HUB5

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What and how? Meet fellow bioinformaticians in Heidelberg and design a game, for anyone from non-bioinformatics scientist to school-children; as ever, you decide.

When? Thursday 21st March 19:00

Where? Griechische Taverne, Zwingerstrasse 20. (At the Bergbahn.)

Who? A team of people working at several different life-science organisations within Heidelberg are organising HUB, with your help (just get in touch or add your comments to this page).

After HUB5

You can see the games we came up with on the night here: HUB5 Games. Please contribute to further development by adding to those pages.

Programme

19:00 Welcome & introduction
19:15 Split in to groups to draft some games: their purpose, target audience, subject, and mechanics.
20:15 Each group to quickly present their game to everyone else.
20:30 Introduction to bioinformatics at a Heidelberg institution: Damien Devos on COS
20:40 Flash talk - ENCODE RNA dashboard, by Maik Röder
20:45 Final discussions
21:00 Drinks and informal discussions (normally we go to a pub, but this HUB is already in one so we'll stay there).

ENCODE RNA dashboard

  • Maik Röder
  • Freelancer
  • Presentation slides: http://www.slideshare.net/maikroeder/encode-rna-dashboard
  • The ENCODE project has produced a massive amount of transcriptome data, made possible by the collaboration of a world wide consortium of laboratories. During the project it was critical to immediately know what data was being produced by which lab. The ENCODE RNA dashboard kept the researchers informed about new results, even before they were officially registered with the ENCODE Data Coordination Center (DCC). It was instrumental for management to have direct insight into the current state of the project at any given point in time. Collaborators could quickly proceed with their own analysis steps once the raw data and processed results were published on the dashboard by other groups. The dashboard was also enriched with direct links to additional summary statistics that had been published using the Grape RNA-Seq pipeline.
  • Now that the project has yielded its results, the ENCODE dashboard still remains the only central place collecting all the RNA data produced by the ENCODE project. The international research community can explore the wide range of experiments, and quickly find and download the exact data sets they need for their own data analysis. The dashboard is not only useful for web access, but command line users will enjoy the friendly batch processing capabilities.
  • There is a huge demand to provide the same kind of dashboard for additional ENCODE projects, and with the new version of our dashboard software package, the system can even be extrapolated to any other bioinformatics project having to deal with a lot of data. For example, the ENCODE Mouse (Mus musculus) dashboard is one of the upcoming dashboards, replicating the success of the ENCODE hg19 (Homo sapiens) dashboard.

Participants

Please add yourself to the list of participants by editing the list below. This will help us to gauge interest and to contact you with more details of the meeting.

List of participants:

  1. Matthew Betts, Uni Heidelberg
  2. Holger Dinkel, EMBL
  3. Gideon Zipprich, DKFZ
  4. Maria Secrier, EMBL
  5. Pierre Khoueiry, EMBL
  6. Jon Fuller, HITS
  7. Grainne Kerr, DKFZ
  8. Sean Powell, EMBL
  9. Paul Costea, EMBL
  10. Verena Tischler, EMBL
  11. Damien Devos, COS HD Uni
  12. Merche Castillo, EMBL
  13. Charles Imbusch, DKFZ
  14. Nati Ha, COS HD Uni
  15. Adam Gristwood, EMBL
  16. Ivan Savora, HITS
  17. Stefan Henrich, HITS
  18. Juliane Diedrich, EMBL
  19. Beifei Zhou, HITS
  20. Kristoffer Forslund, EMBL + guest: Joel Ås, UU
  21. Joana Xavier, EMBL
  22. Th. Soldatos, MH
  23. Aidan Budd, EMBL
  24. Juan Mateo, COS
  25. Clemens Lakner, EMBL
  26. Prakash Balasubramanian, DKFZ
  27. Maik Röder, Freelancer

Organisers

A team of people working at several different life-science organisations within Heidelberg are organising HUB:

Task list

A list of tasks that need to be done on or before the meeting day. Just sign your name to say that you'll do a task, and the same again when the task is done!

To arrange before evening Person responsible Done
Organising warm up exercise Matthew
Gifts (bottles of wine) Adam
List of registered people Matthew
A4 signs in plastic envelopes to help people find the room Adam
Stationary and stickers. (We'll need more than normal, for drafting game boards and pieces.) Adam
Bring paper and postits Holger
Bring lots of pens, "tablecloth" and indexcards Adam
Bring dice and other useful resources everybody
Treasury duties Matthew
Create the poster Matthew Matthew
Print and display poster where relevant
Camera Holger
Beamer Matthew
To do on the evening Person responsible Done
Collect talks on laptop Matthew
Open the room Matthew
Arrange room (tables/chairs) Matthew
Hang up signs to the room not necessary
Setup and welcome attendees Grainne
Setup AV equipment Holger
MC/Chair the meeting Matthew
Tidy and close room not necessary

Planning meetings

Tuesday March 12, 2013

Agenda

  1. Does the programme look OK?
  2. Organisation of the night:
    1. Introduce game ideas already on wiki. Ask for others.
    2. People to vote somehow for the ones they want to work on.
    3. Split in to small groups (max 4 people) accordingly each working on one game idea each.
    4. Each group to summarise their plan to everyone at the end.
  3. What materials will we need? Eg. paper table cloths for writing on, arts and craft stuff for making game pieces etc.
  4. Make sure all the tasks have someone assigned.
  5. Money
    1. Who still owes Holger from last time?
    2. What to do with the money we collected at HUB4? Since HUB5 will be in a restaurant it isn't possible to take beer there, and isn't really practical to pay for people's drinks. Could spend it on wine for speakers and ask the restaurant if we can pay for a crate of beer, or just carry it over to HUB6.
  6. Any other business?

Minutes

Star Coffee, Bismarkplatz, Heidelberg

Present: Matt, Holger, Gideon, Adam, Grainne, Jon

Program

We should make clear at the beginning of the HUB meeting that the goal is not necesarily to make a working game, but to come up with ideas worth pursuing and to have fun discussing different types of games etc. Matt will present the games that are already on the list at this wiki. We should mention licensing / intellectual property and also that there might be possibilities to test-run a final game at a masters course in bioinformatics and ELLS to get in touch with teachers (European Learning Laboratory for the Life Sciences). Ideally we can use a projector for this presentation (needs checking).

After this, people can choose a game to work on, by putting their name on a postit sticker and then use these stickers to assign their name to a particular game/table (Ideally in a row, so we have kind of a bar chart which makes it easy to figure out which ideas are the most interesting to the participants); later, people can change by moving their postit to a different table/group. If a group for a game is too big, we need to split it into tasks (5 people is ideal?). Same if games are too related: It might be good to merge these groups together...

We might have around 8-10 tables, redistribution might be challenging; so probably people need to stay on the game for the whole evening.

Organizing the discussion

At the end of the session, somebody from each group should summarize the game and how to proceed. Ideally somebody is willing to take responsibility to move on afterwards... (how to decide on who takes responsibility / moderator?). We need a timekeeper for these presentations (Grainne?) and we need to be strict about the time (3min max!), otherwise we run out of time for the flash talks

Outlook

After the flash talks, the final discussion will be about summing up the evening, see who want to get involved maybe collect email addresses, ask people to put names, ideas collected etc. at wiki. If there is significant progress on one or more games, there is a chance to play the game at a future .5 HUB meeting? Would be useful to present to everybody but also to get feedback, perform finetuning etc. Also, mention the suggestion for future hub topics page where people can put down ideas that they would like to see at a future HUB.


Wednesday January 30, 2013

Agenda

(Please discuss on the talk page, and add/remove items here.)

  1. HUB4 feedback
  2. Should we have HUB4.5?
  3. Select topic for HUB5
  4. Select date for HUB5
  5. Intro to bioinformatics at a HD institute - who to ask?
  6. Flash talks: how many and how to get proposals?
  7. How to spread the word.
  8. Money spent on HUB4
  9. Any other business

Minutes

Star Coffee, Bismarkplatz, Heidelberg Present: Aidan, Katja, Matt, Holger, Adam, Grainne, Gideon

Welcome Gideon

Welcome to Gideon who joins the HUB organisation team

HUB4 feedback

Interactive aspects (Sam workshop and standing in a line) seen as good ways to get people involved during the meetings – small group stuff seems to work well. Other thoughts included: Ask people at end of meeting if they would like to give a flashtalk; potentially reduce flashtalks to one per meeting; potentially start the meeting off with the interactive idea rather than the institution talk; remember we are bioinformaticians talking to bioinformaticians; Marstall is a good venue for the pub providing there is no football on that evening.

Should we have HUB4.5?

Yes! To take place in February, potentially with a world café style. Aidan and Katja to take lead (and will meet to discuss) – thanks for that, both! Discuss things like ideas for future HUBs (Beyond HUB 5); potential sponsorship and how we might use sponsor money to boost HUB.

Select a date for HUB4.5

Doodle poll - Aidan

Select a topic for HUB5

Two ideas put forward: Solving coding problems (ROSILIND style – http://rosalind.info/problems/locations/) or developing a game that explains bioinformatics (target audience to be decided – using wiki to collect opinions on this somehow?). Team voted for game this time and to keep ROSALIND in mind for a future HUB. Initial suggestions at the table included a Taboo style game and a board game. Ideas developed further via wiki (and at HUB4.5? I can’t remember ☺ ).Also suggested we might invite a games developer to come and give a short talk. Maik to give the one-and-only flashtalk at HUB5? Matt to take the lead for HUB5 – thanks for that Matt!

Heidelberger Spieleverlag I can contact them if requested - Gideon

Date for HUB5

Matt to do a Doodle poll of the organisers, with the meeting to take place in March

Introduction to bioinformatics institute (HUB5)

Ask Misha Savitski or Toby Matheson (Cellzome); anyone else come to mind?

Other points

Contact silent members of committee to see if they want to still be a part of it; Adam to mail Sam and Chris to thank them for talking last week; think about inviting big names to give talk at future HUBs (e.g. Alex Bateman or Janet Thornton from EMBL-EBI)

Ideas Meeting, January 15, 2013

We met on Tuesday morning (15th January 2013) in Star Coffee to discuss the ideas below in more detail.

We decided...

For HUBX (i.e. not HUB5... some other future HUBs) to ask:

  • Alex Bateman if he'd be interested in doing something with us on the topic of using wikipedia as scientists (he already said he'd be interested in principle, but depends on when he's in HD) If/when that works out, we'll ask him (and/or others) about future ISMB/WikiPedia editing competitions, maybe we could incorporate that into the same HUB...?
  • Vicky Schneider if she'd be interested in doing some of her train-the-trainer stuff she was involved in at the EBI as part of a meeting (unfortunately she **doesn't** have time for this in May, but she'll let us know if she'll be back here sometime when she could do this with us i.e. in principle she'd like to do this)

If we're going to do a drive to get more publicity for HUB, let's wait until we have a meeting we think is likely to be particularly appealing to a large audience - e.g. wikipedia editing etc. with Alex

We also thought that, sometime (again like this brainstorming meeting) we could think about ways of getting more interaction with the community via this wiki **between** HUB meetings, making content thus more participant-driven. With this in mind, and prompted by a mail from Jon, I've signed up for this workshop which is about how to promote/deliver effective professional networks http://reedelsevier.reg.meeting-stream.com/researchtrends_elsevierlabs/

We discussed how to choose topics for future meetings:

  1. What we find most fun?
  2. What we think will bring the largest number of people to the meeting?
  3. What we think will bring the most enjoyable/useful/impressive outcome (i.e. if/when it yields a finished project)? [my guess is that this correlates strongly with 2.] Perhaps ideally something that could again end in a publication, although sometime in the future

our feeling was that, obviously, it's a mix of these - but that if we at least don't find the topic/project fun, then nothing is likely to happen with it, so that's key!

We also need to be careful about not scaring people away, thinking in terms of wording of topic/project, not so that it sounds like only very experienced programers could contribute usefully, for example.

We decided that we'd like to give the people at the end of HUB4 the choice between two trajectories for future HUBs:


1. Focusing on coding, getting experience of pair-programing, collaborative coding, something like this

HUB5 - Team Programming and ROSALIND

  • Begin the session with a sociometric stand-on-line thing with the axis being expert programer/no experience programming
  • Define an interface, people can work together with their coding language of preference...
  • To do this, we should check out bringing in a wireless router for someone to set up who can link via Ethernet to the Uni network (Matt...?) during HUB4 (or after HUB4 but before HUB5) to see if we can get this running
    • Useful for looking up quesitons about programming languages
    • If doesn't work out, we need to bring along appropriate books

HUB6 - Play with working collaboratively via git on a small project HUB7 - Plan/consider/discuss together the idea of running a crowdfunded project together


2. Focusing on developing a (probably board, maybe later computer) game for helping wet lab biologists learning about some useful (for them) aspect of bioinformatics

See below/end of page for more ideas about trying to prepare a game...

HUB5 - Coming up with a context/problem in which to develop a game, first ideas about how to design it

  • If we do the game, then colleagues in EBI have developed (and try to write up) a game (a board game, I think) that explore DAS, we could contact them, see if they'd be able to join us (in person?) for some follow-up HUB on this?
  • We also have School workshop bloke with a specialisation in eLearning, Philipp Gebhardt, who we could ask to come along too

HUB6 - Choosing a game to focus on, plan how to develop it further


Try to choose between these at end of HUB4 using one of the sociometric exercises similar to the one Katja will begin the session with:

  • Holger presents ROSALIND idea
  • Matt presents idea of developing together a game
  • We use a two-axis area for people to choose between Rosalind and game idea for HUB5, second axis representing how much they want that particular choice... hmm... maybe this is overkill with the second axis...

Try to fix dates for HUB5 (and maybe also HUB6) ASAP



Other ideas for future HUBs, not focused on

  • Writing together some useful open-source code (a mini-hackathon)
  • Preparing a short "introduction to bioinformatics" training session for bench biologists
    • Some kind of "skills exchange" website - bioinformatians can offer a skill, e.g. "e.g. how to use perl to download data" in exchange for a bench biologist skill "e.g. looking over their shoulder as during an RNAi screen".
  • Writing/improving relevant Wikipedia pages
  • Evaluating ways/tools to better collectively work/write together
  • Crowdfunding idea, get in touch with Grischa Toedt about this again?
  • Asking participants (before meeting) to solve certain challenges from rosalind and then use the meeting to present and discuss different approaches/programming languages/concepts used.
  • Trying to organise surveys/analysis/research into demographics of bioinformatics/bioinformaticians (e.g. have the proportion of people working in bioinforamtics in predominantely bench labs increased over the last years...?)
  • A train-the-trainer-focused evening, a friend who has run these at EBI is visiting HD in May, we could ask her (Vicky Schneider) if she'd be interested in giving a 2-hour session like that in the context of HUB?
  • Something focusing on statistics - one of the topics that's important throughout our field...?
  • People presenting their favourite papers in bioinformatics, maybe trying to choose which ones we'd most like to award a nobel for (for me it's easily Karlin and Altschul, 1990, Proc Natl Acad Sci U S A, 87, 2264-8; imagine life without the EVD in our BLAST etc. statistics...)
  • Productivity in general (discussed by Theo & Holger): get people to introduce and discuss ways of how to organize your everyday life. Sam suggests LifeHacker. Other ideas: GTD, 43folders, InboxZero --Holger Dinkel 16:59, 28 January 2013 (CET)