RDMkit is out of beta and ready to be shown to the world. Check out our change log below to find ... more RDMkit is out of beta and ready to be shown to the world. Check out our change log below to find out what changed in this release compared to our beta release. Thank you to all contributors for their contributions. <strong>Implemented enhancements:</strong> Improve listing of tagged pages #408 Storage guidelines-WP1 DMNetwork #376 Branding - acknowledgement grants #17 Front page changes #466 (bedroesb) <strong>Closed issues:</strong> Adding section descriptions to the frontpage #479 A media page with all our logo's #463 Improve Plant domain page #453 Add link to "ELIXIR Services software tools" on the Data Analysis page. #437 Show CC-BY-4 licence on the website #434 Difference between Data sharing and Open data #430 Licensing vs. Licencing #425 feedback email subject "RDMKit feedback feedback" #422 Fixes to the Marine Metagenomics page #410 Delete "External Links" paragraph #409 Idea for the home page #405 Tools table tags no...
The goal of ELIXIR Converge WP5 is to assess the capacity of ELIXIR and its national nodes to ass... more The goal of ELIXIR Converge WP5 is to assess the capacity of ELIXIR and its national nodes to assist users' projects in implementing Data Management Plans (DMPs) in their projects at a EU scale. To do that, six demonstrator use-cases were created and they are described in the previous deliverable (D5.1). This deliverable includes a description of the main resources that can be used to assess researchers in the process of creating DMPs for at least two use-cases including a gap analysis. The DMPs are related to the demonstrator use-case #1 (Plant sciences) and #3 (Marine metagenomics). Moreover, specific aspects for use-cases #4 (Human data) and #6 (Biomolecular simulation) are also added. The main activities described in this deliverable are related to the ELIXIR Research Data Management Kit (RDMkit) and the Data Stewardship Wizard (DSW) in connection with ELIXIR Converge WP3 activities. For all use-cases except use-case 5 (Toxicology data), a 'Your domain' page in the R...
The scope of deliverable D3.2 is the extension of the content of the WP3 data management toolkit ... more The scope of deliverable D3.2 is the extension of the content of the WP3 data management toolkit (named RDMkit) based on the first wave of demonstrator projects (WP5). In order to achieve the deliverable, we established and applied processes to allow communities to contribute and extend the content of the RDMkit, including the ones involved in the first wave of demonstrator projects. As already reported in D3.1: "The ELIXIR RDMkit is intended to support researchers and data ××stewards to enable lifecycle management for their research data, according to international standards. The aim is to support FAIR by Design: from the first steps of producing FAIR data and Data Management Planning to the final steps of depositing data in public archives." The expansion described in this report adds specific and practical research data management knowledge for several Life Science domains. As the RDMkit is highly interlinked, this deliverable reports all extensions since the started to...
This record contains the data files used in exercises in the NBIS course "Introduction to Da... more This record contains the data files used in exercises in the NBIS course "Introduction to Data Management Practices".
The road to OPSIN (OPen ScIeNce): Come see what it's all about.<br><br>Much like ... more The road to OPSIN (OPen ScIeNce): Come see what it's all about.<br><br>Much like opsins are activated by light, enlightenment on Open Science was the aim of the PhD Event at the Department of Molecular Bioscience, Wenner-Gren Institute, (MBW) on Friday, May 3, 2019. "Open Science" reads like a tautology – a redundant use of words. Being that science strives to expand and spread knowledge, it should be open at its core. However, the system in which science is currently conducted is not set up to do so openly, i.e. transparently. In order to shed some light on the specific problem areas, the MBW PhD students wanted to raise awareness about the ideas of Open Science. <br><br>The document is a collection of the slides presented by the invited speakers Sofie Wennström, Niclas Jareborg, Gustav Nilsonne, Anna Wetterbom and Wilhelm Widmark.<br>
Data Carpentry lesson to learn to navigate your file system, create, copy, move, and remove files... more Data Carpentry lesson to learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards with genomics data.
Video recording of a general lecture about Data Management practices for Life Science in three pa... more Video recording of a general lecture about Data Management practices for Life Science in three parts, and a pdf with the slides.Note! The sound for the movie in part 3 doesn't work. Please go to the Youtube clip and watch it: https://www.youtube.com/watch?v=N2zK3sAtr-4.
The bovine papillomavirus type 1 (BPV-1) genome replicates as a latent plasmid in mouse C127 cell... more The bovine papillomavirus type 1 (BPV-1) genome replicates as a latent plasmid in mouse C127 cells transformed in vitro by the virus. However, we have recently shown that BPV-1 DNA amplification can be induced in a subpopulation of cells under culture conditions which suppress cell proliferation, a finding which led us to hypothesize that expression of a viral replication factor was regulated by cell growth stage. In this report, we describe the detection in these cells of abundant BPV-1 nuclear E2 antigen by immunofluorescence analysis. Expression of E2 antigen in fibropapilloma tissue was similarly localized to nonproliferating epidermal cells of the lower spinous layers--the natural site of induction of vegetative viral DNA replication. Immunoprecipitation analysis showed that the previously characterized 48-kilodalton (transactivator) and 31-kilodalton (repressor) E2 proteins were both induced in growth-arrested cell cultures. In parallel with E2 antigen synthesis under conditio...
RDMkit is out of beta and ready to be shown to the world. Check out our change log below to find ... more RDMkit is out of beta and ready to be shown to the world. Check out our change log below to find out what changed in this release compared to our beta release. Thank you to all contributors for their contributions. <strong>Implemented enhancements:</strong> Improve listing of tagged pages #408 Storage guidelines-WP1 DMNetwork #376 Branding - acknowledgement grants #17 Front page changes #466 (bedroesb) <strong>Closed issues:</strong> Adding section descriptions to the frontpage #479 A media page with all our logo's #463 Improve Plant domain page #453 Add link to "ELIXIR Services software tools" on the Data Analysis page. #437 Show CC-BY-4 licence on the website #434 Difference between Data sharing and Open data #430 Licensing vs. Licencing #425 feedback email subject "RDMKit feedback feedback" #422 Fixes to the Marine Metagenomics page #410 Delete "External Links" paragraph #409 Idea for the home page #405 Tools table tags no...
The goal of ELIXIR Converge WP5 is to assess the capacity of ELIXIR and its national nodes to ass... more The goal of ELIXIR Converge WP5 is to assess the capacity of ELIXIR and its national nodes to assist users' projects in implementing Data Management Plans (DMPs) in their projects at a EU scale. To do that, six demonstrator use-cases were created and they are described in the previous deliverable (D5.1). This deliverable includes a description of the main resources that can be used to assess researchers in the process of creating DMPs for at least two use-cases including a gap analysis. The DMPs are related to the demonstrator use-case #1 (Plant sciences) and #3 (Marine metagenomics). Moreover, specific aspects for use-cases #4 (Human data) and #6 (Biomolecular simulation) are also added. The main activities described in this deliverable are related to the ELIXIR Research Data Management Kit (RDMkit) and the Data Stewardship Wizard (DSW) in connection with ELIXIR Converge WP3 activities. For all use-cases except use-case 5 (Toxicology data), a 'Your domain' page in the R...
The scope of deliverable D3.2 is the extension of the content of the WP3 data management toolkit ... more The scope of deliverable D3.2 is the extension of the content of the WP3 data management toolkit (named RDMkit) based on the first wave of demonstrator projects (WP5). In order to achieve the deliverable, we established and applied processes to allow communities to contribute and extend the content of the RDMkit, including the ones involved in the first wave of demonstrator projects. As already reported in D3.1: "The ELIXIR RDMkit is intended to support researchers and data ××stewards to enable lifecycle management for their research data, according to international standards. The aim is to support FAIR by Design: from the first steps of producing FAIR data and Data Management Planning to the final steps of depositing data in public archives." The expansion described in this report adds specific and practical research data management knowledge for several Life Science domains. As the RDMkit is highly interlinked, this deliverable reports all extensions since the started to...
This record contains the data files used in exercises in the NBIS course "Introduction to Da... more This record contains the data files used in exercises in the NBIS course "Introduction to Data Management Practices".
The road to OPSIN (OPen ScIeNce): Come see what it's all about.<br><br>Much like ... more The road to OPSIN (OPen ScIeNce): Come see what it's all about.<br><br>Much like opsins are activated by light, enlightenment on Open Science was the aim of the PhD Event at the Department of Molecular Bioscience, Wenner-Gren Institute, (MBW) on Friday, May 3, 2019. "Open Science" reads like a tautology – a redundant use of words. Being that science strives to expand and spread knowledge, it should be open at its core. However, the system in which science is currently conducted is not set up to do so openly, i.e. transparently. In order to shed some light on the specific problem areas, the MBW PhD students wanted to raise awareness about the ideas of Open Science. <br><br>The document is a collection of the slides presented by the invited speakers Sofie Wennström, Niclas Jareborg, Gustav Nilsonne, Anna Wetterbom and Wilhelm Widmark.<br>
Data Carpentry lesson to learn to navigate your file system, create, copy, move, and remove files... more Data Carpentry lesson to learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards with genomics data.
Video recording of a general lecture about Data Management practices for Life Science in three pa... more Video recording of a general lecture about Data Management practices for Life Science in three parts, and a pdf with the slides.Note! The sound for the movie in part 3 doesn't work. Please go to the Youtube clip and watch it: https://www.youtube.com/watch?v=N2zK3sAtr-4.
The bovine papillomavirus type 1 (BPV-1) genome replicates as a latent plasmid in mouse C127 cell... more The bovine papillomavirus type 1 (BPV-1) genome replicates as a latent plasmid in mouse C127 cells transformed in vitro by the virus. However, we have recently shown that BPV-1 DNA amplification can be induced in a subpopulation of cells under culture conditions which suppress cell proliferation, a finding which led us to hypothesize that expression of a viral replication factor was regulated by cell growth stage. In this report, we describe the detection in these cells of abundant BPV-1 nuclear E2 antigen by immunofluorescence analysis. Expression of E2 antigen in fibropapilloma tissue was similarly localized to nonproliferating epidermal cells of the lower spinous layers--the natural site of induction of vegetative viral DNA replication. Immunoprecipitation analysis showed that the previously characterized 48-kilodalton (transactivator) and 31-kilodalton (repressor) E2 proteins were both induced in growth-arrested cell cultures. In parallel with E2 antigen synthesis under conditio...
Uploads