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1. Ten simple rules for measuring the impact of workshops

Author

Sufi, Shoaib, Duckles, Beth, Simera, Iveta, Nurmikko-Fuller, Terhi, Bellis, Louisa, Miah, Wadud, Wilde, Adriana, Nenadic, Aleksandra, Silva, Raniere, de Beyer, Jennifer A., Struthers, Caroline, Emsley, Iain, Philippe, Olivier, Balzano, Melissa, Coelho, Sara, Ford, Heather, Jones, Catherine, and Higgins, Vanessa

Subjects
Computer Science - Computers and Society
Abstract

Workshops are used to explore a specific topic, transfer knowledge, solve identified problems or create something new. In funded research projects and other research endeavours, workshops are the mechanism to gather the wider project, community or interested people together around a particular topic. However, natural questions arise: how do we measure the impact of these workshops? Do we know whether they are meeting the goals and objectives we set for them? What indicators should we use? In response to these questions, this paper will outline rules that will improve the measurement of the impact of workshops.

Published
2018
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3. A Different Kind of Carpentry

Author

Nenadic, Aleksandra

Abstract

Invited presentation at the CISMA (Colloquia for Intelligent Sensing, Measurement and Actuators) 2022 webinar, School of Engineering, Edinburgh, 29 March 2022. https://cisma-colloquia.com/2022/03/08/making-coding-work-for-you/.Abstract: Making research methods, data and results more accessible and reproducible can contribute to better science. Taking even small steps towards being more open, reproducible or even a bit better organised than the last time will make you more efficient in your work but will also help make the life easier for your future self or the person that comes to your group/lab after you. The Carpentries is a big international community of enthusiastic volunteers teaching foundational computational skills (version control, basic programming, command line, data organisation, cleaning, analysis and visualisation) founded on best practices (building modular and reusable code, using data structures, reproducibility) for researchers across disciplines. The emphasis is not on advanced, enterprise workflows or tools, but basic “toolbox” skills for everyday use that can be mastered in a relatively short period of time giving researchers the data organisation and computing skills they didn’t even know they needed.

Published
2022
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5. Intermediate Software Development Training in Python - Steve Crouch - CW21 Lightning Talk

Author

Crouch, Stephen, Nenadic, Aleksandra, and Graham, James

Abstract

Lightning talk presented at Collaboration Workshop 2021.Software Carpentry has done an exceptional job providing training for basic computational skills. But what's the next step? As the RSE community continues to grow it's becoming apparent that there is a need for further skills in software development - notably related to working in teams. The SSI is developing a training course - based around Python and being piloted and launched this year - that provides intermediate software development skills as a next step to Software Carpentry.

Published
2021
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9. CarpentryConnect Manchester 2019 Conference (CCMcr19) Report

Author

Nenadic, Aleksandra and Sufi, Shoaib

Subjects
library carpentry, carpentries, software sustainability, research software training, research software, open data, data carpentry, ComputerSystemsOrganization_PROCESSORARCHITECTURES, open research, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), software sustainability institute, ComputingMilieux_MISCELLANEOUS, software carpentry
Abstract

CarpentryConnect Manchester 2019 conference (CCMcr19) took place over three days at The Studio (http://studiovenues.co.uk/venues/manchester/) from 25th to 26th June 2019, and at the School of Computer Science (https://www.cs.manchester.ac.uk/), University of Manchester (http://www.manchester.ac.uk/), on 27th June 2019. It was an opportunity for the members of The Carpentries’ global community of instructors (and anyone else with an interest in helping researchers to improve their computational skills) to get together for a few days to exchange ideas and learn new things about teaching computational skills. The main themes of the conference were increasing the sustainability of scientific software and research through training, good teaching practices, tools and resources for research computing education, the development of novel or existing lessons/curricula in different domains and building local and regional carpentry/training communities at research institutions. This report gives an overview of different parts of the agenda and details of the outputs, impact and feedback., The Software Sustainability Institute, which organised the conference, is supported by EPSRC grant EP/H043160/1, EPSRC, BBSRC and ESRC Grant EP/N006410/1 and EPSRC, BBSRC, ESRC, NERC, AHRC, STFC and MRC grant EP/S021779/1.

Published
2019
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11. Ten simple rules for measuring the impact of workshops

Author

Sufi, Shoaib, primary, Nenadic, Aleksandra, additional, Silva, Raniere, additional, Duckles, Beth, additional, Simera, Iveta, additional, de Beyer, Jennifer A., additional, Struthers, Caroline, additional, Nurmikko-Fuller, Terhi, additional, Bellis, Louisa, additional, Miah, Wadud, additional, Wilde, Adriana, additional, Emsley, Iain, additional, Philippe, Olivier, additional, Balzano, Melissa, additional, Coelho, Sara, additional, Ford, Heather, additional, Jones, Catherine, additional, and Higgins, Vanessa, additional

Published
2018
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12. MOESM1 of BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

Author

Hardisty, Alex, Bacall, Finn, Beard, Niall, Maria-Paula Balcázar-Vargas, Balech, Bachir, Barcza, Zoltán, Bourlat, Sarah, Giovanni, Renato, Jong, Yde, Leo, Francesca, Dobor, Laura, Donvito, Giacinto, Fellows, Donal, Guerra, Antonio, Ferreira, Nuno, Fetyukova, Yuliya, Fosso, Bruno, Giddy, Jonathan, Goble, Carole, Güntsch, Anton, Haines, Robert, Ernst, Vera, Hettling, Hannes, Hidy, Dóra, Horváth, Ferenc, Ittzés, Dóra, Ittzés, Péter, Jones, Andrew, Kottmann, Renzo, Kulawik, Robert, Leidenberger, Sonja, Lyytikäinen-Saarenmaa, Päivi, Cherian Mathew, Morrison, Norman, Nenadic, Aleksandra, Hidalga, Abraham, Obst, Matthias, Oostermeijer, Gerard, Paymal, Elisabeth, Pesole, Graziano, Pinto, Salvatore, Poigné, Axel, Fernandez, Francisco, Santamaria, Monica, Saarenmaa, Hannu, Sipos, Gergely, Karl-Heinz Sylla, Tähtinen, Marko, Vicario, Saverio, Vos, Rutger, Williams, Alan, and Yilmaz, Pelin

Subjects
Data_FILES, GeneralLiterature_MISCELLANEOUS
Abstract

Additional file 1. ‘How-to’ guidelines for the biodiversity virtual e-laboratory.

Published
2016
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13. Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action

Author

Pawlik, Aleksandra, primary, van Gelder, Celia W.G., additional, Nenadic, Aleksandra, additional, Palagi, Patricia M., additional, Korpelainen, Eija, additional, Lijnzaad, Philip, additional, Marek, Diana, additional, Sansone, Susanna-Assunta, additional, Hancock, John, additional, and Goble, Carole, additional

Published
2017
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14. Tools and data services registry: a community effort to document bioinformatics resources

Author

Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C.E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, Brunak, Søren, Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C.E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, and Brunak, Søren

Abstract

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

15. BioVeL : a virtual laboratory for data analysis and modelling in biodiversity science and ecology

Author

Hardisty, Alex R., Bacall, Finn, Beard, Niall, Balcázar-Vargas, Maria-Paula, Balech, Bachir, Barcza, Zoltán, Bourlat, Sarah J., De Giovanni, Renato, de Jong, Yde, De Leo, Francesca, Dobor, Laura, Donvito, Giacinto, Fellows, Donal, Guerra, Antonio Fernandez, Ferreira, Nuno, Fetyukova, Yuliya, Fosso, Bruno, Giddy, Jonathan, Goble, Carole, Güntsch, Anton, Haines, Robert, Hernández Ernst, Vera, Hettling, Hannes, Hidy, Dóra, Horváth, Ferenc, Ittzés, Dóra, Ittzés, Péter, Jones, Andrew, Kottmann, Renzo, Kulawik, Robert, Leidenberger, Sonja, Lyytikäinen-Saarenmaa, Päivi, Mathew, Cherian, Morrison, Norman, Nenadic, Aleksandra, Nieva de la Hidalga, Abraham, Obst, Matthias, Oostermeijer, Gerard, Paymal, Elisabeth, Pesole, Graziano, Pinto, Salvatore, Poigné, Axel, Quevedo Fernandez, Francisco, Santamaria, Monica, Saarenmaa, Hannu, Sipos, Gergely, Sylla, Karl-Heinz, Tähtinen, Marko, Vicario, Saverio, Aldo Vos, Rutger, Williams, Alan R., Yilmaz, Pelin, Hardisty, Alex R., Bacall, Finn, Beard, Niall, Balcázar-Vargas, Maria-Paula, Balech, Bachir, Barcza, Zoltán, Bourlat, Sarah J., De Giovanni, Renato, de Jong, Yde, De Leo, Francesca, Dobor, Laura, Donvito, Giacinto, Fellows, Donal, Guerra, Antonio Fernandez, Ferreira, Nuno, Fetyukova, Yuliya, Fosso, Bruno, Giddy, Jonathan, Goble, Carole, Güntsch, Anton, Haines, Robert, Hernández Ernst, Vera, Hettling, Hannes, Hidy, Dóra, Horváth, Ferenc, Ittzés, Dóra, Ittzés, Péter, Jones, Andrew, Kottmann, Renzo, Kulawik, Robert, Leidenberger, Sonja, Lyytikäinen-Saarenmaa, Päivi, Mathew, Cherian, Morrison, Norman, Nenadic, Aleksandra, Nieva de la Hidalga, Abraham, Obst, Matthias, Oostermeijer, Gerard, Paymal, Elisabeth, Pesole, Graziano, Pinto, Salvatore, Poigné, Axel, Quevedo Fernandez, Francisco, Santamaria, Monica, Saarenmaa, Hannu, Sipos, Gergely, Sylla, Karl-Heinz, Tähtinen, Marko, Vicario, Saverio, Aldo Vos, Rutger, Williams, Alan R., and Yilmaz, Pelin

Abstract

Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on- line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. Conclusions: Our work shows w

Published
2016
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16. Tools and data services registry:a community effort to document bioinformatics resources

Author

Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans-Ioan, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C. E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, Brunak, Søren, Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans-Ioan, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C. E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, and Brunak, Søren

Abstract

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

17. BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

Author

Hardisty, Alex R., primary, Bacall, Finn, additional, Beard, Niall, additional, Balcázar-Vargas, Maria-Paula, additional, Balech, Bachir, additional, Barcza, Zoltán, additional, Bourlat, Sarah J., additional, De Giovanni, Renato, additional, de Jong, Yde, additional, De Leo, Francesca, additional, Dobor, Laura, additional, Donvito, Giacinto, additional, Fellows, Donal, additional, Guerra, Antonio Fernandez, additional, Ferreira, Nuno, additional, Fetyukova, Yuliya, additional, Fosso, Bruno, additional, Giddy, Jonathan, additional, Goble, Carole, additional, Güntsch, Anton, additional, Haines, Robert, additional, Ernst, Vera Hernández, additional, Hettling, Hannes, additional, Hidy, Dóra, additional, Horváth, Ferenc, additional, Ittzés, Dóra, additional, Ittzés, Péter, additional, Jones, Andrew, additional, Kottmann, Renzo, additional, Kulawik, Robert, additional, Leidenberger, Sonja, additional, Lyytikäinen-Saarenmaa, Päivi, additional, Mathew, Cherian, additional, Morrison, Norman, additional, Nenadic, Aleksandra, additional, de la Hidalga, Abraham Nieva, additional, Obst, Matthias, additional, Oostermeijer, Gerard, additional, Paymal, Elisabeth, additional, Pesole, Graziano, additional, Pinto, Salvatore, additional, Poigné, Axel, additional, Fernandez, Francisco Quevedo, additional, Santamaria, Monica, additional, Saarenmaa, Hannu, additional, Sipos, Gergely, additional, Sylla, Karl-Heinz, additional, Tähtinen, Marko, additional, Vicario, Saverio, additional, Vos, Rutger Aldo, additional, Williams, Alan R., additional, and Yilmaz, Pelin, additional

Published
2016
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18. Tools and data services registry: a community effort to document bioinformatics resources

Author

Ison, Jon, primary, Rapacki, Kristoffer, additional, Ménager, Hervé, additional, Kalaš, Matúš, additional, Rydza, Emil, additional, Chmura, Piotr, additional, Anthon, Christian, additional, Beard, Niall, additional, Berka, Karel, additional, Bolser, Dan, additional, Booth, Tim, additional, Bretaudeau, Anthony, additional, Brezovsky, Jan, additional, Casadio, Rita, additional, Cesareni, Gianni, additional, Coppens, Frederik, additional, Cornell, Michael, additional, Cuccuru, Gianmauro, additional, Davidsen, Kristian, additional, Vedova, Gianluca Della, additional, Dogan, Tunca, additional, Doppelt-Azeroual, Olivia, additional, Emery, Laura, additional, Gasteiger, Elisabeth, additional, Gatter, Thomas, additional, Goldberg, Tatyana, additional, Grosjean, Marie, additional, Grüning, Björn, additional, Helmer-Citterich, Manuela, additional, Ienasescu, Hans, additional, Ioannidis, Vassilios, additional, Jespersen, Martin Closter, additional, Jimenez, Rafael, additional, Juty, Nick, additional, Juvan, Peter, additional, Koch, Maximilian, additional, Laibe, Camille, additional, Li, Jing-Woei, additional, Licata, Luana, additional, Mareuil, Fabien, additional, Mičetić, Ivan, additional, Friborg, Rune Møllegaard, additional, Moretti, Sebastien, additional, Morris, Chris, additional, Möller, Steffen, additional, Nenadic, Aleksandra, additional, Peterson, Hedi, additional, Profiti, Giuseppe, additional, Rice, Peter, additional, Romano, Paolo, additional, Roncaglia, Paola, additional, Saidi, Rabie, additional, Schafferhans, Andrea, additional, Schwämmle, Veit, additional, Smith, Callum, additional, Sperotto, Maria Maddalena, additional, Stockinger, Heinz, additional, Vařeková, Radka Svobodová, additional, Tosatto, Silvio C.E., additional, de la Torre, Victor, additional, Uva, Paolo, additional, Via, Allegra, additional, Yachdav, Guy, additional, Zambelli, Federico, additional, Vriend, Gert, additional, Rost, Burkhard, additional, Parkinson, Helen, additional, Løngreen, Peter, additional, and Brunak, Søren, additional

Published
2015
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19. Bringing caBIG services together using Taverna

Author

Nenadic, Aleksandra, Soiland-Reyes, Stian, and Goble, Carole

Abstract

The National Cancer Institute (NCI) from the US has built an integrated biomedical platform called caBIG in order to improve the US cancer research community’s access to key bioinformatics data and tools. The caBIG programme was established in order to allow researchers to more efficiently discover, share, process and integrate disparate clinical and research data, with an ultimate goal of accelerating cancer research. The backbone of the caBIG infrastructure is caGrid – a grid-computing service-oriented environment that integrates various data and analytical services and leverages the combined strengths and expertise of participating organizations in an open and federated environment. caBIG services are categorized as legacy, bronze, silver and gold based on their ability to interoperate with other caBIG services. Legacy does not guarantee any interoperability with external software components or data resources; silver services comply with standardized semantic advertising, discovery and use of the service; gold level is currently being defined by caBIG as an extension to the silver that will enable full syntactic and semantic interoperability of services. Most of the services currently deployed at caGrid are silver.Being able to link caBIG services into a workflow is one of the key requirements for caBIG users, in order for them to automate the design and running of their virtual experiments. Taverna Workbench (henceforth Taverna), a workflow design, management and execution system developed by the myGrid team (now based in Manchester, UK), has emerged as the primary candidate that will meet this need. The myGrid team has joined efforts with the caGrid workflow team from the US (funded by the NCI) in order to integrate caBIG services into Taverna and enable caBIG users to orchestrate data and analytical services in Taverna workflows. This also included integration with the caGrid’s GAARDS security framework for interaction with secure caBIG services.As a side effect of the integration, caBIG services can be combined in mix-and-match style workflows with other existing third party services already accessible from Taverna. This paper describes the details of Taverna-caBIG integration – the extensions added to Taverna in order to be able to discover and invoke caBIG services from Taverna workflows.

Published
2009

23. Software Carpentry: Workshop Template

Author

Ahmadia, Aron, Alderman, Phillip, Allen, James, Banaszkiewicz, Piotr, Barmby, Pauline, Bast, Radovan, Blischak, John, Botvinnik, Olga, Boughton, Andy, Bray, Erik M., Brown, Amy, Brown, C. Titus, Caporaso, Greg, Clayton, Sarah, Cooper, Jonathan, Davis, Matt, Davis, Neal, Duckles, Jonah, Foos, Marianna, Girdhar, Yashasvi, Gonzalez, Ivan, Gosset, John, Grant, Alistair, Guignard, Thomas, Hinsen, Konrad, Ho, Xavier, Irving, Damien, Jackson, Mike, Jolly, Ben, Kim, Jan T., King, W. Trevor, Lebauer, David, Lehtomäki, Joona, Marwaha, Kunal, M.A. Matienzo, Mckay, Sheldon, Michael, Lauren, Michonneau, François, Moss, Steve, Nederbragt, Lex, Nenadic, Aleksandra, Ory, Jeramia, Perez, Fernando, Pritchard, Leighton, Prokopenko, Andrey, Ritchie, Scott, Sane, Maneesha, Silva, Raniere, Smith, Arfon, and Srinath, Ashwin

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

Author

Callum Smith, Paolo Uva, Thomas Gatter, Peter Løngreen, Peter Juvan, Hans Ienasescu, Giuseppe Profiti, Aleksandra Nenadic, Kristoffer Rapacki, Chris Morris, Paola Roncaglia, Steffen Möller, Laura Emery, Søren Brunak, Maria Maddalena Sperotto, Heinz Stockinger, Kristian Davidsen, Federico Zambelli, Helen Parkinson, Olivia Doppelt-Azeroual, Luana Licata, Tatyana Goldberg, Andrea Schafferhans, Elisabeth Gasteiger, Emil Karol Rydza, Camille Laibe, Victor De La Torre, Marie Grosjean, Manuela Helmer-Citterich, Hervé Ménager, Radka Svobodová Vařeková, Rafael C. Jimenez, Martin Closter Jespersen, Anthony Bretaudeau, Jan Brezovsky, Tunca Doğan, Matúš Kalaš, Peter M. Rice, Ivan Mičetić, Rune Møllegaard Friborg, Maximilian Koch, Silvio C. E. Tosatto, Nick Juty, Björn Grüning, Gianmauro Cuccuru, Frederik Coppens, Gianni Cesareni, Jon Ison, Rabie Saidi, Sébastien Moretti, Rita Casadio, Gert Vriend, Guy Yachdav, Niall Beard, Timothy F. Booth, Michael Cornell, Piotr Jaroslaw Chmura, Veit Schwämmle, Karel Berka, Dan Bolser, Vassilios Ioannidis, Jing-Woei Li, Burkhard Rost, Gianluca Della Vedova, Fabien Mareuil, Hedi Peterson, Allegra Via, Paolo Romano, Christian Anthon, Technical University of Denmark [Lyngby] (DTU), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), University of Bergen (UIB), University of Copenhagen = Københavns Universitet (KU), University of Manchester, Palacky University, European Bioinformatics Institute, NEBC Wallingford, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Masaryk University, University of Bologna, Università degli Studi di Roma Tor Vergata [Roma], Ghent University [Belgium] (UGENT), Flanders Institute for Biotechnology, CRS4 Bioinformat, Università degli studi di Milano-Bicocca, Swiss Institute of Bioinformatics, Universität Bielefeld = Bielefeld University, Tumor Biology Center, Centre National de la Recherche Scientifique (CNRS), University of Freiburg, University of Ljubljana, The Chinese University of Hong Kong [Hong Kong], Universita degli Studi di Padova, Bioinformatics Research Centre, Université de Lausanne, CCLRC Daresbury Laboratory, Universität zu Lübeck [Lübeck] - University of Lübeck [Lübeck], Universität Rostock, University of Tartu, Imperial College London, IRCCS Azienda Ospedaliera Universitaria Integrata San Martino (IRCCS AOU San Martino), University of Southern Denmark (SDU), WTCHG, Central European Institute of Technology [Brno] (CEITEC), Instituto Nacional de Bioinformática, Sapienza University of Rome (DIAG), Consiglio Nazionale delle Ricerche, University of Milan, Radboud University Nijmegen, Ison, J, Rapacki, K, Ménager, H, Kalaš, 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, DELLA VEDOVA, G, Dogan, T, Doppelt Azeroual, O, Emery, L, Gasteiger, E, Gatter, T, Goldberg, T, Grosjean, M, Grüning, B, Helmer Citterich, M, Ienasescu, H, Ioannidis, V, Jespersen, M, Jimenez, R, Juty, N, Juvan, P, Koch, M, Laibe, C, Li, J, Licata, L, Mareuil, F, Mičetić, I, Friborg, R, Moretti, S, Morris, C, Möller, S, Nenadic, A, Peterson, H, Profiti, G, Rice, P, Romano, P, Roncaglia, P, Saidi, R, Schafferhans, A, Schwämmle, V, Smith, C, Sperotto, M, Stockinger, H, Vařeková, R, Tosatto, S, de la Torre, V, Uva, P, Via, A, Yachdav, G, Zambelli, F, Vriend, G, Rost, B, Parkinson, H, Løngreen, P, Brunak, S, University of Bergen (UiB), Palacky University Olomouc, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Masaryk University [Brno] (MUNI), Universiteit Gent = Ghent University [Belgium] (UGENT), Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Universität zu Lübeck [Lübeck], Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Copenhagen = Københavns Universitet (UCPH), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, University of Bologna/Università di Bologna, Universiteit Gent = Ghent University (UGENT), Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Université de Lausanne = University of Lausanne (UNIL), Università degli Studi di Padova = University of Padua (Unipd), Universität zu Lübeck = University of Lübeck [Lübeck], Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Università degli Studi di Milano = University of Milan (UNIMI), Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thoma, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Han, Ioannidis, Vassilio, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chri, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C E, de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, and Brunak, Søren

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], registry, Bioinformatics, computer.software_genre, Matematikk og naturvitenskap: 400::Informasjons- og kommunikasjonsvitenskap: 420::Systemutvikling og -arbeid: 426 [VDP], Task (project management), Documentation, Data and Information, Database Issue, Registries, bioinformatique, Data Curation, base de données, Settore BIO/11, gestion de données, tool, SOFTWARE-DEVELOPMENT, bioinformatics, ddc, outil informatique, Tools and data services registry, SEQANSWERS, Web service, MOLECULAR-BIOLOGY, Biology, Ecology and Environment, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Genetics, Implementation, Dissemination, Bioinformatikk / Bioinformatics, Data curation, bioinformatic, business.industry, Computational Biology, Software, Software development, bioinformatics, tools, registry, elixir, Biology and Life Sciences, Mathematics and natural scienses: 400::Information and communication science: 420::System development and design: 426 [VDP], FRAMEWORK, ELIXIR, Settore BIO/18 - Genetica, 030104 developmental biology, tools, Data as a service, COMPILATION, business, COLLECTION, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], computer, WEB SERVICES, LIFE SCIENCES
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.

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

Author

Ison J, Rapacki K, Ménager H, Kalaš 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 GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, and Brunak S

Subjects
Data Curation, Software, Computational Biology, Registries
Abstract

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., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2016
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