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HUB 21 Interactive notebooks – try out programming, Jupyter/IPython, chemoinformatics

January 21, 2016 from 18:00 - 21:00


Read Samo’s short summary of how the event went here (Samo was the lead organiser of the event).

  • When? Thursday January 21st 2016
  • 18.00 pre-unseminar drinks, time to install Anaconda on your laptop
  • 18.30 – 20.30/21.00 unseminar
  • 21.00 onwards chat at Cafe Botanick
  • Where? BioMedX, Im Neuenheimer Feld 583
  • Who? Please sign up to this Doodle poll if you plan on coming, to help us judge numbers. Please indicate if you can bring a laptop along with iPython/anaconda installed on it for the pair programming session
  • Material: GitHub repository for the event

Hosted by BioMedX, this unseminar will give people who’ve never programmed before a chance to write some of their first code, will give more experienced coders a chance to try out pair-programming, and introduce everyone to the opportunities offered by IPython/Jupyter for making our computer-focused data analysis more reproducible, interactive, and sharable.


Organising the computer, what people need to bring. Samo will write a short description, on the wiki, of the tools (Anaconda, some chemoinformatics-specific libraries) for people to install on their laptops if they bring them along.

To start things off, Aidan will create an initial wordpress/wiki page for the unseminar


Need volunteers to:

  • bring along the HUB ‘stationary’ bag
  • hand out sticky labels on the evening, organising setting that up at the door to the BioMedX rooms

Samo will organise a way of making sure that when people ring the bell to get in, someone will hear them, and be able to let them in (maybe leave a phone number on the sign at the door for them to call e.g. Samo if they don’t get anyone answering the bell…?)

At the venue we’ll, before the event, need someone to hang up/stick up signs on the front door, and going up the stairs, (maybe coming from the tram stop?) to get to the venue. Need a volunteer for this


Interactive notebooks – try out programming, Jupyter/IPython, chemoinformatics

Never coded before? Want to try pair programming? Wondering what all the fuss is about iPython/juyper?

Hosted by BioMedX, this unseminar will give people who’ve never programmed before a chance to write some of their first code, will give more experienced coders a chance to try out pair-programming, and introduce everyone to the opportunities offered by iPython/juypiter for making our computer-focused data analysis more reproducible, interactive, and sharable.

dates and time

18.00 for drinks and installing anaconda etc., 18.30 – 20.30 for the unseminar, and then off to Cafe Botankik

Thursday January 21st 2016

how many people to expect?

Expect maybe 20-30 – by spreading to the lobby, we should have no problem fitting 40 people there and in the seminar room

preparing a poster

Eva@BioMedX offered to do this. No one is unhappy with the BioMedX logo going on the poster and, I presume then also, on the wiki/wordpress page for the event.

registering? with/via Doodle?

We’ll use Doodle – on this, we’ll ask them to indicate whether they can bring a laptop, and whether they can put Anaconda on it. In the advert, we’ll encourage them to do this.

We’ll also try and encourage several of us to do this i.e. several organisers to agree to come to the unseminar, and to have anaconda etc. installed on their computers.

setting up the room

We’ll put chairs together in pairs (for the pair-programming part of the evening) and move the chairs closer to the front, so that there’s more space between them.

People can be standing up for the short intro presentations etc., sit down to watch Samo’s demo – I suggest he aim for 15 minutes or so of that. After Samo finishes, Flo will very briefly demo doing the same thing in R.

Introducing HUB and unseminars

Aidan will do this

organising the pair-programming

We’ll put a short description of what we want people to do on the wiki, together with links to exercises – selected ones from Rosalind, together with some that Samo is preparing himself.

Samo will introduce the session with a very quick description of the logistics of the session, and to pair programming – an opportunity to try out explaining what you do to others, helping and teaching others, learning how others approach a problem.

To pair people up, we’ll ask ‘experienced’ who’d be happy to help people with little/no experience to go to one side/part of the room.

People with little/no experience go somewhere else, and we ask them to go to people they don’t know from the experienced group, and then pair up with them.

Then take a vote whether they prefer, and do the one they prefer:

  • us to pair the rest of them randomly (form two lines, they do it with the person they stand opposite)
  • have first the ‘experienced’ people a chance to pair with other experienced ones (if they want) and then do the rest ‘randomly’
  • leave them to pair up on their own

After 30 min, see if any groups want to swap partners to try out with someone else, then do the swap just between them.


For now, unless we someone has inspiration for a different one, we’ll do the ‘classic’ of ‘form a line according to how many Lebkuchen you ate this winter’ – as always, we have one side of the room for “lots” the other for “little”, people organise themselves silently according to how much they think they ate, then we ask people to chat with people around themselves and re-adjust their positions based on this.

Then we ask them to do it again based on how many lines of code they’ve written.

Any volunteers to lead this activity?

Wrap up and thanks

Ask the pairs to reflect on their experience, and decide together if there’s anything interesting or surprising they learnt, that they’d like to share with the others in the room. Give a chance for them to share with the full group, then say thanks and goodbye and we head off together en-masse to Cafe Botanik

Volunteer to lead this?

someone to introduce HUB, unseminars

Aidan will do this


Flo will MC the evening.


Maybe we’d like to run it until 21.00 to give more time for the pair-programming? We can always stop people at 20.30 and say “do you want to do another 30 minutes of this”?

  • Introduction to HUB, unseminars 18.30 – 18.40 (I’ll do it in 5 min, but I assign 10 to give us some buffer as we’ll probably start 5 min late) AIDAN
  • Introduction to this unseminar (what we’ll do, when) FLO 18.40 – 18.45
  • Introduction to BioMedX 18.45 – 18.50 SAMO
  • Ice breaker 18.50 – 19.05 AIDAN
  • iPython demo 19.05 – 19.25 SAMO and FLO
  • Pair programming using Rosalind and chemoinformatics exercises 19.25 – 20.25 SAMO
  • Wrap up and thanks 20.25 – 20.35 AIDAN


January 21, 2016
18:00 - 21:00
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HUB Organisers