When interacting with GitLab at EMBL using git, two protocols are available, HTTPS and SSH. The first is convenient for a quick interaction. However, it quickly gets annoying as it will ask for your credentials every time. A more convenient and versatile option is SSH but it requires going through a few steps to configure it. If incorrectly configured, you will likely see the error message: Permission denied (public key). fatal: Could not read from remote repository.

Ever since it’s launch in 2017, EMBL’s Bio-IT chat has been steadily growing in all directions, expanding the range of topics discussed, the number of daily active users and different functionalities, some fun, some productive. Since around this time last year, the chat has grown to have: over 1600 users of which 410 are active on a monthly basis 700 channels split between 120 public and 580 private 1.5 million posts, which is to say, half million exchanged messages since last year a little over 820 board cards, thanks to the adoption of the new Task Management Boards feature introduced last year With such fast growth and many places to visit, it is normal to find yourself a little lost.

Hello hello everyone! This time around we come to you with different kind of announcement. Thanks to efforts from Federico Marotta, and contributions from Sarah Schulz, we now have a Trivia channel where you can have a little fun and test your scientific and general knowledge. Currently, there will be a trivia session every Thursday at 17:00, but if you are eager to test your knowledge, you are also welcome to issue a trivia start request at any time and a new trivia round will be started for you.

Over the years we have been promoting Git LFS at git.embl.de. With the move to an S3 backed storage, LFS is now the supported way to store large files in our platform. New limit on git push In order to enforce the use of LFS over plain git for large files, as of 2022-09-15 we now reject pushes larger than 100Mb. Introducing git LFS Git LFS is a solution to store large files in Git in a more efficient manner.

Following the feedback we obtained from all of you, we have decided to replace Mattermost, powering https://chat.embl.org, with an older technology, called IRC, following after the successful example of other communities. We hope that with this change you won’t have to deal with the burden of finding the right emoji and meme for every occasion. You will also be able to invite your oldies if /join #channel and /me commands are too unfamiliar or confusing.

Jupyter kernels Jupyter is a server but also an ecosystem of tools for data exploration. JupyterLab is a web interface to notebooks which can be used to document, visualize and perform computations. Computations in Jupyter are performed by a kernel, a separate component that understands how to perform calculations on request and return the result back to Jupyter. As such, a single JupyterLab installation can have multiple kernels with different configurations for different needs.

Bio-IT EMBL chat reached 1M posts EMBL’s Bio-IT chat, initiated in 2017 to facilitate internal real-time interactions between people at EMBL, has reached the milestone of 1.000.000 posts in the first days of February 2022. At close to 5 years of service, and after a significant increase in adoption in the early days of the pandemic, the EMBL chat is now a very active platform with close to 600 channels and a daily exchange of over 2000 messages from over 330 active users.

RStudio is a powerful and user-friendly platform for developing and performing R based data analysis. Coupled with R Markdown, one can easily generate visually rich reports that are one of, if not the, most used feature by the R community at EMBL to communicate results. When the popular GBCS RStudio server backed by the large seneca server is too busy, or if you need a convenient way to generate R Markdown reports in parallel or as part of elaborate pipelines, you can use the following script:

Dear Bio-IT community, Before the end of the year, we would like to take the time to thank you all for your support, participation and contributions. We thankfully recognise that Bio-IT - a project spontaneously born within the EMBL Heidelberg community - still preserves its essence and aim. It is and always has been a community initiative, a way to join forces and share knowledge and ideas, reach common objectives, support each other.

Over the years, the use of symlinks and /g group shares became a de facto standard and recommended practice to workaround the limited storage capacity of the home folder in the EMBL cluster. While functional, these workarounds were unfriendly to beginners and suffered from intermittent problems associated with the overload and automatic cleaning procedures of shared drives and/or /scratch, Thanks to discussions and efforts following from a recent Bio-IT taskforce meetings, this quota has now been expanded to 50 GB.

Over the years, the Bio-IT EMBL Chat has seen an ever increasing list of cute and bouncy happy emoji, dancing cats, parrots, blobs and memes. We are always delighted to see how people customize the space to feel more fun and cheerful and so, to celebrate and recognize this contribution, we have created the Happiness enhancer badge that will be granted to our most active emoji creators: We love to see how you make this place so lively!

Back in early 2020 the Bio-IT project took another step towards ensuring data privacy. Coupled with learning that different groups at EMBL had multiple independent subscriptions to a broad range of survey platforms, the Bio-IT project setup LimeSurvey locally and gained another powerful and reliable service. Since then, this platform has been used to collect feedback from hundreds of workshop attendees, inquire EMBL’s Python User Group (EPUG) and EMBL’s R User Group communities, and to run several internal surveys.

EMBL provides an ownCloud server with (as of March 2021) 50GiB of storage for every EMBL user. To access it navigate to oc.embl.de and login using your EMBL credentials. An alternative to Google Docs/Drive You can use this system much like Google Docs or Google Drive by storing and sharing files or using the built in tools to edit documents. Programmatic access Besides public and private links for download and upload, Owncloud provides a WebDAV interface that can be used for programmatic access.

Initially proposed as an EMBL’s coding club collaborative programming project, the EMBL Bio-IT chat bot, avidly named BIT, took off in 2020 and is already diligently announcing courses and workshops in the Bio-IT-announce channel. Introducing BIT With a modular design, allowing for anyone to contribute new behavior with very little code, BIT, EMBL’s Bio-IT chat bot, is slowly gaining new abilities and showing its usefulness. As of 2021 it already assists EMBL’s Git admin team on specific administrative tasks and monitors EMBL and Bio-IT services keeping us up to date with changes.

EMBL’s (Bio-IT) chat has been initiated in 2017 to facilitate internal real-time interactions between people at EMBL, to promote group discussions and sharing of information. As of 2021 more than 1000 users are registered with over 120 active daily. In part due to the 2020 SARS-CoV-2 pandemic situation, the platform gained particular relevance and became a central hub for communication between members of all EMBL sites. The platform effectively became a pan-EMBL service in 2021, welcoming EMBL-EBI, that would join all other EMBL sites.

This quick tutorial shows you how to connect GitLab at EMBL with a Slack workspace. This can be very useful when you want to stay informed about activities in your repository without having to check your emails all the time - in fact, you may decide to disable email notifications for the repository because Slack notifications are quicker to see, manage and act upon! This tutorial also shows you the power of so-called webhooks!