diff --git a/docs/_Experimental-Procedure-Standards-SOPs/01.1-introduction.md b/docs/_Experimental-Procedure-Standards-SOPs/01.1-introduction.md index da85faf..b534d83 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/01.1-introduction.md +++ b/docs/_Experimental-Procedure-Standards-SOPs/01.1-introduction.md @@ -28,5 +28,5 @@ SOPs serve as valuable educational resources for training new researchers and st The listed experimental SOPs that can be found on this Knowledge Base have been collected by NFDI4Microbiota's consortia members and participants from either (1) well-established and published sources or (2) consist of well-running in-house protocols that have been recently established by various research consortia and their domain expert with wet-lab experiences. -# Get Help +## Get Help If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) diff --git a/docs/_Experimental-Procedure-Standards-SOPs/02-external-sops.md b/docs/_Experimental-Procedure-Standards-SOPs/02-external-sops.md index bc91c62..3c9d53e 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/02-external-sops.md +++ b/docs/_Experimental-Procedure-Standards-SOPs/02-external-sops.md @@ -23,5 +23,5 @@ This page lists well-established and tested protocols from the International Hum |ITS Illumina Amplicon Protocol| Earth Microbiome | DNA Sequencing | [ITS Illumina Amplicon Protocol](https://www.protocols.io/view/emp-its-illumina-amplicon-protocol-14egnqypg5dy/v1) | {: .table .table-hover} -# Get Help +## Get Help If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) diff --git a/docs/_Experimental-Procedure-Standards-SOPs/03-viral-purification-from-bacterial-culture.md b/docs/_Experimental-Procedure-Standards-SOPs/03-viral-purification-from-bacterial-culture.md index 397567a..60a4ac3 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/03-viral-purification-from-bacterial-culture.md +++ b/docs/_Experimental-Procedure-Standards-SOPs/03-viral-purification-from-bacterial-culture.md @@ -5,7 +5,7 @@ layout: default docs_css: markdown --- -# Protocol +## Protocol 1. Centrifuge 40 ml of bacterial culture infected with phage at 6000 g for 30 min, remove the supernatant and filter it through a 0.45 μm syringe filter 2. Centrifuge the filtrate at 35 000 g for 4 h, remove the supernatant and re-suspend the pellet in 600 μl SM buffer 3. Add 2 μl of DNAse I and 20 μl of 10x DNAse buffer and incubate at 37°C for 1.5 h @@ -18,8 +18,8 @@ docs_css: markdown 10. Remove the supernatant and re-suspend the pellet in 100 μl TE buffer 11. Store at 4°C -# Source -In-house protocol provided by Sarah Schulz +## Source +In-house protocol provided by Sarah Schulz. -# Get Help +## Get Help If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) diff --git a/docs/_Experimental-Procedure-Standards-SOPs/04-dna-and-rna-kits-by-sample.md b/docs/_Experimental-Procedure-Standards-SOPs/04-dna-and-rna-kits-by-sample.md index 7110e73..68bb541 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/04-dna-and-rna-kits-by-sample.md +++ b/docs/_Experimental-Procedure-Standards-SOPs/04-dna-and-rna-kits-by-sample.md @@ -6,9 +6,9 @@ docs_css: markdown --- -# Nucleic Acid extraction kits +## Nucleic Acid extraction kits -## DNA extraction +### DNA extraction - Sponges - QIAamp® DNA Micro kit (QIAGEN){% cite Ruocco_2021 %} - Sponges –DNeasy® PowerSoil® Pro Kit (QIAGEN){% cite Ruocco_2021 %} @@ -52,7 +52,7 @@ docs_css: markdown - Bacterial DNA from cultures (automated) - GenFind v3 Kit (Beckman Coulter) - in house protocol provided by Nicole Treichel - Bacterial DNA from low biomass (eg. FACS sorted) samlpes – mericon DNA Bacteria Kit (Qiagen)- in house protocol provided by Nicole Treichel -## RNA extraction +### RNA extraction - Mosquitos - TRIzol LS (Invitrogen) – purified with RNeasy MinElute Cleanup Kit (Qiagen){% cite Ali_2021 %} - Sea Water - RNeasy mini kit (Qiagen){% cite Martínez-Pérez._2022 %} - Antarctic ticks - MagMax mirVana™ Total RNA isolation Kit (ThermoFisher Scientific){% cite Willis_2020 %} @@ -64,7 +64,9 @@ docs_css: markdown - Bile samples - ZymoBIOMICS DNA/RNA Miniprep Kit - in house protocol provided by Nicole Treichel - mouse small intestine content - ZymoBIOMICS DNA/RNA Miniprep Kit - in house protocol provided by Nicole Treichel -# Get Help +--- + +## Get Help If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) ## References diff --git a/docs/_Experimental-Procedure-Standards-SOPs/05-lipid-and-fatty-acid-extraction-protocol-from-biological-samples.md b/docs/_Experimental-Procedure-Standards-SOPs/05-lipid-and-fatty-acid-extraction-protocol-from-biological-samples.md index efadeba..017eeeb 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/05-lipid-and-fatty-acid-extraction-protocol-from-biological-samples.md +++ b/docs/_Experimental-Procedure-Standards-SOPs/05-lipid-and-fatty-acid-extraction-protocol-from-biological-samples.md @@ -47,7 +47,7 @@ Specific instructions for homogenization of frozen tissues (eg; liver) prior to *It is difficult to process tissue samples at weights below 10 mg, so aim for at least 10 mg of tissue to start with -# Get Help +## Get Help If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) ## References diff --git a/docs/_Experimental-Procedure-Standards-SOPs/06-metabolite-extraction-from-adherent-mammalian-cells.md b/docs/_Experimental-Procedure-Standards-SOPs/06-metabolite-extraction-from-adherent-mammalian-cells.md index b7b88e2..3f52182 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/06-metabolite-extraction-from-adherent-mammalian-cells.md +++ b/docs/_Experimental-Procedure-Standards-SOPs/06-metabolite-extraction-from-adherent-mammalian-cells.md @@ -39,7 +39,7 @@ Sample preparation and metabolite extraction: 17. Submit dried sample in 1.5 ml eppendorf tube and can be stored at in dried ice. 18. Blank control: prepare processed blank sample using same procedure but without biological sample (use water or buffer instead). -# Get Help +## Get Help If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) ## References diff --git a/docs/_Experimental-Procedure-Standards-SOPs/07-metabolite-extraction-from-plant-tissue.md b/docs/_Experimental-Procedure-Standards-SOPs/07-metabolite-extraction-from-plant-tissue.md index a8198be..ce52fe5 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/07-metabolite-extraction-from-plant-tissue.md +++ b/docs/_Experimental-Procedure-Standards-SOPs/07-metabolite-extraction-from-plant-tissue.md @@ -35,7 +35,7 @@ h. Collect sample eluent and evaporate the samples to dryness in a SpeedVac conc 7. Sample are reconstituted in mobile phase (or 50% methanol) before analysis -# Get Help +## Get Help If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) ## References diff --git a/docs/_Experimental-Procedure-Standards-SOPs/08-proteomics-tmt-labelled-sp3-method.md b/docs/_Experimental-Procedure-Standards-SOPs/08-proteomics-tmt-labelled-sp3-method.md index c3150a3..02b614b 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/08-proteomics-tmt-labelled-sp3-method.md +++ b/docs/_Experimental-Procedure-Standards-SOPs/08-proteomics-tmt-labelled-sp3-method.md @@ -100,7 +100,7 @@ Sample elution & collection: 10. Elute with 50 µl B Dry samples in Speedvac and reconstitute peptides in 1% formic acid supplemented with 4% acetonitrile. Samples are now ready for the injection on a mass spectrometer -# Get Help +## Get Help If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) ## References diff --git a/docs/_Experimental-Procedure-Standards-SOPs/09-sample-collection-and-storage-by-sample.md b/docs/_Experimental-Procedure-Standards-SOPs/09-sample-collection-and-storage-by-sample.md index d325677..f9d2ab7 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/09-sample-collection-and-storage-by-sample.md +++ b/docs/_Experimental-Procedure-Standards-SOPs/09-sample-collection-and-storage-by-sample.md @@ -13,8 +13,8 @@ Protein storage at -20°C usually requires the addition of 50% glycerol to your Protein samples stored at -80ºC will be frozen. As repeated freeze-thaw cycles usually have a negative influence on protein samples, it is best to prepare small-sized, single-use aliquots that will be used up during the course of an experiment. 5-10% glycerol or other additives that protect against the effect of freezing and thawing can be added as well. After preparing your protein sample aliquots, it is important to flash-freeze them in liquid nitrogen before importing them into the -80ºC freezer for long-term storage. Many proteins are stable for months to years when stored under appropriate conditions at -80°C, but the exact time frame varies from protein to protein and should be determined experimentally. -| Sample | Procedure | Source or Link | -|----------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------| +| Sample | Procedure | Source or Link | +|---------|------------|-----------------| | Activated sludge from wastewater | collected samples stored at 4°C for transport, within 6 h centrifuged at 6 500 g for 15 min at 4°C, supernatant removed and pellets stored at -20°C | {% cite Morin_2020 %} | | Antarctic ticks | collected from rocks, placed in RNALater and stored at -80°C within 4-8 h of collection | {% cite Wille_2020 %} | | Atlantic salmon | dissection samples placed in RNAlater and stored at -80°C | {% cite Karlsen_2022 %} | @@ -43,9 +43,9 @@ Protein samples stored at -80ºC will be frozen. As repeated freeze-thaw cycles | Turkey Trachea swabs | placed in 1 ml PBS, then stored at -20°C | {% cite Kursa_2021 %} | | Vaginal swabs | Skin samples were collected using Catch-All-Swabs (Epicentre Technologies, Wisconsin, USA). The swab was rubbed 5 times, with a circular motion, in the vaginal introitus and then the swab head was placed in a 15 ml sterile screw top collection tube containing 2 ml SCF-1 buffer (see photos above). | (in-house protocol provided by Pamela Ferretti) | | Yoghurt | after purchase, samples were placed immediately at 4°C for transport and within 12 h stared at -80°C | {% cite Islam_2021 %} | +{: .table .table-hover} - -# Get Help +## Get Help If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) ## References diff --git a/docs/_Getting-Started/01-privacy-policy-english-translation.md b/docs/_Getting-Started/01-privacy-policy-english-translation.md index 18fd051..a079eaa 100644 --- a/docs/_Getting-Started/01-privacy-policy-english-translation.md +++ b/docs/_Getting-Started/01-privacy-policy-english-translation.md @@ -11,6 +11,8 @@ hide: true The following policy is an automated translation of the German text. Please refer to the German original for a legally binding document. +--- + ## § 1 Information on data collection, controller, contacting us diff --git a/docs/_Getting-Started/02-contributing.md b/docs/_Getting-Started/02-contributing.md index f1f7c5c..38b9109 100644 --- a/docs/_Getting-Started/02-contributing.md +++ b/docs/_Getting-Started/02-contributing.md @@ -16,13 +16,17 @@ The main steps a user must follow to contribute to the Knowledge Base are: 2. Make changes to files in the repository: - Edit existing files *or* - Create new files -3. Add your name to the [03-contributors.md](https://github.com/NFDI4Microbiota/nfdi4microbiota-knowledge-base/blob/main/docs/_Getting-Started/03-contributors.md) file +3. Add your name to the [03-contributors.md](https://github.com/NFDI4Microbiota/nfdi4microbiota-knowledge-base/blob/main/docs/_Getting-Started/03-contributors.md) file. + +--- ## Create a GitHub account Users will need a GitHub account if they wish to contribute to the Knowledge Base. If you do not already have an account, go to the GitHub [homepage](https://github.com/) and click the `Sign Up` button to create one. Then follow the instructions. Once you have created an account, and signed in, go to the [Knowledge Base repository](https://github.com/NFDI4Microbiota/nfdi4microbiota-knowledge-base.github.io) +--- + ## Make changes to the repository @@ -67,11 +71,14 @@ To create a new issue: [Here](https://docs.github.com/en/issues/tracking-your-work-with-issues/creating-an-issue) is a guide on creating issues on GitHub if you need further help. +--- + ## Add your name to the CONTRIBUTORS file We appreciate your contribution! Please add your name to the [03-contributors.md](https://github.com/NFDI4Microbiota/nfdi4microbiota-knowledge-base/blob/main/docs/_Getting-Started/03-contributors.md) file. +--- ## Contribution Rules @@ -82,13 +89,16 @@ When adding or editing files, please observe the following rules: 2. Use American English 3. Keep the content factual 4. Reference sources appropriately (see below) -5. Use a single `#` for the main file heading and use `##`, `###`, etc, for all subheadings -6. Place image files in the `assets/img/` directory -7. Use internal links to markdown documents with {% raw %}`[Link text]({% link _RDM-Share/26_licenses.md %})`{% endraw %} -8. Non-public links are be restricted to the how-we-operate section and whitelisted in `.github/workflows/ignored-urls.txt` manually +5. Use a single `##` for the main file heading and use `###`, `####`, etc, for all subheadings +6. Before the second and every following `##` add `---` for a visual break line. +7. Place image files in the `assets/img/` directory +8. Use internal links to markdown documents with {% raw %}`[Link text]({% link _RDM-Share/26_licenses.md %})`{% endraw %} +9. Non-public links are be restricted to the how-we-operate section and whitelisted in `.github/workflows/ignored-urls.txt` manually *Note: we might edit your contribution to homogenize the writing style.* +--- + ## Cite sources diff --git a/docs/_How-We-Operate/00-n4m-intro.md b/docs/_How-We-Operate/00-n4m-intro.md index 6d218e6..9518a0f 100644 --- a/docs/_How-We-Operate/00-n4m-intro.md +++ b/docs/_How-We-Operate/00-n4m-intro.md @@ -7,7 +7,7 @@ redirect_from: /How-We-Operate hide: false --- -## Introduction to the NFDI4Microbiota How We Operate +## NFDI4Microbiota: How We Operate ### Aim @@ -17,7 +17,9 @@ Here, all information, guidelines, SOPs, documents, and links required for the w ### Contribution Each member of the consortium can [contribute to this repository](https://knowledgebase.nfdi4microbiota.de/Getting-Started/02-contributing.html). -## Introduction to the Nationale Forschungsdateninfrastruktur (NFDI) e.V. (NFDI association) +--- + +## The Nationale Forschungsdateninfrastruktur (NFDI) e.V. (NFDI association) - The National Research Data Infrastructure (NFDI) aims to systematically index, edit, interconnect, and make available the valuable stock of data from science and research. @@ -29,6 +31,8 @@ Each member of the consortium can [contribute to this repository](https://knowle - In a 30-minute video, the [statute](https://www.youtube.com/watch?v=mXNeZdzCfBg&t=434s) of the NFDI e.V. (German) is explained on their [YouTube channel](https://www.youtube.com/channel/UCTz321rUFOvrKOgkFfhyhLQ). - The Deutsche Forschungsgesellschaft (DFG) funds different NFDI consortia (independently of the NFDI e.V.). Further information and introductory videos can be found on the [DFG website](https://www.dfg.de/en/research-funding/funding-initiative/nfdi). +--- + ## Introduction to NFDI4Microbiota @@ -77,6 +81,8 @@ h) # of training i) # of ambassadors j) # of commits to the knowledge base +--- + ## Governance of NFDI4Microbiota @@ -143,6 +149,8 @@ thus reacting to new and unforeseen scenarios. It is staffed based on suggestion ### NFDI4Microbiota Policy The General Assembly adopted the NFDI4Microbiota Policy in 2023, which will be published on the [NFDI4Microbiota Zenodoo community](https://zenodo.org/communities/nfdi4microbiota) soon. +--- + ## Annual timeline of important dates for the consortium @@ -174,6 +182,8 @@ Middle of November | Announcement | M5.3 | Forwarding Flex Funds decision to app December | Event | TA51 | NFDI4Microbiota Annual Conference 2024 December | Meeting | TA5 | Quarterly coordination coffee +--- + ## NFDI4Microbiota Community, Members, Partners, and Participants @@ -213,6 +223,8 @@ found. All participants are members of the mailing list participants-at-nfdi4mic Ambassadors are young researchers (PhD students, Post Docs, etc.) of microbiology research groups. They actively [registered](https://helmholtz-hzi.limesurvey.net/158936?newtest=Y&lang=en) and are part of the mailing list ambassador-at-nfdi4microbiota.de. Details on the ambassador program can be found on the [web portal](https://nfdi4microbiota.de/community/ambassador.html). +--- + ## Communication @@ -241,6 +253,8 @@ If you are involved in further sections, task forces, or administrative groups ( NFDI mailing lists. For some mailing lists, archives of past emails do exist and can be viewed too. Every NFDI4Microbiota member should at least register to 'nfdi-all' mailing list. All lists can be accessed via [this link](https://lists.nfdi.de/postorius/lists/). +--- + ## Finances diff --git a/docs/_How-We-Operate/01-governance-workflows.md b/docs/_How-We-Operate/01-governance-workflows.md index 5b1068a..70b6e73 100644 --- a/docs/_How-We-Operate/01-governance-workflows.md +++ b/docs/_How-We-Operate/01-governance-workflows.md @@ -12,7 +12,9 @@ hide: false Governance is the process of making and enforcing decisions within an organization or society. The following will introduce the governance structure, and the governance bodies are defined. Details on the bodies of the NFDI4Microbiota can be found in the [introduction to NFDI4Microbiota](00-n4m-intro.html#governance-of-nfdi4microbiota). -## Workflow General Assembly +--- + +## The General Assembly ### Frequency of the General Assembly @@ -70,7 +72,9 @@ consortium for information and review for two weeks. Afterwards, the minutes wil ### Documentation of the General Assembly All files regarding the General Assembly are filed [in Nextcloud](https://nextcloud.nfdi4microbiota.de/f/105454) (internal link). -## Workflow Scientific Advisory Board +--- + +## The Scientific Advisory Board A detailed description of the Scientific Advisory Board (SAB) of NFDI4Microbiota can be found in the [introduction to NFDI4Microbiota](00-n4m-intro.html#governance-of-nfdi4microbiota). @@ -120,7 +124,9 @@ consortium. All files regarding the SAB are filed [here](https://nextcloud.nfdi4microbiota.de/f/105451) (internal link). The members of the SAB are displayed on the web portal. -## Workflow Project Review Board +--- + +## The Project Review Board The Project Review Board (PRB) is responsible for selecting new projects within the scope of the flexible funding and allocation mechanism, thus reacting to new and unforeseen scenarios. It is staffed based on @@ -158,7 +164,9 @@ To update the PRB regularly, they will receive the following information via the - the outcome and the proposals of the annual FlexFunds call, and - a season's greeting email. -## Workflow Circulation Procedure +--- + +## The Circulation Procedure If resolutions have to be made between the meetings of the General Assembly or the Scientific Advisory Board, a circulation procedure can be performed. A simple majority is required to approve a resolution, diff --git a/docs/_How-We-Operate/02-training-guidelines.md b/docs/_How-We-Operate/02-training-guidelines.md index f251ee7..bb1fbd9 100644 --- a/docs/_How-We-Operate/02-training-guidelines.md +++ b/docs/_How-We-Operate/02-training-guidelines.md @@ -29,6 +29,8 @@ software or tools. We only mention certain software products to illustrate our points. We separate the guidelines along the timeline of before, during, and after the training. +--- + ## Before the Training @@ -191,7 +193,7 @@ everyone. A good introduction is given in “[Ten simple rules for making training materials FAIR](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854)”. - +--- ## During the Training @@ -328,7 +330,7 @@ training in the future. Do try to ensure that the feedback can be anonymous and that the questions highlight points of improvement to enable you/the team to provide an even better experience the next time. - +--- ## After the Training @@ -352,5 +354,7 @@ benefit from the work you already provided. If you do so, make sure to state under what license you provide your work. We suggest a permissive license such as [CC BY](https://creativecommons.org/licenses/by/4.0/), or „CC 0“. -# Get Help +--- + +## Get Help If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) diff --git a/docs/_RDM-Collect/12-eln.md b/docs/_RDM-Collect/12-eln.md index 5ed39fd..2cacd6e 100644 --- a/docs/_RDM-Collect/12-eln.md +++ b/docs/_RDM-Collect/12-eln.md @@ -11,11 +11,15 @@ hide: false An Electronic Lab Notebook (ELN) is a software meant for documenting experiments, resulting research data, and processes. In its most basic form, an ELN replicates an interface similar to a page in a physical lab notebook, that allows input via computer or mobile device. More advanced forms often offer other features such as protocol templates, collaboration tools, support for electronic signatures, and the ability to manage the lab inventory. Ultimately, ELNs will replace physical lab notebooks as part of the digital transformation, {% cite kwok_2018 lindstädt_2019 lma_rdmwg vandendorpe:2024 n4m_wc_elns_2023 vieten_2023 %} as it makes sense to document and handle digital data with a digital tool. +--- + ## Uses of ELNs ELNs offer features and functions that can pave the way for significant time savings and knowledge transfer in daily laboratory work. For example, ELNs support the annotation of raw data (e.g. with tags or metadata {% cite rathmann_2021 vandendorpe:2024 %}) without having to switch between different media formats. Annotating data makes it searchable, discoverable, traceable and reusable {% cite vandendorpe:2024 %}. ELNs also bring data and their description closer together through embedded multimedia files (e.g. videos of experimental setups), links to shared resources (e.g. chemical databases or analysis software), links to other experiments, as well as direct links to (raw) data sets and analysis workflows {% cite rehwald_2022 %}. ELNs also allow for the versioning of experiment descriptions {% cite rehwald_2022 %} and the structuring and visualisation of workflows and processes {% cite rathmann_2021 %}. ELNs also have the ability to manage inventories of samples, reagents and other supplies, and track equipment and equipment maintenance schedules {% cite lma_rdmwg %}. ELNs also provide for collaboration {% cite lma_rdmwg %} through a common medium {% cite rehwald_2022 %}. Last but not least, ELNs provide for auditing {% cite lma_rdmwg %}, security and safety. Indeed, ELNs are fireproof, waterproof and cannot be lost, misplaced or stolen. ELNs can also be automatically backed up. They allow timestamping (RFC 3161 using DFN-PKI) and finalisation to prevent further changes {% cite rehwald_2022 %}. They also support electronic signatures {% cite cozatl_2021 %} and require access management {% cite rehwald_2022 %}. +--- + ## Benefits and drawbacks @@ -28,17 +32,23 @@ ELNs offer features and functions that can pave the way for significant time sav ### Drawbacks ELNs still have some disadvantages compared to physical lab notebooks, as network interruptions can temporarily limit access to data {% cite kwok_2018 %}. In addition, they may lack chronological continuity, formatting flexibility, haptic perception and resistance to liquids (for end devices). Another major drawback appears to be data security risks, especially when used to collect and document sensitive data. The best solution to this is the use of private servers on site or private, institutionally based cloud services {% cite Guerrero2016 %}. +--- + ## Ergonomics Several tools and techniques can be used to overcome the difficulties of using a computer when conducting experiments: tablets in the lab, plug-ins (such as voice input and Optical Character Recognition (OCR) plug-ins), linking experiments to raw data files and results, automatic date and time stamping to prove provenance, and integrating ELNs with other research software to capture data and information {% cite lma_rdmwg %}. +--- + ## The role of ELNs in data security and protection Some ELNs can help you keep your data secure by meeting the trustworthiness criteria defined in [FDA 21 CFR Part 11](https://www.fda.gov/regulatory-information/search-fda-guidance-documents/part-11-electronic-records-electronic-signatures-scope-and-application) (USA) and [EU Annex 11](https://www.gmp-compliance.org/guidelines/gmp-guideline/eu-gmp-annex-11-computerised-systems) (EU), including the provision of audit capabilities. ELNs can also provide two-factor authentication and unique credentials. Another way to address data security risks is to use of private servers on site or private, institutionally based cloud services {% cite Guerrero2016 %}. If you are setting up an ELN at your institution, you should also develop a data security plan {% cite lma_rdmwg %}. If you intend to collect sensitive data (e.g. sensitive personal data, sensitive environmental data) with the ELN, you should involve your institution's data protection officer (i.e. the person who oversees the application of and compliance with regulations designed to protect important information from corruption, compromise or loss within an organisation {% cite data_protection_officer:2023 crocetti:2021 %}) in the implementation process to ensure compliance with your institution's data protection regulations and the General Data Protection Regulation (GDPR) (i.e. the regulation “on the protection of natural persons with regard to the processing of personal data and on the free movement of such data” {% cite EU:n.d. %}). These regulations may restrict the physical location and transfer of data, excluding the use of cloud-hosted ELNs {% cite kwok_2018 higgins_2022 %}. You can also contact your RDM support team or relevant initiatives (e.g. the National Research Data Infrastructure for Personal Health Data ([NFDI4Health](https://www.nfdi4health.de/en/))) to find out more about anonymisation and pseudonymisation services, as well as your organisation's existing policies and procedures for handling sensitive data and how an ELN might fit into this picture. Ideally, this should be done at the stage of writing your [Data Management Plan (DMP)]({% link _RDM-Plan/01-dmp.md %}). It is important to note that privacy issues are not addressed by the ELN itself, but rather by how you set it up and store your data {% cite vandendorpe:2024 %}. +--- + ## Selecting an ELN @@ -66,6 +76,8 @@ Specialised systems have the advantage of offering easy entry through free onlin #### High-end systems High-end systems are ELNs that are offered as a module of a comprehensive laboratory management system {% cite Dirnagl:2016 %}. They have all the features of specialised systems and more. High-end ELNs integrate a LIMS (e.g. IBDS E-WORKBOOK, iLAB Laboratory Execution System) that allows complete tracking of samples and reagents through all experiments. They are also directly linked to laboratory equipment such as microscopes, spectrometers and sequencers. High-end systems provide workflows for specific samples, experiments and tasks. They can automatically provide raw data and metadata (e.g. date of last calibration) from laboratory instruments. Finally, high-end systems allow data mining (i.e. the aggregation and clustering of structured data) and analysis of raw data within the system. Such systems include Hivebench and Limsophy. High-end systems have the advantage of completeness of functionality and all their components fit together seamlessly. However, they can be complex to use and few allow users to use a language other than English (by 2020) {% cite Dirnagl:2016 %}. In addition, they are often cloud-hosted solutions, which means that data control and security remain in the hands of the ELN provider {% cite vandendorpe_2020 bobrov_2021 %}, and that they are more expensive {% cite higgins_2022 %}. They also use proprietary formats, which can increase the risk of vendor lock-in (i.e. making users dependent on the ELN and unable to use their data with another ELN without significant switching costs {% cite vendor_lock_in %}) {% cite vandendorpe_2020 bobrov_2021 %}. +--- + ## Implementing the ELN @@ -75,20 +87,23 @@ To successfully select and maintain an ELN, you must first analyse the current s ### Timeframe Testing pre-selected ELNs takes three to six months, depending on when sufficient knowledge of the products’ suitability has been acquired {% cite vandendorpe:2024 %}. Setting up an ELN (especially the inventory functions) initially takes time. However, having an ELN saves time in the long term, e.g. by linking experiments to samples and by managing and ordering supplies {% cite lma_rdmwg %}. +--- + ## eLabFTW eLabFTW is a free and open-source {% cite rathmann_2021 %} ELN developed by Deltablot (France) {% cite cozatl_2021 %}. eLabFTW is a web-based application that runs on all major operating systems. It can be used in research and teaching (e.g. for laboratory exercises) {% cite cozatl_2021 %}. In addition to a search function {% cite rathmann_2021 %} and the ability to take notes, eLabFTW allows you to create experiments and collections of experiments {% cite cozatl_2021 %}, log work steps, document data and results {% cite rathmann_2021 %} with metadata, and create a database for a variety of objects (e.g. lab materials, lab equipment). It is also a good collaborative tool with which you can manage the lab {% cite cozatl_2021 %}. eLabFTW will also help you comply with GRP as it prevents data deletion and provides immutability through timestamps {% cite rathmann_2021 %}. Being open source, it is freely modifiable and highly customisable. It also benefits from community development, by scientists for scientists {% cite cozatl_2021 %}. Its interface has been translated into 17 languages as of June 2024 {% cite Carpi:2021 %}. To see what it looks like, watch this [video tutorial]((https://www.youtube.com/playlist?list=PLJYlS0FDTMq17tvYMeuI2Ct5XtykRFy0K)) with eLabFTW and Labfolder from ZB MED on YouTube. +--- + ## Resources * [ELN Material Collection](https://elb-materialsammlung.gitlab.io/sammlung/) -## Get Help - +--- -If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) +## Get Help * **Best practice examples** (see in {% cite Adam:2021 %}) * ETH Zürich with openBIS @@ -131,6 +146,11 @@ If you have any further questions about the management and analysis of your micr It is also advisable to talk to other members of your research community to find out about their experiences with ELNs (e.g. advantages and disadvantages of different tools, selection process). + +If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) + +--- + ## References diff --git a/docs/_RDM-Collect/13-data-qc.md b/docs/_RDM-Collect/13-data-qc.md index 9d7d730..0cc5296 100644 --- a/docs/_RDM-Collect/13-data-qc.md +++ b/docs/_RDM-Collect/13-data-qc.md @@ -149,6 +149,8 @@ Legend: - **possible reason(s)**: humans are bad with ratios (0.01 = almost 0 and 100 is just large but not the largest bar ever) - **solution/measure**: use any log transformation (e.g. log10: 0.01 => -2, 100 => +2) +--- + ## Single cell ### Quality check @@ -191,5 +193,7 @@ Legend: - **possible reason(s)**: some genes can be interpreted as dates when using excel for data handling - **solution/measure**: never ever use excel or at least make sure that cell type is not "AUTO" +--- + ## Get Help If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/)) diff --git a/docs/_RDM-Plan/01-dmp.md b/docs/_RDM-Plan/01-dmp.md index fb0069f..db5f988 100644 --- a/docs/_RDM-Plan/01-dmp.md +++ b/docs/_RDM-Plan/01-dmp.md @@ -10,6 +10,8 @@ A Data Management Plan (DMP) is a formal and living document that defines respon DMPs are required in [DFG funding proposals since 2022](https://www.dfg.de/en/research_funding/announcements_proposals/2022/info_wissenschaft_22_25/index.html) and in [EU Funding Programs 2021-2027](https://ec.europa.eu/info/funding-tenders/opportunities/docs/2021-2027/common/guidance/aga_en.pdf). For funders, DMPs serve as a reporting tool to hold grantees accountable for conducting good and open science, with regular updates or in case of changes. For researchers and other stakeholders, DMPs are meant to be a living document that accompanies them from proposal writing or project start to the sharing of their data and results. +--- + ## Content of DMPs DMPs typically include the following information: * Administrative project-specific information (including a description of the research project) @@ -27,6 +29,8 @@ DMPs typically include the following information: To find a TDR, see the [Data Repositories page of the Knowledge Base]({% link _RDM-Share/22-data-repositories.md %}). +--- + ## DMP templates and examples **Templates** @@ -38,6 +42,8 @@ To find a TDR, see the [Data Repositories page of the Knowledge Base]({% link _R * [DD-DeCaF Bioinformatics Services for Data-Driven Design of Cell Factories and Communities](https://phaidra.univie.ac.at/o:1139495) * [METASTAVA](https://doi.org/10.5281/zenodo.5841166) +--- + ## Benefits of a DMP If implemented correctly, a DMP can [benefit all stakeholders](https://doi.org/10.1371/journal.pcbi.1006750) in a research project, despite the initial cost of creating the DMP itself. @@ -47,6 +53,8 @@ A DMP can also facilitate and **harmonize the coordination and shared use of dat DMPs offer **other benefits**, such as enabling verification and control: researchers are accountable for how their data are managed during their research project. They also help to identify - and potentially minimize - time and money costs that need to be included in the proposal, such as for Research Data Management (RDM) activities. They also help to comply with Good Research Practice (GRP), support research integrity, and ensure that ethical and legal requirements are met. DMPs also help to meet institutional and funder requirements: funding agencies increasingly require information on the management of research data, and a DMP allows you to structure and formalize this information. Last but not least, DMPs facilitate data reuse, thereby increasing data citation and advancing scientific progress. +--- + ## Writing a DMP **Who is involved in the creation of the DMP?** Entities involved in the creation of a DMP are researchers, RDM staff (check your institution's [research data policy](https://www.forschungsdaten.org/index.php/Forschungsdaten-Policies) and ask for [local support](https://www.forschungsdaten.org/index.php/FDM-Kontakte)) and central infrastructure (e.g. computer center, library). @@ -57,6 +65,8 @@ DMPs offer **other benefits**, such as enabling verification and control: resear **DMP quality check:** A good DMP is well structured and distinguishes between actions to be taken during and after the project. It is a living document that needs to be updated regularly and is for the use of all project stakeholders. It should be started as early as possible, be as concise as possible, as long as necessary, and contain sufficient detail without being redundant. Ideally, the DMP will be published with the research data at the end of the project. +--- + ## DMP tools Although it is generally possible to formulate a DMP in a text document, the use of more dynamic and machine-readable formats finally unlocks its full potential. @@ -69,6 +79,8 @@ RDMO organizes individual DMPs around predefined templates that reflect the requ * **[DMPonline](https://dmponline.dcc.ac.uk/)** was developed by the [Digital Curation Center](https://www.dcc.ac.uk/) (DCC) for the UK funding context but has also been used elsewhere. It is an open-source, web-based tool for researchers. It enables the creation, review, and sharing of DMPs that meet institutional and funder requirements. +--- + ## Further resources * Cessda - [Data Management Expert Guide](https://dmeg.cessda.eu/Data-Management-Expert-Guide) * [Content of a Data Management Plan](https://doi.org/10.18154/RWTH-2019-10064) @@ -90,6 +102,8 @@ RDMO organizes individual DMPs around predefined templates that reflect the requ * [SM Wizard](https://smw.ds-wizard.org/) * [Writing and using a software management plan](https://www.software.ac.uk/guide/writing-and-using-software-management-plan) +--- + ## Get Help If you have any further questions about the management and analysis of your microbial research data, please contact us: [helpdesk@nfdi4microbiota.de](mailto:helpdesk@nfdi4microbiota.de) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/))