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# Pad for the Workshop "Living with Electronic Laboratory Notebooks" *This is a public pad. Please feel free to use it.* The **registration** is still open at the [workshop website](https://rdm.mpdl.mpg.de/mpdl-services/workshops/workshop-living-with-elns-2021/). For general **questions** to the workshop, please write to rdm@mpdl.mpg.de. ## Day 1, 20th September 2021,1:00 pm to 6:15 pm ### 1:00-1:15 Welcome and Short on by Stephan Janosch (Max Planck Institute of Molecular Cell Biology and Genetics), Michael Franke and Yves Vincent Grossmann (both Max Planck Digital Library) * MF: 2016 last [ELN workshop](https://eln.mpdl.mpg.de/?page_id=40) - [central Labfolder licensing](https://www.mpdl.mpg.de/en/about-us/news/news-archive/395-electronic-laboratory-notebook-software-labfolder-licensed-via-mpdl-central-contract.html?highlight=WyJsYWJmb2xkZXIiXQ==) * * SJ: now we have NFDI * YG: who is here? stats and questions * Your questions? * Recording info for first day, breakout room topic collection at the bottom of first day at pad - https://pad.gwdg.de/6GP0a5znT8-RC0MFcVvpfA 🇬🇧 you can type along ### 1:15-2:00 Mark Greiner (Max Planck Institute for Chemical Energy Conversion): Challenges in choosing a full-featured ELN/LIMS for a multi-disciplinary research organization Email: mark.greiner@cec.mpg.de * challenges * analysis * linking data-sample-conditions * linking data collection to notebook, data might mive somewhere else * in search for ELN + inventory system * 75 criteria for reviewing ELNs * NFDI4Cat (also 4Chem, Fairmat + Daphne) * summarized a white paper at the end of the whole process * Questions: * Will criteria catalog be openly available for others? * NFDI - white paper! * Open Sourced vs closed source? * if flexibility built in, then closed source could work (SJ) * exit strategy * on-premises vs. vendor hosted? * why did labfolder (promoted by MPG) not make it to top 3? * We found Labfolder was not so well suited to the chemistry research. It did not have several of the features we had on our list. * Is there a policy to use the system? Will there by usage enforced/mandated? * taking paper away needs more effort * rewards are not visible immediately * little nudging, a lot of support, present best practises - ammbassadors (tech savy domain specialists) * How many people are working in your RDM team? * 1 FTE * (MPFI) Topics that come to mind include: informed consents if you have them, deleting data that must be removed, billing, back up/archiving data, disaster recovery, legal compliance across international boundaries, standardization/best practices. ### 2:00-2:30 Yves Vincent Grossmann (Max Planck Digital Library): ELN Survey 2021 within the Max Planck Society Email: grossmann@mpdl.mpg.de #### Links * [Short summary of the ELN Survey 2021](https://rdm.mpdl.mpg.de/2021/08/02/survey-results-on-the-usage-of-elns-in-the-max-planck-society-2021/) * [Documentation and Analyses of the MPG ELN Survey 2021](https://pure.mpg.de/rest/items/item_3333238_3/component/file_3333355/content) * [ELN Survey from 2016](https://www.mpg.de/10988930/_jb_2017.pdf) * European Commission: Electronic Laboratory Notebooks (ELNs) as key enablers of open science – Open science monitor case study, 31st October 2019, https://data.europa.eu/doi/10.2777/07890 * last survey 2016, half of the users use an ELN * 55 % of users are sastisfied or very satisfied * training opportunities are an issue * ELN Network ![](https://pad.gwdg.de/uploads/upload_8eb2eba436be131a87bccaf720945bbc.png) * inventory managemanent (10 yes, 13 partly)? * Open questions * How to collect (positive) feedback? * ELN user community * product specific questions * general questions * FAQ list * ELN standards * Josh Moore: Just a thought: for the higher organizational levels, I’m somewhat hopeful that ISA can cover a variety of the NFDI projects, and sharing one specification would be useful. For the lower levels, i.e. the details, I don’t know of any such specification. Perhaps though by all agreeing on basic semantics as with Linked Data, the conversion between ELNs could be facilitated, since all properties would have a well-defined, named and versioned context. #### FAQs * 🇬🇧 you can type along ### *2:30-2:45 Coffee Break* ### 2:45-3:15 Knut Finstermeier (Max Planck Unit for the Science of Pathogens): Automating regulatory compliance, the benefit of using an ELN Email: finstermeier@mpusp.mpg.de #### Abstract The Max Planck Unit for the Science of Pathogens (MPUSP) has transitioned from physical lab notebooks to electronical lab notebooks (ELN) at the beginning of 2019. Prior to this transition, several ELNs were evaluated over a period of 3 years and it was concluded that the ELN [Labfolder](https://labfolder.mpdl.mpg.de) was the most appropriate framework for us. To overcome the hesitation of several wet lab scientists (students), the transition was carried out with the full support by the MPUSP director. However, the common problems inherited from physical lab notebooks, i.e. correct and timely documentation of lab experiments or potential falsification, remained an issue. To support the tedious work of PIs and project managers related to ensuring this regulatory requirement for documentation, automated processes and procedures have been implemented to significantly improve the quality of the documentation. With the expected expansion of the Labfolder’s API, more of the necessary manual checkpoints can be transferred to algorithms and thus we are not only closing the supervision gap, but also freeing up time of PIs from management to research. * people did not want to use ELN * directory decision at beginning 2019 * quite some people did use it up to 18 months prior to that decision despite having to keep a physical notebook, too * better project structuring * plan in a notebook #### Questions: * What about resistance and overcoming resistance? * main argument: everyone can than read my entries (not true, you have to share except for supervisors) and a lab notebook is a official documentation (independent of electronical or not) and accessible to labmembers, authorities etc. anyway * in the end, only through the decision by the director, the transition fully happened * Are some using physical and electronic notebooks? * there are no physical notebooks since 2019 * How is information documented inside the lab? Directly on a computer with the ELN? If yes how can you guarantee that equipment doesn't get dirty? If not, you capture it first with a physical notebook and then have double the workload for users? I feel like that is a big issue in chemical labs and/or when wearing gloves etc.  * all labs have computer and people log on to labfolder through the browser from anywhere within the building (through VPN from home) * how is ELN mandate documentated * currently during the onboarding process * there will be ELN specific guidelines (not yet released though) * (SJ) example summary report? * In the future, instead of referencing, we will report the textual changes directly: :::Dear XY, This is the report of the lists of incidences related to the documentation of labwork happening between September 01, 2021 - September 15, 2021. The following people did not create labbook entries for an extended period of time: XXX August 19 - September 14, 2021 (18 weekdays) YYY since Tuesday August 24, 2021 (currently 16 weekdays) ZZZ since Tuesday August 03, 2021 (currently 31 weekdays) Furthermore, the following late edits were taken in this time period: AAA entry from August 09, 2021 in "******" edited on September 01, 2021 (after 23 days) entry from June 22, 2021 in "********" edited on September 09, 2021 (after 79 days) BBB entry from August 23, 2021 in "********" edited on September 09, 2021 (after 17 days) CCC entry from August 05, 2021 in "********" edited on September 01, 2021 (after 27 days) entry from July 29, 2021 in "********" edited on September 01, 2021 (after 34 days) entry from July 20, 2021 in "********" edited on September 01, 2021 (after 43 days) Please reach out to these lab members to resolve that issue. Thank you very much, [...]::: more questions * (SJ) share the code behind reports? * certainly possible, please reach out to me directly: finstermeier@mpusp.mpg.de * (SJ) How to handle alumni? * manually curated filter list, a new version of the tool could potentially use the LDAP to match active email addresses to identify alumni * (SJ) Transparency of ELN reporting? * people know about the reporting through onboarding, reminder emails to users directly and one on one supervisor meetings for feedback #### group activity of one research group at MPI-CBG ![](https://pad.gwdg.de/uploads/upload_01b3f7152a427a78329ffea0b4154cef.png) user 1 uses Labfolder sporadically ### 3:15-3:45 Lu Yu (Max Planck Digital Library): From LabCam to other Addons Email: yu@mpdl.mpg.de #### Abstract LabCam is a camera app for mobile devices. It is a helper to capture and upload your photos to the associated keeper (https://keeper.mpdl.mpg.de) account. In this session, I will explain why we developed this Addon app and explore other beneficial apps for your laboratory work. * 🇬🇧 you can type along * colony counter app * Questions: * (SJ) How go microscopy images into the device running Labcam? * What API functionality is available with Keeper? ### 3:45-4:15 Carsten Fortmann-Grote and Kristian Ullrich (Max Planck Institute for Evolutionary Biology): OpenBIS and SEEK Emails: carsten.fortmann-grote@evolbio.mpg.de and ullrich@evolbio.mpg.de #### Abstract We present openBIS, an ELN+LIMS solution and SEEK, a data catalogue and commons platform. Combined, these opensource tools support the entire data lifecycle from lab work documentation to publishing and deposition. We will present how we integrate openBIS and SEEK into the lab and data management strategy at our institute, describe various use cases, and discuss extensions for domain specific applications such as Next Generation Sequencing and Microscopy. * 🇬🇧 you can type along Questions: * OpenBIS * (YVG) Do you have a strategy to bring your whole institute towards using openBIS&Seek? * Good question, on the department level it will be hard to enforce (Harnack-Prinzip). However, since one director is leaving in less than two years, this will open the possibilty to go beyond dual-usage of A(nalog)LN and ELN. * How does the process of adding custom types of inventory look like? (e.g. not just storing chemicals, but maybe also lenses, etc.) * There is a dedicated admin GUI to add new tpyes, which can be any vocabulary (https://openbis.ch/index.php/docs/admin-documentation/new-entity-type-registration/) * Is there some easy way to search through the database using properties of the inventory item? (e.g. for lenses, suitable wavelength) * Yes, there is a dedicated search engine (https://openbis.ch/index.php/docs/user-documentation/openbis-features/search/) * Seek * (MF) About minting DOIs: Are you already doing this? Where do you get them from? Where are they pointing to? * Q2 ### *4:15-4:45 Coffee Break* ### 4:45-5:15 Pablo I. Ampuero Ruiz (Max Planck Institute for Social Anthropology): Can ELN become the new ethnographic field diary? Email: ampuero@eth.mpg.de #### Abstract For generations social anthropologists have filled the pages of paper diaries with thick descriptions, images, drawings, and whatever else that constitutes a “fieldnote”. More tech-savvy anthropologists have tried to substitute the old paper diary with a variety of digital commercial alternatives, with varied levels of frustration. In this presentation I explore how ELNs like [Joplin](https://joplinapp.org/) can be useful to those working with qualitative data and in which ways it can be developed to fit the needs of researchers in the humanities and social sciences. * 🇬🇧 you can type along ### 5:15-5:30 Stephan Janosch (Max Planck Institute of Molecular Cell Biology and Genetics): Implementing documentation for genetically modified organism Email: janosch@mpi-cbg.de #### Abstract There are strict requirements of documenting genetically modified organisms (GMO) in life sciences. This contribution will explain, which organisatorical challenges were overcome and how Labfolder was used to implement these to overcome paper and enable collaboration. * 🇬🇧 you can type along ### 5:30-6:15 Interactive Part Day 1 – topic poll + breakout rooms * 🇬🇧 youdd can type along #### possible Topics for breakout rooms 1. training opportunities for ELN users 2. administrative aspects of running a ELN service - reporting 3. How to convince your directors of adopting/enforcing ELN usage? 4. ELN UX in other national research institute's (Helmholtz, Leibniz, ..., overlap of same research topics (chemistry, biology, social, ...) might be stronger as within MPG) 5. Topic ## Day 2, 21st September 2021, 9:00 am to 1:30 pm ### Welcome SJ: From RSE to ELN supporter * SJ: requirements: diverse environments, methods, use cases, interfaces - high overlap with RDM, eln-internal mailing list * recording info ### 9:00-9:45 Michael Mende (Max Planck Institute of Animal Behavior): Notebook Origines – why document? Email: mmende@ab.mpg.de #### Abstract This suggested session or contribution looks at the Good Scientific Practice side of notebooks: The DFG requires all universities and research institutes and organisations to implement the new (2019) DFG Codex for research integrity. Part of the Codex describes the minimum requirements for Data Management and Documentation in particular. So what are these? What would be the appropriate use of a manual lab notebook, and how is this translated into ELN solutions? * https://embassy.science * shocked when talking to young poeple * missing motivation * transparency, reproduceabilty, * who owns the data? * safeguarding institutional access, collaboration scenarios! * institution or any other rule implemented describing ownership * ownership <> intelectual property (IP) * IP get documented via lab notebook * MPI for Meteorology (MPI-M) * They have policies: https://mpimet.mpg.de/en/science/good-scientific-practice * Steneck 2004 * https://ori.hhs.gov/ori-introduction-responsible-conduct-research * https://rdm.mpdl.mpg.de * code are guidelines - but it's not an implementation * ideal world: Introduction for ELN by ombusman on good scientific practice Questions: * (SJ) Aware of combined introductions to GSP and ELN within Ombudsman Network? * (SJ) Do we miss culture of mentoring and time for reflection? * (SJ) Ombudsman Network as chance for further networking? * So putting ELN exports into the ELN would make sense as well? ### 9:45-10:15 Heike Böhm (Max Planck Institute for Medical Research): Teaching the use of ELN by building a community recipe book Email: heike.boehm@mr.mpg.de [**Presentation slides for the talk**](https://pure.mpg.de/rest/items/item_3341771_1/component/file_3341772/content) #### Abstract - Teaching Master students (and beginning PhD student) to take ‘good’ lab notes – especially in interdisciplinary sciences - How to document a kitchen experiment (the difference between recipes and lab book entries) - Facilitating interaction and community by a fun, low risk joint project * interdisciplinatory work introduces new things, struggle * connection to publication lost #### Questions/Thoughts * (SJ) No recording which ELN template version has been used. So templates need to have their own id. * (SJ) Comments are not exported in Labfolder. They seem not be first class citiziens in the system * referenced inventory must not be deleted, of ### *10:15-10:30 Coffee Break* ### 10:30-11:00 Sean Leavey (Max Planck Institute for Gravitational Physics): Building a plugin for sustainable academic research for the largest blogging platform on the web Email: sean.leavey@aei.mpg.de #### Abstract Having gotten fed up with the shortcomings of the numerous ELNs I've used throughout my academic career, I've spent a thousand hours since 2018 developing my own as a plugin on top of WordPress - blogging software used by 35% of all websites. The plugin is now in daily use by ca. 300 people and ca. 20 groups. In this talk I discuss the problems with other ELNs, give a brief tour of the features (and anti-features!) of the one I developed, and touch upon the question of sustainability of ELN platforms and long term archival of scientific work. [Slides](https://wolke7.aei.mpg.de/s/KMDJyFSWDxtzb3s) * Is your plugin available through the normal WP plugin marketplace? No, not yet. But ask per mail by Sean (sean.leavey@aei.mpg.de) ### 11:00-11:30 Stephan Janosch (Max Planck Institute of Molecular Cell Biology and Genetics): Using ELNs as source for a competence database Email: janosch@mpi-cbg.de #### Abstract ELNs collect what people are doing. What if you could mine this treasure and create a ressource which allows competence lookup of your colleagues. https://onthesamepage.online/gihodaf * competences * hidden REF * backward propagation of references * from publication back to entry * sample tracking * URLs in ELN should trigger web archive crawl and add the web archive link * https://ithenticate.mpdl.mpg.de * https://www.protocols.io ### 11:30-12:00 Ilja Bezrukov and Rebecca Schwab (Max Planck Institute for Developmental Biology): Using Confluence, an enterprise collaboration system as ELN Emails: {ibezrukov, rschwab}@tuebingen.mpg.de #### Abstract Atlassian Confluence is an enterprise collaboration system with wiki-like functionality and a large plugin ecosystem. We will present advantages and disadvantages of using it as ELN, and as a discussion and shared resources platform. We will also give an overview of the technical and licensing aspects. * https://www.atlassian.com * six years in usage * intuitive * lab work and administration can work together * end of support for local installation announced * https://www.atlassian.com/migration/journey-to-cloud ### *12:00-12:15 Coffee Break* ### 12:15-12:45 Anthony Piro (Max Planck Institute for Plant Breeding Research): Using electronic lab notebooks to foster collaborative efforts in the lab Email: piro@mpipz.mpg.de #### Abstract Electronic lab notebooks are an ideal means of compiling notes from multiple investigators working on collaborative projects. Furthermore, the ability to link electronic notebooks to electronic inventories of lab supplies - such as oligonucleotides - aids sharing common materials during collaboration and avoids unnecessary duplicate ordering. * 🇬🇧 you can type along ### 12:45-1:30 Open Discussion Round * Chemicals (SJ) * updating safety sheets is a lot of work * be more efficient * from individual CBGs to GV and back * interfaces into/exports of SAP * Is there MPG funding for development of ELN software? * perhaps MPDL SoLi https://www.soli.mpdl.mpg.de/en/proposals_funding/ * ELN specific meetings per software * European ELN user meeting - contact aviral (aviral.vaid@cec.mpg.de) * there's a UK ELN network that we could contact as well, run by JISC * use existing networks (here MPG Bioimaging or Ombudspersons) * Labfolder community meeting with vendor (private + public part) * MPG RSE team room: https://extranet.mpg.de/teams/RSE (@SJ invite Aviral) * core facility meeting #### Communication * https://listsrv.mpdl.mpg.de/mailman/listinfo/eln-mpg-internal #### Other workshop/event ideas? 1. Scientific Software 2. Topic 3. Topic ### 1:30 End of Workshop * 🇬🇧 you can type along ## Other Events within the MPG on ELNs * DV Meeting on 30th September 2021: Speaker: Bernd Rinn (ETH Zürich - Scientific IT Services) on openBIS https://dv-treffen.mpg.de/posts/programm/