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Tool for predicting effects of variants for any genome in Ensembl or with genome annotation (via GFF). This includes vertebrates and also plants, fungi, protists, metazoa and bacteria. There is a web and a REST API version but the most powerful is the Perl script version. See McLaren et al., 2016, Genome Biology

The gCube System - workspace-application-handler -------------------------------------------------- The workspace-application-handler discovers from Application Profile the url of the application (gCube Apps) that can open the type of workspace item passed in input This software is part of the gCube Framework (https://www.gcube-system.org/): an open-source software toolkit used for building and operating Hybrid Data Infrastructures enabling the dynamic deployment of Virtual Research Environments by favouring the realisation of reuse oriented policies. The projects leading to this software have received funding from a series of European Union programmes including: * the Sixth Framework Programme for Research and Technological Development - DILIGENT (grant no. 004260); * the Seventh Framework Programme for research, technological development and demonstration - D4Science (grant no. 212488), D4Science-II (grant no. 239019),ENVRI (grant no. 283465), EUBrazilOpenBio (grant no. 288754), iMarine (grant no. 283644); * the H2020 research and innovation programme - BlueBRIDGE (grant no. 675680), EGIEngage (grant no. 654142), ENVRIplus (grant no. 654182), Parthenos (grant no. 654119), SoBigData (grant no. 654024); Version -------------------------------------------------- 1.2.0-4.6.1-126630 (2017-09-19) Please see the file named "changelog.xml" in this directory for the release notes. Authors -------------------------------------------------- * Francesco Mangiacrapa (francesco.mangiacrapa-AT-isti.cnr.it), Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" - CNR, Pisa (Italy). Maintainers ----------- * Francesco Mangiacrapa (francesco.mangiacrapa-AT-isti.cnr.it), Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" - CNR, Pisa (Italy). Download information -------------------------------------------------- Source code is available from SVN: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/portlets/user/workspace-application-handler Binaries can be downloaded from the gCube website: https://www.gcube-system.org/ Installation -------------------------------------------------- Installation documentation is available on-line in the gCube Wiki: https://wiki.gcube-system.org/gcube/index.php Documentation -------------------------------------------------- Documentation is available on-line in the gCube Wiki: https://wiki.gcube-system.org/gcube/index.php Support -------------------------------------------------- Bugs and support requests can be reported in the gCube issue tracking tool: https://support.d4science.org/projects/gcube/ Licensing -------------------------------------------------- This software is licensed under the terms you may find in the file named "LICENSE" in this directory.

The source code is used to display pneumococcal compendium: gene expression values, fold changes and correlation values

Beta version of the software and R functions that align and average trajectories of endocytic events imaged with epifluorescence imaging.

The gCube System - tabular-data-unionwizard-widget -------------------------------------------------- tabular-data-unionwizard-widget allows the union of tabular resources This software is part of the gCube Framework (https://www.gcube-system.org/): an open-source software toolkit used for building and operating Hybrid Data Infrastructures enabling the dynamic deployment of Virtual Research Environments by favouring the realisation of reuse oriented policies. The projects leading to this software have received funding from a series of European Union programmes including: * the Sixth Framework Programme for Research and Technological Development - DILIGENT (grant no. 004260); * the Seventh Framework Programme for research, technological development and demonstration - D4Science (grant no. 212488), D4Science-II (grant no. 239019),ENVRI (grant no. 283465), EUBrazilOpenBio (grant no. 288754), iMarine (grant no. 283644); * the H2020 research and innovation programme - BlueBRIDGE (grant no. 675680), EGIEngage (grant no. 654142), ENVRIplus (grant no. 654182), Parthenos (grant no. 654119), SoBigData (grant no. 654024); Version -------------------------------------------------- 1.5.0-4.6.0-125889 (2017-08-01) Please see the file named "changelog.xml" in this directory for the release notes. Authors -------------------------------------------------- * Giancarlo Panichi (giancarlo.panichi-AT-isti.cnr.it), Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" CNR, Pisa IT Maintainers ----------- * Giancarlo Panichi (giancarlo.panichi-AT-isti.cnr.it), Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" CNR, Pisa IT Download information -------------------------------------------------- Source code is available from SVN: https://svn.research-infrastructures.eu/public/d4science/gcube/trunk/portlets/user/tabular-data-unionwizard-widget Binaries can be downloaded from the gCube website: https://www.gcube-system.org/ Installation -------------------------------------------------- Installation documentation is available on-line in the gCube Wiki: https://gcube.wiki.gcube-system.org/gcube/index.php/Tabular_Data_Manager Documentation -------------------------------------------------- Documentation is available on-line in the gCube Wiki: https://gcube.wiki.gcube-system.org/gcube/index.php/Tabular_Data_Manager Support -------------------------------------------------- Bugs and support requests can be reported in the gCube issue tracking tool: https://support.d4science.org/projects/gcube/ Licensing -------------------------------------------------- This software is licensed under the terms you may find in the file named "LICENSE" in this directory.

This repository contains the last release of the code of the variable misuse tool deployment for the DECODER project. This tools allows to detect and repair bugs or errors corresponding to variables within source code files written in Java, C and C++.

This repository contains the Python bindings to the PROSPECT and SAIL leaf and canopy reflectance models, respectively. Both models have been rewritten and coupled in Python, with some changes to improve on efficiency. The bindings implement the following models: PROSPECT: versions 5 and D. Flexibility to add/modify leaf absorption profiles. SAIL: FourSAIL version. The thermal extension of the model is also implemented, although this hasn't been widely tested. Simple Lambertian soil reflectance model

Fiji plugins for qualitative image annotations + analysis workflows This Zenodo entity contains - the supplementary figures to the published article (see reference below) - an archived of the releases (.zip) from the GitHub repository To install the plugins, just activate the Qualitative Annotations update site in Fiji. The latest version of the workflows are available on the GitHub repository or on the KNIME Hub. See the GitHub repository for the documentation or the YouTube tutorials. Zip releases The zip file of the releases contains: - the source code for the Fiji plugins as py files - the KNIME analysis workflows Citation Thomas LSV, Schaefer F and Gehrig J. Fiji plugins for qualitative image annotations: routine analysis and application to image classification [version 1; peer review: awaiting peer review]. F1000Research 2020, 9:1248 (https://doi.org/10.12688/f1000research.26872.1) Version history - v1.0.2bis : Add suppl Figures (pptx) - v1.0.1bis: initial zenodo release with DOI (same as 1.0.1, just newly release to get a DOI) - v1.0.1: initial GitHub release (not archived on Zenodo). A preconfigured Fiji installation is attached to this release on GitHub

ESMF sources used for the regridding benchmark corresponding to the branch ESMF_8_2_0_beta_snapshot_08, which can be obtained with the git command “git clone https://github.com/esmf-org/esmf.git --branch ESMF_8_2_0_beta_snapshot_08 --depth 1”.

Code used for modeling radiocarbon dated wood samples from Ploča Mičov Grad (2018). Software used: OxCal v4.4.2 (Bronk Ramsey, 2020) Presented and analyzed in: Hafner et al. (forthcoming), First Absolute Chronologies of Neolithic and Bronze Age Settlements at Lake Ohrid based on Dendrochronology and Radiocarbon Dating, 2021