Report BUP1

This is a brief report on the first Budapest Unseminar in Bioinformatics which was organized as part of an EMBO practical workshop, also several local bioinformaticians joined the fun.

As an icebreaker, participants were separated into different groups based on their cloths’ color, which worked quite well.
Next, the groups were asked to interview individuals to find out some interesting / unique / funny fact about this person. Then these traits where noted and collected and in the end read out aloud, so other groups could guess who this trait belonged to.
People seemed to enjoy this ice-breaker quite a bit (leading to it taking longer than anticipated) and it also helped getting to know each other, which was useful for the rest of the week long EMBO course…

For the main activity, we created five broad topics (Apps, Websites, Software Tools, Communication Tool, non-software Tools) and then participants joined the respective group they’re interested in to discuss these topics.
The task at hand was then to come up with tools which they find particularly useful in their day-to-day work or just makes life easier, discuss them, rank them and finally present them to everybody. We also asked a facilitator per group to keep track of these tools by using a piratepad.

The atmosphere was great, people enjoyed themselves and had a lot of fun!

Here are some impressions:

BUP1

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Holger

Report HUB22 – Visual perspectives in science

This page includes a short summary of what took place at HUB22 – Visual perspectives in science, together with feedback and reflection on the event from several of the HUB organisers.

Summary of HUB22

This HUB was the second time we’ve tied an unseminar in with the VizBi conference series, using the unseminar as a social event for conference participants, as well as a chance for the local HUB community to meet up with the conference participants.

We were very happy with the turn-out for the event (50 or so), and that it was a good mix of locals and conference participants. It’s always exciting to have some out-of-town speakers at the unseminars, which we had this time through one of the flash talks, and from Jan Aert’s super-quick introduction to ideas associated with data visualisation for science.

We also tried out something new for HUB – a session using improvisational dance, in this case to visualise London Underground station usage data. This was led by local dance teacher and dance therapist Ariane Konrad, who everyone we spoke with greatly enjoyed working with. Hopefully we can find some interesting contexts for some further collaborations with her in the future!

Another highlight was the amazing work done in the dative exercise at the HUB on making a video to visualise London Underground passenger usage data by David Ma and Francis Rowland!

We were also glad to have food and refreshments made available through the support of de.NBI – thanks to them, and all participants of the event!

Feedback from HUB organisers

Laura Howes

If there was one thing I think was clear to me on reflection, a simpler programme has benefits and allows you to concentrate on:

  • delivering what you want well
  • allowing time and effort for issues like diversity
  • reducing stress

In that spirit and as requested… things I liked

  • props on the signage
  • loved trying something new (dance)
  • the numbers and engagement of participants was great

Things to be improved

  • it generally felt a bit rushed (too much on?)
  • all male and pale speakers
  • mismatch between info on web and where we actually went for post HUB-drinks.

That said I agree that Flo did a great job and I’ve heard some very good feedback so I think again it’s a case of making sure that knowing we could do better doesn’t cloud the ability to appreciate what we achieved.

 

 

Adam Gristwood

Things I liked:

  • having a choice of activities – the dance routine was awesome.
  • talks – although a bit more visualisation stuff would have been good, eg. more videos.
  • the starting time! Personal preference but was nice not to have to rush out of work early.
  • range of participants – is fantastic to have people who work outside HD at these events.
  • organisation/mcing was great.

Things to do differently:

  • give people opportunity to present what they learnt (dance routine got some time, but would have been great to hear some of the others)
  • calmer programme
  • someone to take responsibility for guiding people to the pub afterwards?
  • check the destination on a bus when responsible for guiding a large group of people across town!
  • female speakers

Aidan Budd

I really enjoyed seeing some ‘old friends’ again at the HUB – including Gustavo (one of the people who kick-started the Cape Town unseminars, he’s now at EMBL-EBI in Hinxton) and Maria, who was in Paris for several years, and is now back nearish to here, and it turns out worked in Florian’s lab before she left. Small world, eh?!

I thought Florian did a great job yesterday – looked like the evening was very well received. Thanks for that, Florian! And to all the others who worked hard to make it a success.

Things I particularly liked:

  •  the venue fitted the purpose and our activities well
  • the ice breaker was super-simple (in some ways) and went very well
  • trying something different (and I think fun) with the dance
  • Florian’s MCing

Things I think we could do differently:

  • a less full program, for exactly the reasons Laura gives above. I know it’s really hard to keep the number of things you do in an event low (whenever I organise a course, it’s always so hard to say ‘we can do without that’) – but I think, in retrospect, we could have made two HUBs out of this – one on optical illusions, one on data viz, and then both would not have felt so rushed etc.
  • no questions after Flash talks – if people want to talk with the flashtalkes, they can grab them afterwards
  • have more diverse speakers

Malvika’s SciFund writing assignment about HUB

The text below is a blog written by HUB/WUBSyB participant Malvika Sharan, as an assignment for an online course she participated in offered by SciFund challenge for scientific outreach.

Un-seminar in Bioinformatics, it’s finally happening!

I am Malvika Sharan, a PhD student at the University of Würzburg. My target audience includes graduate students and researchers in and around Würzburg, Germany, who are working in the fields of bioinformatics and systems biology.

As a PhD student of bioinformatics (working in a research group where most people are experimental biologists), attending bio-computational conferences has always made me feel like home where everyone talks the same technical language as me (maybe a bit more fluently)!

HUBsession

One of the sessions of Heidelberg Unseminars in Bioinformatics at EMBL. Image by Adam Gristwood. Source: www.hub-hub.de

In one such conference in 2013, while I was still trying to figure out my scientific interests as a ‘first-year-PhD-student’, I signed up for a side-event called ‘Birds of a feather (BoF)’ on ‘Unseminars’. At this event, I learnt that an ‘unseminar’ (which was apparently not a printing mistake for ‘seminar’) refers to a participant-driven unconventional seminar. We, as participants, could choose topics and share our scientific interests with like-minded people in a completely laid-back environment.

AidanBuddAddressingAnUnseminar

Aidan Budd addressing an unseminar. Image by Matthew Betts

Without doubt, this was one of the most welcoming events I ever attended. Aidan Budd, who worked as a computational biologist at European Molecular Biology Laboratory (EMBL) in Heidelberg, was the organizer of this event. He enthusiastically shared his approach of using unseminar as a tool for community building and introduced us to Heidelberg Unseminars in Bioinformatics (HUB) that he had co-founded in Heidelberg.

This experience motivated my supervisor, Konrad, and me to organize a similar event to bring bioinformatics enthusiasts together in our university. We kept in touch with Aidan and contributed to a crowd-sourced effort of writing a scientific article on unseminars and unconferences that got published early this year.

Video filmed at HUB7

Meanwhile, during several events in my university, I met quite a few researchers who have been working in diverse fields of computational biology: those who don’t get an opportunity or platform for interacting with other groups that share their interests.

JUST_DO_IT._(NIKE)

Nike’s famous philosophy: “JUST DO IT”. Source: WikiMedia commons https://commons.wikimedia.org/wiki/File:JUST_DO_IT._%28NIKE%29.gif

Now, more than ever, I felt a desperate need to revisit the idea of bringing the bioinformatics community together in my university. As a ‘final-year-PhD-student’, I have developed teaching skills, organized several events in my graduate school, participated in several hours of unseminar-discussions with my colleagues and gained outreach knowledge from the SciFund challenge training. It looks like the right time has come to “JUST DO IT” (so says the Nike-box on my shoe-stand)!

Well, there it is! A not-too-elaborate background story of the unseminar event that is finally happening in our institute (Institute for Molecular Infection Biology, University of Würzburg) on November 18, 2015 at 5:00 pm. We have set up a basic webpage and sent out invitations to everyone in the university. The response so far is encouraging and I am eager to see how this turns out.

If you have any suggestions, experiences, or anecdotes to share, feel free to get in touch with us!


 

Now that the first Würzburg WUBSyB has been held, I can report that it was attended by more than 30 researchers from different institutes in University of Würzburg. Due to common interest we would be organizing it on second Thursday of each month.

Report HUB20 – Storytelling in Science

This is a short summary of what took place at HUB20 – Storytelling in Science.

HUB 20 was held on Tuesday, the 8th of December 2015. The theme of the meeting was storytelling in science, with the aim that participants work together to think about how they might use creative ways to talk about their work and aspects relating to their work. More than 30 people from institutes across Heidelberg and beyond attended the event. The evening began with a warm up exercise, where people were given pieces of a Christmas card and then asked to find the people with the other parts to complete the puzzle. Then participants sellotaped the cards together and wrote a message of good will to one of the other HUBs around the world that have been inspired by the Heidelberg Unseminars in Bioinformatics.

Next came a talk by Adam Gristwood, an Editor from EMBL who gave an overview of the potential for weaving narrative into how one speaks about science. One take home message was to think about the audience. One example to give some context to this was given by Adam who recalled a speaker from a performing arts school began what seemed initially to be a fairly mundane talk on this topic, before grabbing a guitar and strumming a tune telling people to *LOVE* their audience, whoever they are and singing a personal story about his experiences with different audiences and their very varied responses. The idea is that people generally like stories about people, so starting your story at a human level – such as why you became a scientist in the first place –, can be a good place to begin. Especially in communicating to the public, but also to peers in different fields of expertise, it can be useful to take a step back – think about why your research is important? What is the bigger picture? It is also important to remember storytelling and narrative is just one tool of many that one can use to communicate – so appropriateness is also important to consider.

Some examples of creative ways to do this can be found here: http://storycollider.org

With this in mind, participants were asked to get into groups of three and assign one interviewer, one interviewee, one reporter.

The
Interviewer asked questions to interviewee – with aim to extract unique facts about the person. Reporter to write briefly three “unique” facts they observe from the interview on card provided.

The aim was to encourage participants to think about 1) the way they tell stories about themselves; 2) the way they seek stories and information from others; 3) the kind of information that is interesting to take from

Next up was two talks:

Eva-Maria Gottman, head of marketing at the BioMed-X Innovation Centre, explored how Disney Pixar develops stories for their movies, and some of the simple principles behind it that can be translated to science communication. Eva-Maria also looked at story structure, and how considering this structure can help get your message across.

Lucas Czech, a PhD student at the Heidelberg Institute for Theoretical Studies, gave an brilliantly-illustrated presentation to explain his work science-slam style. He told the Story of Small-land and Tinyton”, to shed light on his work analysing microbial communities via shotgun sequencing and evolutionary placements of the resulting reads on a reference tree.

Participants were then asked to come up with analogies for their research, in order to give a visual hook to the listener who can take their understanding of everyday things and use these to have a better idea about scientific work. But some caution was urged! – as science journalist Jacob Aron once said: “Analogies in science writing are like forklift trucks – when used correctly they do a lot of heavy lifting, but if you don’t know what you’re doing you’ll quickly drive them into a wall of laboured metaphors and cause some major damage.”

This was discussed in small groups, the groups then selected their favourite one and from these selections, people voted for their overall favourites. Ideas included:

  • Is being sick during childhood like being vaccinated against asthma?
  • Building open source software is like being in an open playground where parents gave you the tools and you can do whatever you want with those tools.
  • Bioinformatics is like a recycling machine – put in raw material and get a useful output.
  • 3d chromatin architecture is like a spaghetti with meatballs – it is a mess!
  • And the winner… Nanobodies can be used like a chewing gum in a keyhole so the key does not fit anymore.

For anyone interested in the concept of analogy itself, the following book is a good read: Surfaces and Essences, by Douglas Hofstadter and Emmanuel Sander – http://surfacesandessences.com/

The authors write: “…the spotting of analogies pervades every moment of our thought, thus constituting thought’s core. To put it more explicitly, analogies do not happen in our minds just once a week, once a day, once an hour, or once a minute; they spring up inside our minds numerous times every second. We swim non-stop in an ocean of small, medium-sized and large analogies, ranging from mundane trivialities to brilliant insights… This incessant mental sparkling, lying somewhere below the conscious threshold gives rise to our most basic, humdrum low-level acts of categorisation, whose purpose is to allow us to understand the situations we encounter (or at least their most primordial elements) and to let us communicate with others about them.”

The evening concluded with a gluhwein (or two!) at the Christmas market.

(Report written by Adam Gristwood)

Report HUB 21 – Interactive notebooks

You can find more details of how the event was run here.

Interest in IPython/Jupyter notebooks was enormous so we actually had to close the doodle pool once we reached 50 participants due to space constraints at BioMed X. As expected from the doodle results around 50 people actually showed up. For the icebreaker people had to arrange themselves in the corridor based on their coding experience from the least experienced to the most experienced. Ice breaker was followed by short information about BioMed X presented by one of BioMed X’s group leaders Simone Fulle. Samo Turk then gave short introduction in Python programming and Jupyter notebooks showing some basic concepts in Python programming and explaining the benefits of interactive notebooks. Florian Huber followed with R in Jupyter demonstrating the power of excellent Bioconductor package. Finally Samo explained the basic idea behind pair programming which was also an introduction into the group activity – pair programming. Based on the icebreaker it was clear that roughly half people were inexperienced in programming so people formed pairs with one experienced and one inexperienced member. They were allowed to use any programming language to solve Rosalind problems (http://rosalind.info/). People really enjoyed this exercise and some pairs were actively coding even after the official program ended at 9:30pm and the last pair stopped coding at 11pm!

Report on HUB19 – Intuistics

HUB wiki page for this unseminar

Another successful evening! With around 60 people* and several helping hands on deck, people were intrigued from the beginning with their werewolf diagnoses and testing kits, with several groups chatting quite happily. It seemed almost a shame to interrupt this with a welcome and intro to the evening’s programme. Bernd Klaus then gave a fun flash talk on ‘cheating with charts’, warming people up to the theme of the evening and getting people laughing at graphing (hats off to him for that). For the ice-breaker, several people guessed that there was a high chance of pairs of people with the same birthday. This was partly because there were twice as many people as we expected and partly because it’s a well-known example… but of course this didn’t matter – people liked getting off their feet to move around and talk to each other. Holger’s magic trick was intriguing, even to him I think – I still don’t know how he managed to guess people’s cards every time (perhaps parapsychology could be a topic for a future HUB, as long as we cross Holger’s palms with silver). Sam Caddick was a natural host for the game show. People seemed to intuitively know the right answer but for the wrong reason, but that was fine as whatever people said it stimulated discussion (or heated debate). The simulation with playing cards was enjoyed by all and (remarkably) gave the right answer, which was handy as none of us were that confident in explaining it analytically… The confidence quiz showed that people are indeed overconfident, with most groups giving correct ranges for between three and six of the answers. We then found the werewolf, with a brief chat and cartoon explanation of Bayesian statistics, disease prevalence and false-positive rates. It just remained to make some closing remarks, thank our guest presenters (Bernd and Sam) with wine, apologise for not buying wine for our in-house magician (Holger), and then retire to the foyer for wine and snacks kindly provided by HFLYS.

Thanks to everyone who made it happen. I’m looking forward to the next one.

Explanatory slides used on the night

(* – about twice as many who put their names on the doodle.)

Tuesday 18th November

Time: 08:00

Place: Cafe Fresco, Heidelberg

In attendance: Aidan, Bronagh, Holger, Florian, Agnes, Thomas Wolf, Matt, Adam

Topics: Planning for 2015

Minutes

  • flip charts and masking tape are needed for HUB15
  • Matt to make the HUB 15 poster
  • HUB 15 will finish at 8.30, so everyone can go to the Christmas on Kornmarkt

Ideas for HUBS 2015

  1.  Open data/reproducible data. Florian, Iman
  2.  Statistics and Intuition; Matt, Thomas Wolf, Agnes
  3.  Storytelling in science; Adam, Iman
  4. Raspberry Jam; Holger
  5.  Working with REST in bioinformatics and beyond; Holger, Xiaofeng, Pierre
  6.  Open Space Technologies; Aidan
  7. Choosing a collaborative project for HUB/CUB; Bronagh

What is HUB?

Heidelberg Unseminars in Bioinformatics are participant-driven meetings where people with an interest in bioinformatics come together to discuss hot topics and exchange ideas and then go for a drink and a snack afterwards.