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1. The bio.tools registry of software tools and data resources for the life sciences

Author

Ison, J., Ienasescu, H., Chmura, P., Rydza, E., Menager, H., Kalas, M., Schwammle, V., Gruning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Varekova, R.S., Racek, T., Vondrasek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R., Nyronen, T., Valencia, A., Capella, S., Gelpi, J., Zambelli, F., Savakis, B., Leskosek, B., Rapacki, K., Blanchet, C, Jimenez, R., Oliveira, A., Vriend, G., Collin, O., Helden, Jacques van, Longreen, P., Brunak, S., Ison, J., Ienasescu, H., Chmura, P., Rydza, E., Menager, H., Kalas, M., Schwammle, V., Gruning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Varekova, R.S., Racek, T., Vondrasek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R., Nyronen, T., Valencia, A., Capella, S., Gelpi, J., Zambelli, F., Savakis, B., Leskosek, B., Rapacki, K., Blanchet, C, Jimenez, R., Oliveira, A., Vriend, G., Collin, O., Helden, Jacques van, Longreen, P., and Brunak, S.

Abstract

Contains fulltext : 208582.pdf (publisher's version ) (Open Access), Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.

Published
2019

2. The bio.tools registry of software tools and data resources for the life sciences

Author

Ison, J., Ienasescu, H., Chmura, P., Rydza, E., Menager, H., Kalas, M., Schwammle, V., Gruning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Varekova, R.S., Racek, T., Vondrasek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R., Nyronen, T., Valencia, A., Capella, S., Gelpi, J., Zambelli, F., Savakis, B., Leskosek, B., Rapacki, K., Blanchet, C, Jimenez, R., Oliveira, A., Vriend, G., Collin, O., Helden, Jacques van, Longreen, P., Brunak, S., Ison, J., Ienasescu, H., Chmura, P., Rydza, E., Menager, H., Kalas, M., Schwammle, V., Gruning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Varekova, R.S., Racek, T., Vondrasek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R., Nyronen, T., Valencia, A., Capella, S., Gelpi, J., Zambelli, F., Savakis, B., Leskosek, B., Rapacki, K., Blanchet, C, Jimenez, R., Oliveira, A., Vriend, G., Collin, O., Helden, Jacques van, Longreen, P., and Brunak, S.

Abstract

Contains fulltext : 208582.pdf (publisher's version ) (Open Access), Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.

Published
2019

3. The bio.tools registry of software tools and data resources for the life sciences

Author

Ison, J., Ienasescu, H., Chmura, P., Rydza, E., Menager, H., Kalas, M., Schwammle, V., Gruning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Varekova, R.S., Racek, T., Vondrasek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R., Nyronen, T., Valencia, A., Capella, S., Gelpi, J., Zambelli, F., Savakis, B., Leskosek, B., Rapacki, K., Blanchet, C, Jimenez, R., Oliveira, A., Vriend, G., Collin, O., Helden, Jacques van, Longreen, P., Brunak, S., Ison, J., Ienasescu, H., Chmura, P., Rydza, E., Menager, H., Kalas, M., Schwammle, V., Gruning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Varekova, R.S., Racek, T., Vondrasek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R., Nyronen, T., Valencia, A., Capella, S., Gelpi, J., Zambelli, F., Savakis, B., Leskosek, B., Rapacki, K., Blanchet, C, Jimenez, R., Oliveira, A., Vriend, G., Collin, O., Helden, Jacques van, Longreen, P., and Brunak, S.

Abstract

Contains fulltext : 208582.pdf (publisher's version ) (Open Access), Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.

Published
2019

4. Tools and data services registry: a community effort to document bioinformatics resources

Author

Ison, J., Rapacki, K., Menager, H., Kalas, M., Rydza, E., Chmura, P., Anthon, C., Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., Vedova, G.D., Dogan, T., Doppelt-Azeroual, O., Emery, L., Gasteiger, E., Gatter, T., Goldberg, T., Grosjean, M., Gruning, B., Helmer-Citterich, M., Ienasescu, H., Ioannidis, V., Jespersen, M.C., Jimenez, R., Juty, N., Juvan, P., Koch, M., Laibe, C., Li, J.W., Licata, L., Mareuil, F., Micetic, I., Friborg, R.M., Moretti, S., Morris, C., Moller, S., Nenadic, A., Peterson, H., Profiti, G., Rice, P., Romano, P., Roncaglia, P., Saidi, R., Schafferhans, A., Schwammle, V., Smith, C., Sperotto, M.M., Stockinger, H., Varekova, R.S., Tosatto, S.C., Torre, V., Uva, P., Via, A., Yachdav, G., Zambelli, F., Vriend, G., Rost, B., Parkinson, H., Longreen, P., Brunak, S., Ison, J., Rapacki, K., Menager, H., Kalas, M., Rydza, E., Chmura, P., Anthon, C., Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., Vedova, G.D., Dogan, T., Doppelt-Azeroual, O., Emery, L., Gasteiger, E., Gatter, T., Goldberg, T., Grosjean, M., Gruning, B., Helmer-Citterich, M., Ienasescu, H., Ioannidis, V., Jespersen, M.C., Jimenez, R., Juty, N., Juvan, P., Koch, M., Laibe, C., Li, J.W., Licata, L., Mareuil, F., Micetic, I., Friborg, R.M., Moretti, S., Morris, C., Moller, S., Nenadic, A., Peterson, H., Profiti, G., Rice, P., Romano, P., Roncaglia, P., Saidi, R., Schafferhans, A., Schwammle, V., Smith, C., Sperotto, M.M., Stockinger, H., Varekova, R.S., Tosatto, S.C., Torre, V., Uva, P., Via, A., Yachdav, G., Zambelli, F., Vriend, G., Rost, B., Parkinson, H., Longreen, P., and Brunak, S.

Abstract

Contains fulltext : 171819.pdf (publisher's version ) (Open Access), Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Published
2016

5. Tools and data services registry: a community effort to document bioinformatics resources

Author

Ison, J., Rapacki, K., Menager, H., Kalas, M., Rydza, E., Chmura, P., Anthon, C., Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., Vedova, G.D., Dogan, T., Doppelt-Azeroual, O., Emery, L., Gasteiger, E., Gatter, T., Goldberg, T., Grosjean, M., Gruning, B., Helmer-Citterich, M., Ienasescu, H., Ioannidis, V., Jespersen, M.C., Jimenez, R., Juty, N., Juvan, P., Koch, M., Laibe, C., Li, J.W., Licata, L., Mareuil, F., Micetic, I., Friborg, R.M., Moretti, S., Morris, C., Moller, S., Nenadic, A., Peterson, H., Profiti, G., Rice, P., Romano, P., Roncaglia, P., Saidi, R., Schafferhans, A., Schwammle, V., Smith, C., Sperotto, M.M., Stockinger, H., Varekova, R.S., Tosatto, S.C., Torre, V., Uva, P., Via, A., Yachdav, G., Zambelli, F., Vriend, G., Rost, B., Parkinson, H., Longreen, P., Brunak, S., Ison, J., Rapacki, K., Menager, H., Kalas, M., Rydza, E., Chmura, P., Anthon, C., Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., Vedova, G.D., Dogan, T., Doppelt-Azeroual, O., Emery, L., Gasteiger, E., Gatter, T., Goldberg, T., Grosjean, M., Gruning, B., Helmer-Citterich, M., Ienasescu, H., Ioannidis, V., Jespersen, M.C., Jimenez, R., Juty, N., Juvan, P., Koch, M., Laibe, C., Li, J.W., Licata, L., Mareuil, F., Micetic, I., Friborg, R.M., Moretti, S., Morris, C., Moller, S., Nenadic, A., Peterson, H., Profiti, G., Rice, P., Romano, P., Roncaglia, P., Saidi, R., Schafferhans, A., Schwammle, V., Smith, C., Sperotto, M.M., Stockinger, H., Varekova, R.S., Tosatto, S.C., Torre, V., Uva, P., Via, A., Yachdav, G., Zambelli, F., Vriend, G., Rost, B., Parkinson, H., Longreen, P., and Brunak, S.

Abstract

Contains fulltext : 171819.pdf (publisher's version ) (Open Access), Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Published
2016

6. Tools and data services registry: a community effort to document bioinformatics resources

Author

Ison, J., Rapacki, K., Menager, H., Kalas, M., Rydza, E., Chmura, P., Anthon, C., Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., Vedova, G.D., Dogan, T., Doppelt-Azeroual, O., Emery, L., Gasteiger, E., Gatter, T., Goldberg, T., Grosjean, M., Gruning, B., Helmer-Citterich, M., Ienasescu, H., Ioannidis, V., Jespersen, M.C., Jimenez, R., Juty, N., Juvan, P., Koch, M., Laibe, C., Li, J.W., Licata, L., Mareuil, F., Micetic, I., Friborg, R.M., Moretti, S., Morris, C., Moller, S., Nenadic, A., Peterson, H., Profiti, G., Rice, P., Romano, P., Roncaglia, P., Saidi, R., Schafferhans, A., Schwammle, V., Smith, C., Sperotto, M.M., Stockinger, H., Varekova, R.S., Tosatto, S.C., Torre, V., Uva, P., Via, A., Yachdav, G., Zambelli, F., Vriend, G., Rost, B., Parkinson, H., Longreen, P., Brunak, S., Ison, J., Rapacki, K., Menager, H., Kalas, M., Rydza, E., Chmura, P., Anthon, C., Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., Vedova, G.D., Dogan, T., Doppelt-Azeroual, O., Emery, L., Gasteiger, E., Gatter, T., Goldberg, T., Grosjean, M., Gruning, B., Helmer-Citterich, M., Ienasescu, H., Ioannidis, V., Jespersen, M.C., Jimenez, R., Juty, N., Juvan, P., Koch, M., Laibe, C., Li, J.W., Licata, L., Mareuil, F., Micetic, I., Friborg, R.M., Moretti, S., Morris, C., Moller, S., Nenadic, A., Peterson, H., Profiti, G., Rice, P., Romano, P., Roncaglia, P., Saidi, R., Schafferhans, A., Schwammle, V., Smith, C., Sperotto, M.M., Stockinger, H., Varekova, R.S., Tosatto, S.C., Torre, V., Uva, P., Via, A., Yachdav, G., Zambelli, F., Vriend, G., Rost, B., Parkinson, H., Longreen, P., and Brunak, S.

Abstract

Contains fulltext : 171819.pdf (publisher's version ) (Open Access), Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Published
2016

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