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1. EOSC-Life Final report on EOSC-Life training activities and their impact

Author

Ludwig, Rebecca, Duquenne, Lauranne, Gurwitz, Kim, Swan, Anna, Thomas Lopez, Daniel, Lloret Llinares, Marta, and Delgado, Claudia

Subjects
FAIR data, Open Science, Life science research infrastructures, Training, European Open Science Cloud
Abstract

This document outlines the training activities that have been completed since the beginning of the grant and their impact. The EOSC-Life training programme is built on the training needs analysis, which was presented in D9.1 Final report of analysis of the training needs of different EOSC-Life users in month 12. EOSC-Life training is aimed at two target communities that have distinct needs and different roles towards establishing a European Open Science Cloud (EOSC): (i) the Research Infrastructures (data) staff and (ii) the end-user of the (data) services offered. The deliverable gives an overview on the wide range of training offers completed, which highlight that EOSC-Life managed extremely well to ensure cross WP involvement and adapted the training to remote offers during the pandemic restrictions. Since the training activities described in D9.2 Review of EOSC-Life training activities, their impact and potential adaptations, our focus has been on developing and publishing the e-learning materials, while activities around courses, workshops and open calls continued. In total, since the beginning of the project we have supported over 1000 participants with in-person/virtual training and over 6000 participants with e-learning. Training in EOSC-Life has been organised in a top-down as well as bottom-up approach; top-down training activities have been organised by the technical work packages in EOSC-Life as well as the training work package, while the Training Open Call process allows for training activities organised by the EOSC-Life community to receive EOSC-Life support. All training activities relate to the needs analysis. Three rounds of the Training Open Call have been completed, in total we received 22 applications and 15 proposals received funding. In conclusion, EOSC-Life training activities were a driver and sustainer of the EOSC-Life community and an important pillar in reaching external audiences.&nbsp

Published
2023
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2. InterPro in 2011: new developments in the family and domain prediction database

Author

Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, and Yong, Siew-Yit

Published
2012
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4. InterPro: the integrative protein signature database

Author

Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, Bork, Peer, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Laugraud, Aurélie, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, Mistry, Jaina, Mitchell, Alex, Mulder, Nicola, Natale, Darren, Orengo, Christine, Quinn, Antony F., Selengut, Jeremy D., Sigrist, Christian J. A., Thimma, Manjula, Thomas, Paul D., Valentin, Franck, Wilson, Derek, Wu, Cathy H., and Yeats, Corin

Published
2009

5. InterPro in 2011: new developments in the family and domain prediction database

Author

Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, Yong, Siew-Yit, Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, and Yong, Siew-Yit

Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces

Published
2017

6. InterPro: the integrative protein signature database

Author

Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, Bork, Peer, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Laugraud, Aurélie, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, Mistry, Jaina, Mitchell, Alex, Mulder, Nicola, Natale, Darren, Orengo, Christine, Quinn, Antony F., Selengut, Jeremy D., Sigrist, Christian J. A., Thimma, Manjula, Thomas, Paul D., Valentin, Franck, Wilson, Derek, Wu, Cathy H., Yeats, Corin, Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, Bork, Peer, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Laugraud, Aurélie, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, Mistry, Jaina, Mitchell, Alex, Mulder, Nicola, Natale, Darren, Orengo, Christine, Quinn, Antony F., Selengut, Jeremy D., Sigrist, Christian J. A., Thimma, Manjula, Thomas, Paul D., Valentin, Franck, Wilson, Derek, Wu, Cathy H., and Yeats, Corin

Abstract

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total ∼58 000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/)

Published
2017

7. Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes

Author

Chun-Long Chen, Rappailles, Aurelien, Duquenne, Lauranne, Huvet, Maxime, Guilbaud, Guillaume, Farinelli, Laurent, Audit, Benjamin, d'Aubenton-Carafa, Yves, Arneodo, Alain, Hyrien, Olivier, and Thermes, Claude

Subjects
DNA replication -- Research, Mammals -- Genetic aspects, Gene mutations -- Analysis, DNA repair -- Evaluation, Health
Published
2010

9. InterPro in 2011: new developments in the family and domain prediction database

Author

Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, Yong, Siew-Yit, Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, and Yong, Siew-Yit

Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces

10. InterPro: the integrative protein signature database

Author

Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, Bork, Peer, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Laugraud, Aurélie, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, Mistry, Jaina, Mitchell, Alex, Mulder, Nicola, Natale, Darren, Orengo, Christine, Quinn, Antony F., Selengut, Jeremy D., Sigrist, Christian J. A., Thimma, Manjula, Thomas, Paul D., Valentin, Franck, Wilson, Derek, Wu, Cathy H., Yeats, Corin, Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, Bork, Peer, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Laugraud, Aurélie, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, Mistry, Jaina, Mitchell, Alex, Mulder, Nicola, Natale, Darren, Orengo, Christine, Quinn, Antony F., Selengut, Jeremy D., Sigrist, Christian J. A., Thimma, Manjula, Thomas, Paul D., Valentin, Franck, Wilson, Derek, Wu, Cathy H., and Yeats, Corin

Abstract

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total ∼58 000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/)

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