The Carpentries workbench The Carpentries teach foundational coding and data science skills to researchers worldwide. The Carpentries is a community of people that gathers together with the aim to make technical skills training effective, accessible and scalable. Most of the training happens in the form of short and very hands-on training courses, collaboratively designed (and openly shared) in the community, and delivered by certified The Carpentries instructors (ream more on how to become a certified instructor) and multiple helpers, to ensure that all trainees are properly followed.

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.

Recently, Bio-IT took some steps towards the standardisation of its activities description. In the context of the Data Sciences strategy at EMBL and in particular in WorkStream 1 - “Internal and external training & support”, we collected a glossary of competencies that we are going to use for different purposes. Bio-IT competencies This glossary includes two types of terms: the skills, representing expertise, abilities to use tools, and the topics, matters of knowledge.

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!