VRE

Improvement
* [TVB-2880] - Export only view model H5 in simulation ZIP


Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A,
van der Vlag M, Diaz-Pier S, Peyser A, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A,
Akintoye S, Stahl C, Deco G, McIntosh, Hilgetag C, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie J, Amunts K,
Mersmann J, Jirsa V, Ritter P. https://arxiv.org/abs/2102.05888
Brain simulation as a Service: The Virtual Brain on the European Research Platform EBRAINS.