Submit your session proposals for CarpentryConnect and BioNT Community Event - Heidelberg 2024! The CarpentryConnect and BioNT community event - Heidelberg 2024 is expected to be the key community-building and networking event for The Carpentries and BioNT’s community in Europe, with worldwide participation. Taking place 12 - 14 November 2024 at EMBL Heidelberg, this event will provide the opportunity to bring together newer and more experienced community members to share knowledge, network, develop new skills, and develop strategies for training beyond academia and building strong local and regional training communities.

Announcing a community event in EMBL Heidelberg, 12-14 November 2024. Join us for CarpentryConnect Heidelberg 2024 at EMBL! More information at: carpentries.org/blog/2024/01/announcing-cchd24 Bio-IT welcomes you to a community event, that we are co-organising with the project BioNT and The Carpentries. We will talk about and act on how to connect people through training across sectors (Academia and Industry, as well as job seekers), how to enhance the impact of training activities, and how to increase diversity within our training communities.

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.

The Bio-IT website includes courses announcements not only from Bio-IT, but from various EMBL entities including the EMBL centers and ALMF. Would you also like to know how to announce a course and manage the related registrations and communication through our website? Here’s a short overview for you! Upcoming courses in the Bio-IT website The page available at bio-it.embl.de/upcoming-courses includes two lists. The Upcoming courses on top shows courses planned with a date and time, while you can consider the Training plan on the bottom our wishlist of courses we are planning or would like to organise in the future.

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.

We want you(r training requests)! New year, new resolutions. It has always been central in the Bio-IT’s mission to plan and deliver a curriculum of training courses designed on the needs and wishes of the (biocomputational) community at EMBL. From this year, we have a tool to collect them in a systematic way: the Bio-IT training catalogue. The platform was initiated, and developed to an advanced state, from Bio-IT’s summer intern Emily Simons, who joined us through the DAAD RISE project.

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.

Visit the official BioNT website: biont-training.eu Short term training courses, DIGITAL Europe The DIGITAL Europe Programme call DIGITAL-2022-TRAINING-02-SHORT-COURSES aims at increasing the training offer in digital skills of people in the workforce and job-seekers, through free and open short-term courses. Bio-IT, leading a consortium of 9 institutions in 4 countries, applied to the call with a project for the computational training of people in the Life Sciences sector. The project got funded and will start its activities in early 2023.

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!

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.

The EMBL Python User Group (EPUG) is a collective of python programmers at EMBL who meet regularly (every other Tuesday at 4 PM) to discuss python-related topics, demonstrate tools and modules, and experiment with python-related software and hardware. After the summer break, we reached out to the community to discuss EPUG format, addressed level of expertise, ideas for improvements and answer potential newcomers questions. This post includes a summary of what happened.

✈️ Hello, this is your community manager speaking. Bio-IT community manager, but - since recently - also Zenodo community manager. What does this mean? Here explained. FAIR, sustainable and (eventually) open science FAIR stands for Findable, Accessible, Interoperable, Reusable. It refers to a list of 15 principles published in The FAIR Guiding Principles for scientific data management and stewardship in 2016, aimed at “improving the infrastructure supporting the reuse of scholarly data”.

What? Well, a shared calendar 📆. Who? From Bio-IT, for you EMBLites 💚. When? All year long, update in real-time ⌚. Where? Online 💻 or on site 🏢, wherever something is happening. Why? Here’s why: The Bio-IT calendar The Bio-IT calendar lists courses, events, and activities open to all EMBL members. You can simply consult it there or add it to your EMBL calendar. This is a friendly calendar of things you may want to do - not of things you have to do, of opportunities to interact with EMBL researchers and learn new skills.

“CommunityRule is a governance toolkit for great communities”. The website homepage provides this definition, and then challenges you with two questions: How does your community work? Are you ready to make hard decisions? Defining our governance structure The purpose of the CommunityRule project is to make you think about how your community is organised, who is in charge of making decisions and who can influence this decisions. The project is still work in progress, but a wide range of definitions and tags is already available - even if not all of them are thoroughly described - to define your community governance structure.

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!

A lot has happened in the past few weeks, as everyone at EMBL has been adapting to working from home. It’s been a busy time for the Bio-IT community: as computational researchers and support staff, most of our community members are able to continue working on most of their normal tasks/research, the only major change being that they do that from home. Many such members are facing additional challenges, though, from struggling with reduced Internet connection speeds to balancing their work tasks with the need to care for children and other family members.

Restrictions are increasingly being rolled out with a view to slowing the spread of the novel Coronavirus. So far, the EMBL sites in Rome and Barcelona have been closed and our colleagues at those stations are having to find ways to work from home (where possible). Similarly, members at all other stations have been asked to work from home whenever they can, and in-person events both large and small are being cancelled to reduce the risk of viral transmission.

Post by Malvika Sharan on behalf of the Bio-IT Team To express our appreciation and gratitude for your contribution to the Bio-IT project and further support your involvement in such activities within and outside EMBL, we are launching the Bio-IT Outreach & Travel Fellowship program 2020. Any EMBL member who has actively led, facilitated, contributed to or participated in a Bio-IT event or project can request a fellowship of up to 500 Euros to attend or organise an event in 2020 by submitting an application.

By Malvika Sharan, a Community Outreach Coordinator of EMBL Bio-IT project. This post was originally written for the Software Sustainability Institute’s blog series. Let me start by saying that I am a positive person (generally speaking!). If you tell me about a disaster, I will try to find something positive in it. Having made that disclaimer, I can now safely say that I am a bit pessimistic too. Therefore, no matter how positive I am about my training and outreach events as a community manager, I am ready to fight the disaster that hasn’t occurred yet.

On 4 July 2019, we hosted the very first Bio-IT hackathon. We invited our community members from various research groups/departments a few months ahead of the event and asked them to think of projects that they could pitch for this hackathon. In order to provide a selection of topics, we encouraged project ideas ranging from developing technical tools to writing documents. We were successful at drawing 16 contributors from different research and non-research groups to participate in this event.

Post by Malvika Sharan. Written as a part of her participation at Bioinformatics Open Source Conference 2019 supported by the Open Bionformatics Foundation (OBF) sponsors a Travel Fellowship program fellowship, this post first appeared on the Open Bionformatics Foundation (OBF) website. The phrase ‘water cooler effect’ is derived from informal gatherings and connections made around water coolers (or vending machines these days!) at the workplace or other formal situations. Such unplanned encounters lead to genuine connections between people resulting in meaningful and productive collaborations.

Dear Community Managers, Have you been working on multiple projects with multiple groups of people? Have you ever (or every day) felt like that you are not specialised enough? Then these next 90 seconds are for you (because I just lost 30 seconds introducing myself). You may think that you are less specialised than many in your community, but that’s mostly because you know too many people of specific expertise. Remember?