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Deliverable Report D6.6 Enanomapper Final Dissemination Report

Bengt Fadeel Malahat Mousavi
The key objectives of WP6 are to disseminate and raise awareness of the scientific results, tools and applications developed in the eNanoMapper project among the user communities in academia and industry, and to provide training on these eNanoMapper tools, through online seminars, tutorials, and training events (workshops). In the third year of the project, the partners have produced a series of tutorials on tools developed in the technical workpackages and organized several workshops including the...

Deliverable Report D5.7 Final Report On User Applications

Philip Doganis Lucian Farcal
Deliverable 5.7 reports on the Tasks 5.3 and 5.9 on the user applications achievements. The application infrastructure developed within eNanoMapper project aims to support the data management in the area of nanosafety research and to enable an integrated approach for the risk assessment of nanomaterials. To achieve these, eNanoMapper developed an ontology, a data infrastructure and modelling tools with applicability in risk assessment of nanomaterials. eNanoMapper developed resources and tools for predicting toxicity of nanomaterials...

Deliverable Report D3.1 Technical Specification And Initial Implementation Of The Protocol And Data Management Web Services

Bengt Fadeel Philip Doganis
We reviewed the current state of the art of availability and requirements for nanomaterial databases, through reviewing the literature, online resources, engaging in discussions with the NanoSafety Cluster working groups and using the results of a community-based requirement analysis. The eNanoMapper data architecture was developed and consists of a set of web services, providing access to experimental protocols and data, search service and modules, facilitating linking and data transfer between third party databases. This design...

Bridgedb/Bridgedb: Bridgedb 2.2.2

Christian Y. Brenninkmeijer, Stian Soiland-Reyes, Egon Willighagen, Anders Riutta, Alexander Pico, Randy Kerber, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
BridgeDb v2.2.2 is a minor bug fix release since v2.2.1. Fixes: recognition of the new HMDB identifiers reduces the size of Ant-based distributions (with jars that support OSGi) fixed the MIRIAM urn for some UniProt identifiers

Bridgedb/Bridgedb: Bridgedb 2.2.0 Released

Christian Y. Brenninkmeijer, Stian Soiland-Reyes, Egon Willighagen, Anders Riutta, Alexander Pico, Randy Kerber, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
Major BridgeDb release, to be picked up by all downstream projects and users. The changes include more liberal loading of Derby files, new data sources (EPA CompTox Dashboard, BRENDA Ligands, MetaboLights), updated link out patterns, and the QC tool reports more information, including the overall identifier and mapping counts. Furthermore, it includes a considerable amount of work by the Open PHACTS projects, as detailed in a few past internal releases.

Bridgedb/Bridgedb: Bridgedb 2.2.1

Christian Y. Brenninkmeijer, Stian Soiland-Reyes, Egon Willighagen, Anders Riutta, Alexander Pico, Randy Kerber, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
BridgeDb v2.2.1 is a minor bug fix release since v2.2.0. Fixes: IDMapperUniprot does not follow relative redirects org.bridgedb jars published in Maven Central The release to Maven Central mean you do no longer need to compile BridgeDb or add a <repository> to use BridgeDb JARs as a binary dependencies. The Maven build system will take care of transitive dependencies (e.g. other parts of BridgeDb that is needed) The below examples assume you need just org.bridgedb.bio,...

Bridgedb/Bridgedb: Bridgedb 2.3.0

Christian Y. Brenninkmeijer, Egon Willighagen, Stian Soiland-Reyes, Anders Riutta, Ian Dunlop, Alexander Pico, Randy Kerber, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
Major BridgeDb release, to be picked up by all downstream projects and users. The changes include an update for the PICR client, better documentation, updated Open PHACTS URIs, minor updates to various data sources, added "Brachypodium distachyon" as recognized species, removed Uniprot-SwissProt as data source (just use Uniprot-TrEMBL), and the URL of the webservice can now be changed from the command line.

Enabling Open Science: Wikidata For Research

Daniel Mietchen, Gregor Hagedorn, Egon Willighagen, Mariano Rico, Asuncion Gomez-Perez, Eduard Aibar, Karima Rafes, Cécile Germain, Alastair Dunning, Lydia Pintscher, Daniel Kinzler & Anonymous
Wiki4R will create an innovative virtual research environment (VRE) for Open Science at scale, engaging both professional researchers and citizen data scientists in new and potentially transformative forms of collaboration. It is based on the realizations that (1) the structured parts of the Web itself can be regarded as a VRE, (2) such environments depend on communities, (3) closed environments are limited in their capacity to nurture thriving communities. Wiki4R will therefore integrate Wikidata, the...

Openrisknet, An Open E-Infrastructure To Support Data Sharing, Knowledge Integration And In Silico Analysis And Modelling In Risk Assessment

Thomas Exner, Joh Dokler, Daniel Bachler, Lucian Farcal, Chris Evelo, Egon Willighagen, Marc Jacobs, Philip Doganis, Haralambos Sarimveis, Iseult Lynch, Stefan Kramer, Cedric Notredame, Danyel Jennen, Georgios Gkoutos, Ola Spjuth, Paul Jennings, Tim Dudgeon, Frederic Bois & Barry Hardy
OpenRiskNet (https://openrisknet.org/) is an EU funded infrastructure project with the main objective to develop an open e-infrastructure providing resources and services to a variety of industries requiring risk assessment, including chemicals, cosmetic ingredients, drugs and nanomaterials. The OpenRiskNet approach is to work on different case studies to test and evaluate requirements to overcome the fragmentation of data and tools and to provide solutions improving the harmonization of data, usability and interoperability of application programming interfaces...

Openrisknet, An Open E-Infrastructure To Support Data Sharing, Knowledge Integration And In Silico Analysis And Modelling In Risk Assessment

Thomas Exner, Joh Dokler, Daniel Bachler, Lucian Farcal, Chris Evelo, Egon Willighagen, Marc Jacobs, Philip Doganis, Haralambos Sarimveis, Iseult Lynch, Stefan Kramer, Cedric Notredame, Danyel Jennen, Georgios Gkoutos, Ola Spjuth, Paul Jennings, Tim Dudgeon, Frederic Bois & Barry Hardy
OpenRiskNet (https://openrisknet.org/) is an EU funded infrastructure project with the main objective to develop an open e-infrastructure providing resources and services to a variety of industries requiring risk assessment, including chemicals, cosmetic ingredients, drugs and nanomaterials. The OpenRiskNet approach is to work on different case studies to test and evaluate requirements to overcome the fragmentation of data and tools and to provide solutions improving the harmonization of data, usability and interoperability of application programming interfaces...

Cdk: Cdk Release 1.5.11

Egon Willighagen, John May, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Yap Chun Wei, Daniel Szisz, Stephan Beisken, Tomáš Pluskal, Mark Williamson, Arvid Berg, Aclarkxyz, Ralf Stephan, Ngn, Klas Jönsson, Dmitry Katsubo, Oliver Stueker, AndyHowlettGitHub, Uli Köhler, Cyrus Harmon, Sambitgaan, Zachcp, Rafeli … & Carl Mäsak
https://github.com/cdk/cdk/wiki/1.5.11-Release-Notes

Cdk: Cdk Release 1.5.12

John May, Egon Willighagen, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Yap Chun Wei, Daniel Szisz, Stephan Beisken, Tomáš Pluskal, Mark Williamson, Arvid Berg, Alex Clark, Ralf Stephan, Nina Jeliazkova, Klas Jönsson, Kdole, AndyHowlettGitHub, Dmitry Katsubo, Oliver Stueker, Uli Köhler, Cyrus Harmon, Sambitgaan, Zachcp … & Carl Mäsak
1.5.12 Release Note

Cdk: Cdk Release 1.5.7

Egon Willighagen, John May, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Daniel Szisz, Stephan Beisken, Yap Chun Wei, Mark Williamson, Arvid Berg, Rwst, Ngn, Aclarkxyz, KlasJoensson, Dmitry Katsubo, Oliver Stueker, AndyHowlettGitHub, Tomas-Pluskal, Uli Köhler, Cyrus Harmon, Sambitgaan, Rafeli, PeterOdeus … & Carl Mäsak
1.5.7 Release Notes

Cdk: Cdk Release 1.5.8

Egon Willighagen, John May, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Daniel Szisz, Stephan Beisken, Yap Chun Wei, Mark Williamson, Arvid Berg, Rwst, Ngn, Aclarkxyz, KlasJoensson, Dmitry Katsubo, Oliver Stueker, AndyHowlettGitHub, Tomas-Pluskal, Uli Köhler, Cyrus Harmon, Sambitgaan, Rafeli, PeterOdeus … & Carl Mäsak
1.5.8 Release Notes

Cdk: Cdk Release 1.5.9

Egon Willighagen, John May, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Daniel Szisz, Stephan Beisken, Yap Chun Wei, Mark Williamson, Arvid Berg, Ralf Stephan, Ngn, Aclarkxyz, KlasJoensson, Dmitry Katsubo, Oliver Stueker, AndyHowlettGitHub, Tomas-Pluskal, Uli Köhler, Cyrus Harmon, Sambitgaan, Rafeli, PeterOdeus … & Carl Mäsak
Full Release Notes

Cdk: Cdk Release 1.5.10

Egon Willighagen, John May, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Daniel Szisz, Stephan Beisken, Yap Chun Wei, Mark Williamson, Tomas-Pluskal, Arvid Berg, Ralf Stephan, Ngn, Aclarkxyz, KlasJoensson, AndyHowlettGitHub, Dmitry Katsubo, Oliver Stueker, Uli Köhler, Cyrus Harmon, Sambitgaan, Rafeli, PeterOdeus … & Carl Mäsak
https://github.com/cdk/cdk/wiki/1.5.10-Release-Notes

Cdk: Cdk Release 1.5.7

Egon Willighagen, John May, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Daniel Szisz, Stephan Beisken, Yap Chun Wei, Mark Williamson, Arvid Berg, Rwst, Ngn, Aclarkxyz, KlasJoensson, Dmitry Katsubo, Oliver Stueker, AndyHowlettGitHub, Tomas-Pluskal, Uli Köhler, Cyrus Harmon, Sambitgaan, Rafeli, PeterOdeus … & Carl Mäsak
1.5.7 Release Notes

Cdk/Cdk: Cdk 1.5.15

John Mayfield, Egon Willighagen, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Tomáš Pluskal, Yap Chun Wei, Daniel Szisz, Mark Williamson, Nikolay Kochev, Nina Jeliazkova, Arvid Berg, Alex Clark, Ralf Stephan, Oliver Stueker, Kdole, Klas Jönsson, Kaibioinfo, Dmitry Katsubo, AndyHowlettGitHub, Uli Köhler, Cyrus Harmon, Sambitgaan … & LuisFF
The Chemistry Development Kit

Cdk/Cdk: Cdk 2.0

John Mayfield, Egon Willighagen, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Tomáš Pluskal, Kazuya Ujihara, Yap Chun Wei, Daniel Szisz, Mark Williamson, Nikolay Kochev, Nina Jeliazkova, Arvid Berg, Alex Clark, Ralf Stephan, Oliver Stueker, Kdole, Klas Jönsson, Kaibioinfo, Dmitry Katsubo, AndyHowlettGitHub, Uli Köhler, Cyrus Harmon … & LuisFF
The Chemistry Development Kit

Cdk/Cdk: Cdk 1.5.14

John Mayfield, Egon Willighagen 0000-0001-7542-0286, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Tomáš Pluskal, Yap Chun Wei, Daniel Szisz, Mark Williamson, Nikolay Kochev, Nina Jeliazkova, Arvid Berg, Alex Clark, Ralf Stephan, Klas Jönsson, Kdole, Stephan Beisken, Kaibioinfo, Dmitry Katsubo, Oliver Stueker, AndyHowlettGitHub, Cyrus Harmon, Uli Köhler … & PeterOdeus
The Chemistry Development Kit

Enanomapper Applications To Support The Risk Assessment Of Nanomaterials

Lucian Farcal, Philip Doganis, George Drakakis, Haralambos Sarimveis, Micha Rautenberg, Christoph Helma, Denis Gebele, Nikolay Kochev, Vedrin Jeliazkov, Nina Jeliazkova, Malahat Mousavi, Bengt Fadeel, Vesa Hongisto, Penny Nymark, Pekka Kohonen, Roland Grafström, Jiakang Chang, Gareth Owen, Friederike Ehrhart, Linda Rieswijk, Egon Willighagen, Spela Hardy & Barry Hardy
The infrastructure developed within eNanoMapper project aims to support the data management in the area of nano safety research and to enable an integrated approach for the risk assessment of nanomaterials. To achieve these, eNanoMapper developed an ontology, a data infrastructure and modelling tools with applicability in risk assessment of nanomaterials. By merging the expertise of partners in statistical and data mining tools and in predictive toxicology, biology and nanotechnology research, eNanoMapper developed resources and...

Cdk/Cdk: Cdk 2.1

John Mayfield, Egon Willighagen, Rajarshi Guha, Gilleain Torrance, Kazuya Ujihara, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Tomáš Pluskal, Yap Chun Wei, Daniel Szisz, Mark J. Williamson, Nikolay Kochev, Nina Jeliazkova, Arvid Berg, Alex Clark, Ralf Stephan, Oliver Stueker, Kdole, Klas Jönsson, Kaibioinfo, Dmitry Katsubo, AndyHowlettGitHub, Uli Köhler, Cyrus Harmon … & Philopon
Release Notes

Cdk/Cdk: Patch Release Of 2.1

John Mayfield, Egon Willighagen, Rajarshi Guha, Gilleain Torrance, Kazuya Ujihara, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Tomáš Pluskal, Yap Chun Wei, Daniel Szisz, Mark J. Williamson, Nikolay Kochev, Nina Jeliazkova, Arvid Berg, Alex Clark, Ralf Stephan, Oliver Stueker, Kdole, Klas Jönsson, Kaibioinfo, Dmitry Katsubo, AndyHowlettGitHub, Uli Köhler, Cyrus Harmon … & Philopon
This patch release removes the SNAPSHOT dependency.

Deliverable Report D6.1 Enanomapper Year 1 Dissemination Report

Roland Grafström Bengt Fadeel
WP6 (Dissemination and Training) focuses on the development of news, events, findings, practices, resources, services created and scientific discoveries or progress from the eNanoMapper project. The Deliverable 6.1 describes the overall dissemination activities in the first twelve months of the project with a focus on the Task 6.1 (Community web site), Task 6.2 (Virtual seminars), Task 6.3 (Workshops) developments and other important scientific events in which eNanoMapper partners participated with lecture and/or poster presentations. Online...

Resource Types

  • Software
    62
  • Text
    36
  • Dataset
    1

Publication Year

  • 2018
    10
  • 2017
    26
  • 2016
    15
  • 2015
    30
  • 2014
    14
  • 2013
    4

Registration Year

  • 2018
    17
  • 2017
    49
  • 2016
    3
  • 2015
    21
  • 2014
    9

Data Centers

  • ZENODO - Research. Shared.
    99