Verified Commit da329253 authored by Renato Alves's avatar Renato Alves 🌱
Browse files

Correct broken links and additional references to blogs

parent b164b45a
......@@ -11,9 +11,9 @@ menu:
Hello!
Thank you for visiting the [EMBL Bio-IT Community](https://bio-it.embl.de/) Blogs.
Thank you for visiting the [EMBL Bio-IT Community](https://bio-it.embl.de/) Blog.
**Bio-IT Community Blogs** is an Open Source project where you as a community member are the contributor of its contents.
**Bio-IT Community Blog** is an Open Source project where you, as a community member, are a contributor to its content.
**Short summary**
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......@@ -34,7 +34,7 @@ Would you like to contribute to this project?
### Submitting posts:
Please use this [markdown template](https://git.embl.de/grp-bio-it/bio-it-blogs/blob/master/content/posts/2019-02-16-bio-it-community-blogs.md) to write your post and submit via email, issue or pull request.
Please use this [markdown template](https://git.embl.de/grp-bio-it/blog/blob/master/content/posts/2019-02-16-bio-it-community-blog.md) to write your post and submit via email, issue or pull request.
You can read more about the GitLab Pages and data protection [here](https://bio-it.embl.de/gitlab-pages/)
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......@@ -3,17 +3,17 @@ date: 2019-02-16T19:29:59+01:00
description:
featured_image: "images/fZ_0JXvH1il_rawpixel_unsplash.jpeg"
tags: []
title: "Bio-IT Community Blogs"
title: "Bio-IT Community Blog"
omit_header_text: true
---
## Bio-IT Community Blogs
## Bio-IT Community Blog
*Disclaimer: This post is a summary of [about](https://grp-bio-it.embl-community.io/bio-it-blogs/about/) and [contribute](https://grp-bio-it.embl-community.io/bio-it-blogs/contribute/) pages of this website. So if you have read them, you should probably skip it! :)*
*Disclaimer: This post is a summary of [about](https://grp-bio-it.embl-community.io/blog/about/) and [contribute](https://grp-bio-it.embl-community.io/blog/contribute/) pages of this website. So if you have read them, you should probably skip it! :)*
**Bio-IT Community Blogs** is an Open Source project where you as a community member are the contributor of its contents. This project will be developed by me (*Hi! I am Malvika Sharan, a coordinator of EMBL Bio-IT*) to engage with the members of Bio-IT community at EMBL.
**Bio-IT Community Blog** is an Open Source project where you as a community member are the contributor of its contents. This project will be developed by me (*Hi! I am Malvika Sharan, a coordinator of EMBL Bio-IT*) to engage with the members of Bio-IT community at EMBL.
[Bio-IT](bio-it.embl.de) is a community initiative, which aims to build, support, and promote computational biology activity at EMBL Heidelberg. Bio-IT community members are scientists who share a varying level of interests and expertise in bioinformatics and help each other by sharing their skills, experience, and tools with others. The community has been growing since 2012 and has gained diverse members of different research interests who are bioinformatics learners, trainers, resource-developers, problem-solvers, decision-makers, knowledge-sharers, visitors and supporters.
[Bio-IT](https://bio-it.embl.de) is a community initiative, which aims to build, support, and promote computational biology activity at EMBL Heidelberg. Bio-IT community members are scientists who share a varying level of interests and expertise in bioinformatics and help each other by sharing their skills, experience, and tools with others. The community has been growing since 2012 and has gained diverse members of different research interests who are bioinformatics learners, trainers, resource-developers, problem-solvers, decision-makers, knowledge-sharers, visitors and supporters.
## Creating more opportunities to participate
......@@ -25,7 +25,7 @@ Interviews and open dialogues on relevant social issues with our community membe
## You can contribute too!
If you want to [contribute](https://grp-bio-it.embl-community.io/bio-it-blogs/contribute/) to the development of this project, [write me an email](mailto:malvika.sharan@embl.de).
If you want to [contribute](https://grp-bio-it.embl-community.io/blog/contribute/) to the development of this project, [write me an email](mailto:malvika.sharan@embl.de).
Everyone who will **become an author** for this project will **receive a complimentary USB stick**.
......
......@@ -25,14 +25,14 @@ On the International Women’s Day, on 8 March, we wanted to show our gratitude
TheyForShe is a non-binary take on [HeForShe](https://www.heforshe.org/en), which is a solidarity campaign for the advancement of gender equality, initiated by the United Nations. This is to imply, that even though the event is to celebrate for our female colleagues, we invited everyone interested in joining one or multiple sessions at the event.
![](https://git.embl.de/grp-bio-it/blogs/raw/master/content/images/IWD_Picture2.png)
![](../../images/IWD_Picture2.png)
### Skill-building sessions
Sponsored by Bio-IT and EDC, we ran 5 sessions: guided discussion on Ally Skills, transferable skill in Project Management, technical skill in GitHub for collaborative Documentation, hands-on storytelling skill, and group discussion on Open Science for gaining visibility. The different sessions were attended by participants from varying backgrounds and interests.
The Ally-Skill training is originally developed by Valerie Aurora in Frameshift Consulting. A Intentionally kept as the first session of the day, Ally-Skill session invited participants to understand the terminologies and basic skills of being an ally. A one-hour session was delivered by [Paul Sanchez](https://twitter.com/poljiology), [Sofya Mikhaleva](https://twitter.com/MikhalevaSofya), [Katja Ovchinnikova](https://twitter.com/Katja_HB4) and me.
A number of scenarios were given for the group discussions and discussed together with everyone. With a combination of informative presentation and interactive format in the group discussion, participants were exposed to general situations where they can step up as an ally to their colleagues and extend support to people from socially marginalised groups. Our participants appreciated this session and showed interest in organizing a longer version of this training. Read this [a blog by Katja](https://grp-bio-it.embl-community.io/blogs/posts/2019-03-14-ally-skills/) for more detail.
A number of scenarios were given for the group discussions and discussed together with everyone. With a combination of informative presentation and interactive format in the group discussion, participants were exposed to general situations where they can step up as an ally to their colleagues and extend support to people from socially marginalised groups. Our participants appreciated this session and showed interest in organizing a longer version of this training. Read this [a blog by Katja](https://grp-bio-it.embl-community.io/blog/posts/2019-03-14-ally-skills/) for more detail.
The Project Management session was one of the most popular sessions of the day. Project management is the practice of initiating, planning, executing, controlling, and closing the work of a team to achieve specific goals and meet specific success criteria at the specified time. This session was conducted by the professional project managers [Simone Bell](https://www.huber.embl.de/people/simone-bell/) (Huber Group) and [Ulrike Trojahn](https://intranet.embl.de/research/scb/zeller/members/index.php?s_personId=CP-60021738) (Bork/Zeller). This hands-on transferable-skill session introduces participants to the main principles and practices of project management that they can use in their work.
......@@ -52,10 +52,10 @@ Overall the event was a success and was well received by the participants. Unlik
The main motivations behind this event were 1) to openly talk about the nature of support women need in science, 2) how one can become an ally to their colleagues who face certain disadvantages, and 3) how to engage with the underrepresented minority groups, including women on campus and encourage them to exchange technical skills. Given the participation, engagement, and feedback, the event was a success. However, there are some existing issues that pose challenges to organise such events. For example, I had asked the event attendees if they would like to be involved in EDC activities on campus, to which only less than 25 percent participants indicated their willingness which makes it hard for us to gauge the interest of people in participating at such events.
![](https://git.embl.de/grp-bio-it/blogs/raw/master/content/images/IWD_Picture4.png)
![](../../images/IWD_Picture4.png)
Other challenges include lack of low-barrier funding to pay for basic requirements of the event, availability of EMBL staff as trainers, topics of interests for the networking and skill-building sessions, and lack of support in organising such events. Over the next month, I will be exploring these issues with the different communities at EMBL and I hope to host similar events in the future. You can check the official page and a complete schedule of this event is available on the [official page](https://bio-it.embl.de/international-womens-day-2019).
If you are interested in getting more information on any of these sessions, feel free to drop me a line by emailing sharan@embl.de.
*Header image of the hosts from the evening round-table networking session: Picture by [Sandra Correia](https://intranet.embl.de/research/cbb/ellenberg/members/index.php?s_personId=CP-60022664)*
\ No newline at end of file
*Header image of the hosts from the evening round-table networking session: Picture by [Sandra Correia](https://intranet.embl.de/research/cbb/ellenberg/members/index.php?s_personId=CP-60022664)*
......@@ -14,13 +14,13 @@ TLDR: I am collecting/sharing academic stories of my colleagues and friends (at
## Digital Storytelling for Culture Change
#### Project Page: [Bio-IT Community Blogs](https://grp-bio-it.embl-community.io/blogs)
#### Project Page: [Bio-IT Community Blog](https://grp-bio-it.embl-community.io/blog)
> *“Stories matter. Many stories matter. Stories have been used to dispossess and to malign, but stories can also be used to empower and to humanize. Stories can break the dignity of a people, but stories can also repair that broken dignity.”* - [Chimamanda Ngozi Adichie](https://twitter.com/ChimamandaReal), [The Danger of a Single Story](https://ngl.cengage.com/21centuryreading/resources/sites/default/files/B3_TG_AT7_0.pdf)
## Project background
**Digital storytelling** is a tool that allows people to share certain aspects of their personal stories. The digital equivalent of traditional storytelling can include any electronic (non-physical) media such as blogs, audio, motion videos or stills that help individuals to **tell their story or present an idea**.
**Digital storytelling** is a tool that allows people to share certain aspects of their personal stories. The digital equivalent of traditional storytelling can include any electronic (non-physical) media such as posts, audio, motion videos or stills that help individuals to **tell their story or present an idea**.
[Source: [Digital Storytelling](https://en.wikipedia.org/wiki/Digital_storytelling), also see: [Web 2.0](https://en.wikipedia.org/wiki/Web_2.0)]
......@@ -63,15 +63,15 @@ The study plan of the OL7 culture track, complemented with the personal discussi
The following elements have helped me in accomplishing my open leadership and open culture goals towards involving diverse voices in my work:
1. 📈 [Community Assessment Survey](https://grp-bio-it.embl-community.io/blogs/posts/2019-02-17-bio-it-community-survey/) (started in February, need to give a final push)
1. 📈 [Community Assessment Survey](https://grp-bio-it.embl-community.io/blog/posts/2019-02-17-bio-it-community-survey/) (started in February, need to give a final push)
This survey is being conducted to support the ongoing work in Bio-IT towards developing equitable strategies by identifying needs of the individual members for training, consulting and other bioinformatics resources. The data collected in this survey will be useful in identifying member groups who are currently underrepresented and what support is needed to engage with them. This survey helped us see the impact of our training and social activities organized for our members on a regular basis. It also allowed our respondents point out the exact bioinformatics needs from the community.
2. 👯‍♀🏳‍🌈 [International Women’s day: ‘TheyForShe’ Networking and Skill-Building Event](https://grp-bio-it.embl-community.io/blogs/posts/2019-03-10-iwd-2019/) (local effort)
2. 👯‍♀🏳‍🌈 [International Women’s day: ‘TheyForShe’ Networking and Skill-Building Event](https://grp-bio-it.embl-community.io/blog/posts/2019-03-10-iwd-2019/) (local effort)
On 8 March 2019, with the support from the members of Bio-IT, Staff Association, Equality and Diversity Committee and LGBTQ+ committee at EMBL Heidelberg, I co-organised a skill-building and networking event under the title “International Women’s day: ‘TheyForShe’ Networking and Skill-Building Event“. With this event, in addition to expressing our gratitude towards the women researchers and colleagues, I created a platform to involve ‘non-bioinformatic participants’ who are generally missing from our community. This event was attended by ~70 participants from both scientific and non-scientific domains at EMBL. From a number of short skill-building and networking session, participants could select which session they wanted to attend, without affecting their normal workday schedule.
3. 📭Launching of the the [Community Blog Platform](https://grp-bio-it.embl-community.io/blogs/posts/2019-02-16-bio-it-community-blogs/) (digital effort)
3. 📭Launching of the the [Community Blog Platform](https://grp-bio-it.embl-community.io/blog/posts/2019-02-16-bio-it-community-blog/) (digital effort)
As a main component for the Digital Storytelling, I launched the Bio-IT Community Blog Platform, inviting contributions from our community members. The content development for this platform will take place during the Mozilla sprint. I have already reached out to a number of members, with a special focus on the members of underrepresented groups. We will start documenting their stories in coming weeks.
......@@ -117,4 +117,4 @@ Finally, my mentor, Caleb, kindly offered (agreed!) to be the first person to be
*Creative Commons Attribution 4.0 International License by Malvika Sharan*
Cover image from by [@socialcut](https://unsplash.com/photos/FluPNkHfCTs) on Unsplash
\ No newline at end of file
Cover image from by [@socialcut](https://unsplash.com/photos/FluPNkHfCTs) on Unsplash
......@@ -9,7 +9,7 @@ omit_header_text: true
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](https://hackmd.io/79efcMTLSBmWzbmvxwg_AA) from different research and non-research groups to participate in this event.
![](https://git.embl.de/grp-bio-it/blogs/raw/master/content/images/2019_poster_1.png)
![](../../images/2019_poster_1.png)
In the past, we have organised and participated in several hackathon-style events in different community spaces. These events aimed at achieving different collaborative outcomes such as developing functioning software to learning resources, publications, and web-pages. Through our experiences at these events we had concluded that, for a hackathon to be successful, the participants must be able to work in an environment that is inspiring and productive for everyone involved. With the motivation of providing this experience for others in our community, one goal that we set for the event was to gather project proposals that would be interesting and accessible to people with different expertise and interests in programming and technical topics. In this regard, we were very happy with the selection of projects pitched by several members a month before the hackathon. 8 different projects (check the [Issues](https://git.embl.de/grp-bio-it/hackathons/issues)) were proposed, which were both creative and useful for the community and catered to both our programmer (web scraping, R Shiny development, developing website infrastructure) and non-programmer (graphic design, tutorial writing, digital storytelling) community members. Historically, ‘hackathons’ in tech-spaces have not been the most inclusive events, therefore we paid attention in making sure that we personally reached out to individuals, especially women researchers who would bring diverse perspectives and distinct expertise, but may not consider to join us at the event.
......@@ -34,19 +34,19 @@ Here is a brief list of the tasks that went into organising this hackathon, and
We received 10 responses to our survey, of which 7 participants rated the event as good and 3 found it excellent.
![](https://git.embl.de/grp-bio-it/blogs/raw/master/content/images/hack_new.png)
![](../../images/hack_new.png)
*Everyone indicated that they learned something new in the event.*
60% of the respondents thought that the event duration was too short, and 1 person thought that it was too long. 50% of the participants indicated that they will keep on working on the projects afterwards. The nature of a project or a particular challenge may affect peoples' engagement and the amount of time that they invest enthusiastically.
![](https://git.embl.de/grp-bio-it/blogs/raw/master/content/images/hack_members.png)
![](../../images/hack_members.png)
*60% of the respondent got to know at least one new member who they didn't know before.*
7 participants indicated that they will come back to this event if we organise it again, and the remaining respondents replied in 'maybe'.
![](https://git.embl.de/grp-bio-it/blogs/raw/master/content/images/hack_recommend.png)
![](../../images/hack_recommend.png)
*90% of the respondents indicated that they will recommend this event to others.*
......@@ -102,7 +102,7 @@ According to our participants, these are the things that we can do to make the n
- Save some time for the end to get a final report-out from each group and thank everyone
- Plan to kickoff this event an evening in advance where people can introduce their topics, set some goals, and come back the next day to directly work on the projects without losing time
<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Now a much larger bbq. Thanks to <a href="https://twitter.com/tbyhdgs?ref_src=twsrc%5Etfw">@tbyhdgs</a> and <a href="https://twitter.com/ZellerGroup?ref_src=twsrc%5Etfw">@ZellerGroup</a> for arranging it and taking care of all dietary requirements 🙌🏽 <a href="https://t.co/0HgWsG5YyM">pic.twitter.com/0HgWsG5YyM</a></p>&mdash; Malvika Sharan (@MalvikaSharan) <a href="https://twitter.com/MalvikaSharan/status/1146825893240856576?ref_src=twsrc%5Etfw">July 4, 2019</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Now a much larger bbq. Thanks to <a href="https://twitter.com/tbyhdgs">@tbyhdgs</a> and <a href="https://twitter.com/ZellerGroup">@ZellerGroup</a> for arranging it and taking care of all dietary requirements 🙌🏽 <a href="https://t.co/0HgWsG5YyM">pic.twitter.com/0HgWsG5YyM</a></p>&mdash; Malvika Sharan (@MalvikaSharan) <a href="https://twitter.com/MalvikaSharan/status/1146825893240856576">July 4, 2019</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
**A few more ideas for the next year**
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......@@ -14,24 +14,24 @@ Let me start by saying that I am a positive person (generally speaking!). If you
I have organised a number of events ranging from formal conferences, semi-formal training courses, to informal social meetings. In the last three years, I have become very comfortable with the kind of work that goes into organising such events. I have also become quite aware of the fact that my events will face unexpected threats even though I have planned everything well. This is where I want to use the term “pessimistic organiser”: someone who organises an event assuming that some disasters may appear.
![](https://git.embl.de/grp-bio-it/blogs/raw/master/content/images/risk_aspects.png)
![](../../images/risk_aspects.png)
*Important aspect of planning an event, DOI: 10.5281/zenodo.3368395*
One of the first tasks in my current job, while I was still recovering from my PhD life, was to host a week-long bioinformatics workshop for a group of 40 people that included new pre-docs and senior researchers from a European PhD training network. I had never organised any international event before, and this was the first project where I had a chance to lead and execute an event as the main organiser. This included designing and delivering the protein informatics workshop, organising travel and accommodation of everyone, handling the budget, choosing and booking locations for all the events, hosting an official dinner, finalising menus, coordinating with all the members and trainers involved, and everything in between. To my surprise, starting from the day that everyone arrived until everyone left, this event faced a number of challenging surprises. Did I expect them? No! I wasn’t a pessimistic organiser yet.
I had no contingency plan for what I would do if something went wrong. I was only excited about ticking the boxes on my task list and didn't take unexpected threats into account. Things did go wrong. For example, a new student showed up without a registration, a senior researcher decided to not show up on the first day that led to automatic cancellation of their hotel booking, one department was on vacation on the day they were supposed to host a tour to their facility, and the committee meeting went on one hour longer than scheduled and I wasn’t sure if I had the authority to interrupt them. These were exceptional situations that I couldn’t have predicted. However, I could have worked on my risk-management plan to already think of the challenges and put some possible solutions in place.
![](../../images/risk_mitigate.png)
![](https://git.embl.de/grp-bio-it/blogs/raw/master/content/images/risk_mitigate.png)
*Prioritising tasks and risks to address (green tick mark) and monitor (magnifying glass) before, during, and after an event, DOI: 10.5281/zenodo.3368395*
So... that was exciting, and it was a great learning experience too. Instead of making a big deal about any of these, my supervisor [Toby Gibson](https://www.embl.de/research/units/scb/gibson/members/index.php?s_personId=CP-60003209) told me to always remember that “things will go wrong, and that is alright”, and he was right. These minor challenges did not affect the overall success of the event.
I have come a long way since then. In the last year alone, I have chaired three international scientific conferences. I have organised and taught in a number of workshops, and have hosted various informal and formal outreach event series. Many of these events faced logistical problems (no show, low budget, and high demand), technical problems (no internet, lost packages, unsuitable venue, and projector failure) and natural disasters such as flood (Rome, Nov 2018) and earthquake (La Plata, Dec 2018). In the process of organising these, I have identified the important aspects of planning a scientific event. Furthermore, I have also created comprehensive lists of responsibilities that appear in the different stages of event organisation, risk assessment, task prioritisation, and risk mitigation.
![](https://git.embl.de/grp-bio-it/blogs/raw/master/content/images/risk_types.png)
![](../../images/risk_types.png)
*Adapted from an Illustration from Barron & Barron Project Management for Scientists and Engineers.*
Few of my top tips for planning an event as a pessimistic organiser are the following:
......
......@@ -24,7 +24,7 @@ meet the challenges these lockdowns pose to our work
and to support other members who are less able to keep working "as usual"
while the sites are closed.
[In our first post on this topic](https://grp-bio-it.embl-community.io/blogs/posts/2020-03-13-bio-it-activity-online-covid-19/),
[In our first post on this topic](https://grp-bio-it.embl-community.io/blog/posts/2020-03-13-bio-it-activity-online-covid-19/),
published as EMBL sites were beginning to close their doors,
I outlined how existing Bio-IT resources and support could be accessed
and might help keep our community connected while Covid-19 restrictions are in place.
......
---
title: "Blogs"
title: "Blog"
date: 2019-02-16T19:29:59+01:00
featured_image: "images/alexisrbrown_unsplash.jpeg"
---
## Bio-IT Community Blogs
## Bio-IT Community Blog
This project aims to offer a platform for sharing ideas, resources, tools & techniques, interesting publications, interviews and stories from all our community members.
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