EpiCass and CassavaNet4Dev advanced bioinformatics workshop
EpiCass and CassavaNet4Dev are collaborative projects funded by the Swedish Research Council between the Swedish University of Agriculture (SLU) and the International Institute of Tropical Agriculture (IITA). The projects aim to investigate the influence of epigenetic changes on agricultural traits...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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EMBnet Stichting
2023
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/132149 |
| _version_ | 1855543062574399488 |
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| author | Gisel, A. Stavolone, L. Olagunju, T. Landi, M. Damme, R. van Niazi, A. Falquet, L. Shah, T. Bongcam-Rudloff, E. |
| author_browse | Bongcam-Rudloff, E. Damme, R. van Falquet, L. Gisel, A. Landi, M. Niazi, A. Olagunju, T. Shah, T. Stavolone, L. |
| author_facet | Gisel, A. Stavolone, L. Olagunju, T. Landi, M. Damme, R. van Niazi, A. Falquet, L. Shah, T. Bongcam-Rudloff, E. |
| author_sort | Gisel, A. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | EpiCass and CassavaNet4Dev are collaborative projects funded by the Swedish Research Council between the Swedish University of Agriculture (SLU) and the International Institute of Tropical Agriculture (IITA). The projects aim to investigate the influence of epigenetic changes on agricultural traits such as yield and virus resistance while also providing African students and researchers with advanced bioinformatics training and opportunities to participate in big data analysis events. The first advanced bioinformatics training workshop took place from May 16th to May 18th, 2022, followed by an online mini-symposium titled "Epigenetics and crop improvement" on May 19th. The symposium featured international speakers covering a wide range of topics related to plant epigenetics, cassava viral diseases, and cassava breeding strategies. A new online and on-site teaching concept was developed for the three-day workshop to ensure maximum student participation across Western, Eastern, and Southern Africa. Initially planned in Nigeria, Kenya, Ethiopia, Tanzania, and Zambia, the workshop ultimately focused on Nigeria, Kenya, and Ethiopia due to a lack of qualified candidates in the other countries. Each classroom hosted 20 to 25 students, with at least one bioinformatician present for support. The classrooms were connected via video conferencing, whereas teachers located in different places in Africa and Europe joined the video stream to conduct teaching sessions. The workshop was divided into theoretical classes and hands-on sessions, where participants could run data analysis with support from online teachers and local bioinformaticians. To enable participants to run guided, CPU and RAM-intensive data analysis workflows and overcome local computing and internet access restrictions, a system of virtual machines (VMs) hosted in the cloud was developed. The teaching platform provided teaching and exercise materials to support the use of the VMs. Although some students could not run heavy data analysis workflows due to unforeseen restrictions in the cloud, these issues were solved. All participants had the opportunity to run the analysis steps independently in the cloud using the protocols hosted on the teaching platform. |
| format | Journal Article |
| id | CGSpace132149 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | EMBnet Stichting |
| publisherStr | EMBnet Stichting |
| record_format | dspace |
| spelling | CGSpace1321492025-11-11T11:07:52Z EpiCass and CassavaNet4Dev advanced bioinformatics workshop Gisel, A. Stavolone, L. Olagunju, T. Landi, M. Damme, R. van Niazi, A. Falquet, L. Shah, T. Bongcam-Rudloff, E. next generation sequencing epigenetics plant biology cassava EpiCass and CassavaNet4Dev are collaborative projects funded by the Swedish Research Council between the Swedish University of Agriculture (SLU) and the International Institute of Tropical Agriculture (IITA). The projects aim to investigate the influence of epigenetic changes on agricultural traits such as yield and virus resistance while also providing African students and researchers with advanced bioinformatics training and opportunities to participate in big data analysis events. The first advanced bioinformatics training workshop took place from May 16th to May 18th, 2022, followed by an online mini-symposium titled "Epigenetics and crop improvement" on May 19th. The symposium featured international speakers covering a wide range of topics related to plant epigenetics, cassava viral diseases, and cassava breeding strategies. A new online and on-site teaching concept was developed for the three-day workshop to ensure maximum student participation across Western, Eastern, and Southern Africa. Initially planned in Nigeria, Kenya, Ethiopia, Tanzania, and Zambia, the workshop ultimately focused on Nigeria, Kenya, and Ethiopia due to a lack of qualified candidates in the other countries. Each classroom hosted 20 to 25 students, with at least one bioinformatician present for support. The classrooms were connected via video conferencing, whereas teachers located in different places in Africa and Europe joined the video stream to conduct teaching sessions. The workshop was divided into theoretical classes and hands-on sessions, where participants could run data analysis with support from online teachers and local bioinformaticians. To enable participants to run guided, CPU and RAM-intensive data analysis workflows and overcome local computing and internet access restrictions, a system of virtual machines (VMs) hosted in the cloud was developed. The teaching platform provided teaching and exercise materials to support the use of the VMs. Although some students could not run heavy data analysis workflows due to unforeseen restrictions in the cloud, these issues were solved. All participants had the opportunity to run the analysis steps independently in the cloud using the protocols hosted on the teaching platform. 2023 2023-10-05T13:32:21Z 2023-10-05T13:32:21Z Journal Article https://hdl.handle.net/10568/132149 en Open Access application/pdf EMBnet Stichting Gisel, A., Stavolone, L., Olagunju, T., Landi, M., van Damme, R., Niazi, A., ... & Bongcam-Rudloff, E. (2023). EpiCass and CassavaNet4Dev advanced bioinformatics workshop. EMBnet. journal, 29: 1045, 1-6. |
| spellingShingle | next generation sequencing epigenetics plant biology cassava Gisel, A. Stavolone, L. Olagunju, T. Landi, M. Damme, R. van Niazi, A. Falquet, L. Shah, T. Bongcam-Rudloff, E. EpiCass and CassavaNet4Dev advanced bioinformatics workshop |
| title | EpiCass and CassavaNet4Dev advanced bioinformatics workshop |
| title_full | EpiCass and CassavaNet4Dev advanced bioinformatics workshop |
| title_fullStr | EpiCass and CassavaNet4Dev advanced bioinformatics workshop |
| title_full_unstemmed | EpiCass and CassavaNet4Dev advanced bioinformatics workshop |
| title_short | EpiCass and CassavaNet4Dev advanced bioinformatics workshop |
| title_sort | epicass and cassavanet4dev advanced bioinformatics workshop |
| topic | next generation sequencing epigenetics plant biology cassava |
| url | https://hdl.handle.net/10568/132149 |
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