# Hello attendees of the HDBI training symposium! 2023-09-12 I'm Richard one of the organisers of the day and one of the workshop presenters. To get the most out of the day **you will need a few things set-up before hand**. :warning: **You will need to bring a laptop with you to participate in the workshop sessions!** *Getting to the venue:* Upon arrival to the Francis Crick Institute (1 Midland Road, London, NW1 1AT), please report to reception, where they’ll direct you to the meeting room (Seminar Suite) [Crick's Visit us page](https://www.crick.ac.uk/about-us/visit-us) <iframe width="425" height="350" src="https://www.openstreetmap.org/export/embed.html?bbox=-0.14259696006774905%2C51.52702866914611%2C-0.11781334877014162%2C51.53541156643091&amp;layer=mapnik&amp;marker=51.53122031074359%2C-0.1302051544189453" style="border: 1px solid black"></iframe><br/><small><a href="https://www.openstreetmap.org/?mlat=51.53122&amp;mlon=-0.13021#map=17/51.53122/-0.13021">View Larger Map</a></small> *Arrival time:* This is set from 9:30-10:00am *Zoom link to join online:* https://ucl.zoom.us/j/91852549377?pwd=WVFWNldsQkoza3ZDcWQxSGY4MXlKZz09 (Meeting ID: 918 5254 9377; Passcode: 079201) Remember to double check that you have: - A laptop charger (if your device won't last all day under continuous use) - The ability to access the internet at the Crick institute, there is eduroam, 'Crick Events WiFi (PWD: Cr!ck2023)' & 'The Cloud WiFi' available on site (see: https://www.crick.ac.uk/about-us/visit-us/facilities) For the Renku session, the OMERO session, & my session **you will need an account on [Renkulab.io](Renkulab.io)**, I will also need to know your [Renkulab.io](Renkulab.io) usernames so that I can add you to a group and share some materials with you on the platform. (FYI Renku is an open source project developed by the swiss data science centre not a commercial platform so they won't be clogging up your inbox with marketing emails) It is possible to complete the [OMERO](https://www.openmicroscopy.org/omero/) session on your own device without using the [cloud environment that we have pre-prepared for the session](https://renkulab.io/projects/hdbi/omero-workshop) in Renku if you want to install all of the tools that we will be using during this session on your system. The software that you will need to install **if** you wish to locally on your own machine is as follows: - [OMERO.insight](https://www.openmicroscopy.org/omero/downloads/) the OMERO desktop client - [OMERO.python](https://www.openmicroscopy.org/omero/downloads/) the CLI client for OMERO allowing bulk uploads, and API access for programatic analysis of data on an OMERO server (If you have no CLI experience and don't know how to install a python package I'd suggest following along in the cloud environment) (You could also try running the [Renku session on your local machine](https://renku.readthedocs.io/en/stable/how-to-guides/own_machine/index.html) if you have docker installed - bonus points from me for anyone who uses this method) You will get the most out of both the [protocols.io](protocols.io) session and my session if you set up an account on [protocols.io](protocols.io) (FYI [protocols.io](protocols.io) is a commercial entity - [recently purchased by Springer-nature](https://group.springernature.com/gp/group/media/press-releases/publisher-acquires-protocolsio-driving-open-research/25844774), so I can't speak as confidently to what they'll do with you email address but they've not abused my inbox in the time I've had an account with them.) If you'd like me to add you to the [protocols.io HDBI workspace]() then please share your [protocols.io](protocols.io) username with me. Both [protocols.io](protocols.io) & [Renkulab.io](Renkulab.io) support sign-in via [ORCID](https://orcid.org/) so this is probably the easiest way to set-up accounts on both platforms, if you don't yet have an [ORCID](https://orcid.org/) now would be a good excuse to kill 3 birds with one stone. :warning: Please complete [this form](https://cryptpad.fr/form/#/2/form/view/xipCYkZTgIAyAoq2XCTmFwZ0taQS3bF4A8KZ5s6VIJc/) with your [Renkulab.io](Renkulab.io) username and optionally [protocols.io](protocols.io) username. Whilst I'm asking you to create accounts if you'd like to have a place to chat with other attendees, before, during or after the symposium to ask follow up questions or directions if you get lost on the way to the venue etc. I created a matrix space for HDBI and a room for this training symposium: https://matrix.to/#/#hdbi:matrix.org in which I am currently all alone 😢. (FYI matrix is an open source messaging protocol developed by a non-profit so again unlikely to abuse your email, it's similar to slack, discord, or teams) If you'd like to get a head start on my workshop whilst making delicious chocolate chip cookies :cookie: then checkout the [recipe](https://dx.doi.org/10.17504/protocols.io.n92ldmy9nl5b/v2) # Links ## Protocols.io - [Protocols.io](https://www.protocols.io/) - [Tutorials](https://www.protocols.io/tutorials) - [Webinars](https://www.protocols.io/webinars) - [Slides](https://docs.google.com/presentation/d/14WFoTvuaLcAsUFz3hdngzsCkKUSI1jfbqtAjwuApzLo/edit#slide=id.p1) ## Renku - [Presentation slides](https://docs.google.com/presentation/d/1xQiX_x93mA3eABiMFCPELwZ8_n4MFnhu) - [Renkulab.io](https://renkulab.io/) - [Documentation](https://renku.readthedocs.io/en/latest/) - [Forum](https://renku.discourse.group/) - [Source Code](https://github.com/SwissDataScienceCenter) - [Tutorial Link](bit.ly/renku-hdbi-tutorial) - ## OMERO - [Open Microscopy Environment](https://www.openmicroscopy.org/index.html) - [Documentation](https://www.openmicroscopy.org/docs/) - [Guides](https://omero-guides.readthedocs.io/en/latest/) - [image.sc forum](https://forum.image.sc/c/data-management/29) - [Source Code](https://github.com/ome/) - - [Renkulab.io Environment for today's workshop](https://renkulab.io/projects/hdbi/omero-workshop) - Slides and other resources from OME training [downloads.openmicroscopy.org](http://downloads.openmicroscopy.org/) - [Slides & other resources for today](https://downloads.openmicroscopy.org/presentations/2023/HDBI-Crick/) - Demo server address: [outreach.openmicroscopy.org](http://outreach.openmicroscopy.org) - :warning: Credentials will be reset and this server wiped on a regular basis so __DO NOT__ store any data here that you want to keep. You can apply for a longer term account on an OMERO demo at: https://www.openmicroscopy.org/explore/ - Contact Regarding OME training: [training-support@openmicroscopy.org](mailto:training-support@openmicroscopy.org) ## HCA data portal - [Human Cell Atlas Data Portal](https://data.humancellatlas.org/) - [Human Cell Atlas Metadata Structure](https://github.com/HumanCellAtlas/metadata-schema/blob/master/docs/structure.md) - [Slides](https://docs.google.com/presentation/d/194HDRORDrPmaQlg7sHsCc1SZL2EIiGUsflB6vXF-WJg/edit#slide=id.g27bfda8b93c_0_239) ## Open, Collaborative, and Reproducible Scientific Workflows - [CCCOOCI project page](https://renkulab.io/projects/hdbi/data-management/cccooci) - [Slides](https://hdbi.gitlab.io/data-management/hdbi-data-outputs-quarto-presentations/training-symposium_2023-09-12.html) (These will likely be changing up until the event)