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Difference between revisions of "Codefest 2017"

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* Preparing and publishing [http://www.biomedcentral.com/1471-2105/15/S14/S7 papers about the work accomplished].
 
* Preparing and publishing [http://www.biomedcentral.com/1471-2105/15/S14/S7 papers about the work accomplished].
 +
 +
== Outcomes ==
 +
 +
* [https://docs.google.com/presentation/d/1f81Aj5-AzKrsRdMk8bvZqSrZ88bQVSMsQA9X4jZe0GE/edit?usp=sharing Summary slides for presentation at BOSC]
 +
* [https://docs.google.com/document/d/1PHN1qAWq1a2zM91oPYBy0DP2KKq5MbT6mdEQpH_kjbQ/edit?usp=sharing Google document of project and progress at Codefest]
 +
* Photos: [https://photos.app.goo.gl/IgUcLp8pBlRApAxy1 Ntino's]
  
 
== Why attend ==
 
== Why attend ==
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We plan to have lunch and coffee available for everyone attending. The rough schedule for the two days is:
 
We plan to have lunch and coffee available for everyone attending. The rough schedule for the two days is:
  
* Thursday July 20th 9am: Meet at Brmlab, introductions and organization into projects, coffee (from [http://www.oukydouky.cz Ouky Douky café])
+
* Thursday July 20th 9am: Meet at Brmlab, introductions and organization into projects, coffee (from [http://www.oukydouky.cz Ouky Douky café]), local fruits & pastries (from the [http://holesovickytrh.cz/ farmers' market])
 
* Thursday July 20th 10-1: Work in groups
 
* Thursday July 20th 10-1: Work in groups
 
* Thursday July 20th 1pm: Provided Lunch at Brmlab ([http://www.pizzaletna.cz/en/ Pizza Letná]] + post-lunch presentations on progress and organization
 
* Thursday July 20th 1pm: Provided Lunch at Brmlab ([http://www.pizzaletna.cz/en/ Pizza Letná]] + post-lunch presentations on progress and organization
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* Thursday July 20th late evening: Additional work at your discretion
 
* Thursday July 20th late evening: Additional work at your discretion
  
* Friday July 21st 9am: Meet at Brmlab, provide status updates and organize, coffee (from [http://www.oukydouky.cz Ouky Douky café])
+
* Friday July 21st 9am: Meet at Brmlab, provide status updates and organize, coffee (from [http://www.oukydouky.cz Ouky Douky café]), local fruits & pastries (from the [http://holesovickytrh.cz/ farmers' market])
 
* Friday July 21st 10-1: Work
 
* Friday July 21st 10-1: Work
* Friday July 21st 1pm: Provided lunch at Brmlab ([http://www.pizzaletna.cz/en/ Pizza Letná]] + post-lunch presentations on progress
+
* Friday July 21st 1pm: Provided lunch at Brmlab ([http://www.pizzaletna.cz/en/ Pizza Letná]) + post-lunch presentations on progress
 
* Friday July 21st 2-6: Work
 
* Friday July 21st 2-6: Work
* Friday July 21st 6pm: Wrap up presentations, pay-your-own-way group dinner, and get ready for [[BOSC 2017]]
+
* Friday July 21st 6pm: Wrap up presentations + clean-up of Brmlab, and get ready for [[BOSC 2017]]
 +
* Friday July 21st 7.30pm: Pay-your-own-way group beer + optional pub food (not vegan) at [http://www.zlycasy.eu/ Zlý Časy]. SEE [https://www.open-bio.org/wiki/Codefest_2017#Beer DIRECTIONS]
  
 
This is completely flexible based on progress and needs of attendees. Some resources while the hackathon is ongoing:
 
This is completely flexible based on progress and needs of attendees. Some resources while the hackathon is ongoing:
  
* [https://hangouts.google.com/call/5vqcefziwnhi3kcz6u4kxdytkey Google Hangout] for remote participants that will be on when we're working in Prague.  
+
* [https://hangouts.google.com/call/46cq2fdgbvhmjds4nybn4tipiay Google Hangout] for remote participants that will be on when we're working in Prague.  
 
* Feel free to ask in the [https://gitter.im/chapmanb/obf-codefest Gitter Chat channel] if you're wondering about the current status at any time.
 
* Feel free to ask in the [https://gitter.im/chapmanb/obf-codefest Gitter Chat channel] if you're wondering about the current status at any time.
 +
* [https://docs.google.com/presentation/d/1f81Aj5-AzKrsRdMk8bvZqSrZ88bQVSMsQA9X4jZe0GE/edit?usp=sharing Summary slides for presentation at BOSC]
 
* [https://docs.google.com/document/d/1PHN1qAWq1a2zM91oPYBy0DP2KKq5MbT6mdEQpH_kjbQ/edit?usp=sharing Google document with documentation of on-going Codefest work]
 
* [https://docs.google.com/document/d/1PHN1qAWq1a2zM91oPYBy0DP2KKq5MbT6mdEQpH_kjbQ/edit?usp=sharing Google document with documentation of on-going Codefest work]
 
  
 
== Dinner ==
 
== Dinner ==
  
On the first evening, Thursday July 20th, we're having a group dinner in [www.crossclub.cz/en Cross Club]. Directions:
+
On the first evening, '''Thursday July 20th''', we're having a group dinner in [http://www.crossclub.cz/en Cross Club] at 7pm. Directions:
  
 
* Option one: [https://www.google.com/maps/dir/brmlab,+Bubensk%C3%A1+1477%2F1,+170+00+Praha+7-Hole%C5%A1ovice,+Czechia/Cross+Club+Kav%C3%A1rna,+Plyn%C3%A1rn%C3%AD+1096%2F23,+170+00+Praha+7-Hole%C5%A1ovice,+%C4%8Cesko/@50.1032505,14.4306477,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x470b94b80ce899d9:0xcc81f00a71b39b29!2m2!1d14.4359171!2d50.0984431!1m5!1m1!1s0x470b94b5151af143:0x2d943b3cb67afc96!2m2!1d14.4432531!2d50.1081792!3e3?hl=en One stop with the underground] (alternatively a couple of stops with a tram, see [https://www.google.com/maps/dir/brmlab,+Bubensk%C3%A1+1477%2F1,+170+00+Praha+7-Hole%C5%A1ovice,+Czechia/Cross+Club+Kav%C3%A1rna,+Plyn%C3%A1rn%C3%AD+1096%2F23,+170+00+Praha+7-Hole%C5%A1ovice,+%C4%8Cesko/@50.1032505,14.4306477,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x470b94b80ce899d9:0xcc81f00a71b39b29!2m2!1d14.4359171!2d50.0984431!1m5!1m1!1s0x470b94b5151af143:0x2d943b3cb67afc96!2m2!1d14.4432531!2d50.1081792!3e3?hl=en Google Maps])
 
* Option one: [https://www.google.com/maps/dir/brmlab,+Bubensk%C3%A1+1477%2F1,+170+00+Praha+7-Hole%C5%A1ovice,+Czechia/Cross+Club+Kav%C3%A1rna,+Plyn%C3%A1rn%C3%AD+1096%2F23,+170+00+Praha+7-Hole%C5%A1ovice,+%C4%8Cesko/@50.1032505,14.4306477,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x470b94b80ce899d9:0xcc81f00a71b39b29!2m2!1d14.4359171!2d50.0984431!1m5!1m1!1s0x470b94b5151af143:0x2d943b3cb67afc96!2m2!1d14.4432531!2d50.1081792!3e3?hl=en One stop with the underground] (alternatively a couple of stops with a tram, see [https://www.google.com/maps/dir/brmlab,+Bubensk%C3%A1+1477%2F1,+170+00+Praha+7-Hole%C5%A1ovice,+Czechia/Cross+Club+Kav%C3%A1rna,+Plyn%C3%A1rn%C3%AD+1096%2F23,+170+00+Praha+7-Hole%C5%A1ovice,+%C4%8Cesko/@50.1032505,14.4306477,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x470b94b80ce899d9:0xcc81f00a71b39b29!2m2!1d14.4359171!2d50.0984431!1m5!1m1!1s0x470b94b5151af143:0x2d943b3cb67afc96!2m2!1d14.4432531!2d50.1081792!3e3?hl=en Google Maps])
  
{|
+
* Option two: 20 minutes [https://www.google.com/maps/dir/brmlab,+Bubensk%C3%A1+1477%2F1,+170+00+Praha+7-Hole%C5%A1ovice,+Czechia/Cross+Club+Kav%C3%A1rna,+Plyn%C3%A1rn%C3%AD+1096%2F23,+170+00+Praha+7-Hole%C5%A1ovice,+%C4%8Cesko/@50.1032505,14.4306477,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x470b94b80ce899d9:0xcc81f00a71b39b29!2m2!1d14.4359171!2d50.0984431!1m5!1m1!1s0x470b94b5151af143:0x2d943b3cb67afc96!2m2!1d14.4432531!2d50.1081792!3e2?hl=en walk]
|   
+
 
| [[File:Crossclubmetro.png|620px|center|Brmlab to Cross Club by transport|link=https://www.google.com/maps/dir/brmlab,+Bubensk%C3%A1+1477%2F1,+170+00+Praha+7-Hole%C5%A1ovice,+Czechia/Cross+Club+Kav%C3%A1rna,+Plyn%C3%A1rn%C3%AD+1096%2F23,+170+00+Praha+7-Hole%C5%A1ovice,+%C4%8Cesko/@50.1032505,14.4306477,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x470b94b80ce899d9:0xcc81f00a71b39b29!2m2!1d14.4359171!2d50.0984431!1m5!1m1!1s0x470b94b5151af143:0x2d943b3cb67afc96!2m2!1d14.4432531!2d50.1081792!3e3?hl=en]]
+
Please try to be there before 7.30pm, otherwise we'll loose our table reservations.
|   
+
 
|}
+
 
 +
== Beer ==
 +
 
 +
On the second evening, '''Friday July 21st,''' we're having a group beer at [http://zlycasy.eu Zlý Časy] at '''7.30pm'''. They have some traditional pub food, too (no vegan and no gastro but authentic). The vegetarian options are various cheese dishes. The vegan option is eating elsewhere beforehand or afterwards.
  
* Option two: 20 minutes [https://www.google.com/maps/dir/brmlab,+Bubensk%C3%A1+1477%2F1,+170+00+Praha+7-Hole%C5%A1ovice,+Czechia/Cross+Club+Kav%C3%A1rna,+Plyn%C3%A1rn%C3%AD+1096%2F23,+170+00+Praha+7-Hole%C5%A1ovice,+%C4%8Cesko/@50.1032505,14.4306477,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x470b94b80ce899d9:0xcc81f00a71b39b29!2m2!1d14.4359171!2d50.0984431!1m5!1m1!1s0x470b94b5151af143:0x2d943b3cb67afc96!2m2!1d14.4432531!2d50.1081792!3e2?hl=en walk]
+
It's a walking distance from the red C line, exactly from the '''stop at the congress center (Vyšehrad)'''. Coming from the ISMB/ECCB keynote|registration|reception is thus very possible! [https://www.google.com/maps/dir/brmlab,+Bubenská,+Holešovice,+Praha-Praha+7,+Česko/Zlý+Časy,+Čestmírova,+Praha,+Česko/@50.0816251,14.4333811,14z/data=!4m16!4m15!1m5!1m1!1s0x470b94b80ce899d9:0xcc81f00a71b39b29!2m2!1d14.4359171!2d50.0984431!1m5!1m1!1s0x470b947e932889db:0xe7fd48b92656f255!2m2!1d14.4420491!2d50.0643445!2m1!5e1!3e3?hl=en Directions:]
  
 
{|
 
{|
 
|   
 
|   
| [[File:Crossclubwalk.png|620px|center|Brmlab to Cross Club by foot|link=https://www.google.com/maps/dir/brmlab,+Bubensk%C3%A1+1477%2F1,+170+00+Praha+7-Hole%C5%A1ovice,+Czechia/Cross+Club+Kav%C3%A1rna,+Plyn%C3%A1rn%C3%AD+1096%2F23,+170+00+Praha+7-Hole%C5%A1ovice,+%C4%8Cesko/@50.1032505,14.4306477,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x470b94b80ce899d9:0xcc81f00a71b39b29!2m2!1d14.4359171!2d50.0984431!1m5!1m1!1s0x470b94b5151af143:0x2d943b3cb67afc96!2m2!1d14.4432531!2d50.1081792!3e2?hl=en]]
+
| [[File:Zlycasy.png|467px|center|Brmlab to Zlý Časy (optionally via ISMB)|link=https://www.google.com/maps/dir/brmlab,+Bubensk%C3%A1,+Hole%C5%A1ovice,+Praha-Praha+7,+%C4%8Cesko/Zl%C3%BD+%C4%8Casy,+%C4%8Cestm%C3%ADrova,+Praha,+%C4%8Cesko/@50.0816251,14.4333811,14z/data=!4m16!4m15!1m5!1m1!1s0x470b94b80ce899d9:0xcc81f00a71b39b29!2m2!1d14.4359171!2d50.0984431!1m5!1m1!1s0x470b947e932889db:0xe7fd48b92656f255!2m2!1d14.4420491!2d50.0643445!2m1!5e1!3e3?hl=en]]
 
|   
 
|   
 
|}
 
|}
 
Please try to be there before 7.30pm, otherwise we'll loose our table reservations.
 
 
 
  
 
== Sponsors ==
 
== Sponsors ==
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We are grateful to and welcome [https://repositive.io/ Repositive Limited] (connecting the genomics community with the data they need) and  [https://www.sevenbridges.com/ Seven Bridges] (the Biomedical Data Analysis Platform) as new sponsors for the Codefest and BOSC 2017. We also thank the [http://www.uochb.cz/web/structure/31.html Institute of Organic Chemistry and Biochemistry] for lending us practical coffee equipment.
+
We are grateful to and welcome [https://repositive.io/ Repositive Limited] (connecting the genomics community with the data they need) and  [https://www.sevenbridges.com/ Seven Bridges] (the Biomedical Data Analysis Platform) as new sponsors for the Codefest and BOSC 2017. We thank the gorgeous [https://brmlab.cz Brmlab] and its members for providing us their great space, equipment, and help. We also thank the [http://www.uochb.cz/web/structure/31.html Institute of Organic Chemistry and Biochemistry] for lending us additional equipment.
  
 
We're looking for sponsors interested in being involved with the open source community. Sponsorship money helps provide food and drink for the Codefest and [https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md Open Bioinformatics Foundation Travel Fellowships] for BOSC and Codefest. If interested, please get in touch with [https://github.com/chapmanb Brad] (Codefest) or the [mailto:bosc@open-bio.org BOSC committee] (general).
 
We're looking for sponsors interested in being involved with the open source community. Sponsorship money helps provide food and drink for the Codefest and [https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md Open Bioinformatics Foundation Travel Fellowships] for BOSC and Codefest. If interested, please get in touch with [https://github.com/chapmanb Brad] (Codefest) or the [mailto:bosc@open-bio.org BOSC committee] (general).
Line 141: Line 147:
  
 
* [http://github.com/chapmanb Brad Chapman]
 
* [http://github.com/chapmanb Brad Chapman]
* [https://twitter.com/matuskalas Matúš Kalaš] (If in trouble at Brmlab, find Matúš or call him at +421905868848)
+
* [https://twitter.com/matuskalas Matúš Kalaš]
 
* [https://twitter.com/HLWiencko Heather Wiencko]
 
* [https://twitter.com/HLWiencko Heather Wiencko]

Latest revision as of 06:38, 22 July 2017

OpenBio Codefest 2017 is July 20th and 21st, 2017 (the Thursday and Friday before BOSC 2017 and the ISMB/ECCB 2017 meeting) at Brmlab: a non-profit, community-run hackerspace in Prague.

This is an opportunity for anyone interested in open science, biology and programming to meet, discuss and work collaboratively. Everyone is welcome to attend. We will have a mix of experienced developers, newcomers to bioinformatics and everything in between.

This is the 8th annual pre-BOSC Codefest. Previous fun and successful events were Codefest 2010 in Boston, Codefest 2011 in Vienna, Codefest 2012 in Los Angeles, Codefest 2013 in Berlin, and Codefest 2014 in Boston, Codefest 2015 in Dublin and Codefest 2016 in Orlando.

Objectives

The goal of Codefest is to bring open source bioinformatics programmers together to have an enjoyable and productive two days. Practically this results in a number of useful outcomes:

  • Developing new communities working on shared problems. For example, the Common Workflow Language developed from discussions at Codefest 2014.
  • Establishing new friendships, helping to expand the open source bioinformatics community.

Outcomes

Why attend

  • For current community members: expand your network and strengthen existing relationships. Teach and learn from new community members. Focus on open source work without interruptions. Discuss questions and problems in real time.
  • For everyone: discuss and learn from the community. Teach others what you know. Build new friendships and collaborations.

If you have any questions or thoughts, please get in touch with Brad directly, in the Gitter chat room or on the Codefest 2017 mailing list.

What to expect

The OpenBio Codefest is a collaborative two day working session. The only requirement for attendance is that you have an interest in open source software and solving scientific problems. We will have contributors to open source bioinformatics tools present to collaboratively work with, and we welcome new attendees who want to learn and contribute to open source code or documentation.

The rough structure of the two days is:

  • Start with introductions from everyone attending about their goals and plans for the two days.
  • Assemble into working groups based on shared interests like programming languages, open source projects or biological questions. We use the collaboratively brainstormed Google document as the basis for setting up groups. Attendees determine the goals for the two days. If you have an idea for a project, please add it before the event. Any and all suggestions are welcome.
  • Work and discuss. Enjoy the productive time.
  • We'll have regular breaks where each group can deliver short reports on their progress.
  • We have informal lunches, dinners and drinks as a way for everyone to get to know each other better.
  • At the end of the two days, we summarize contributions and work accomplished in a BOSC presentation and meeting report.

Please feel free to get in touch with any of the organizers with questions. You are very welcome at Codefest.

Attending

You are very welcome to attend. There is no cost, we only ask you to register to help organize numbers. Please add yourself if you are interested to this Google spreadsheet We'll coordinate through the Codefest 2017 mailing list, so please sign up to discuss and receive updates.

If you're not able to physically attend, we're still more than happy to have you participate in Codefest. Please sign up on the the Google spreadsheet and list yourself as remote only. We have a Gitter chat room we can use to coordinate and discuss in real time and will have an open Google Hangout to make it easier to be part of Codefest remotely.

Add your project ideas to the shared google document. The ideas include smaller focused projects and larger work. We want suggestions from everyone and will organize into groups around these during Codefest.

Logistics

Codefest is kindly hosted by Brmlab, a non-profit, community-run hackerspace in Prague.

Brmlab

We plan to have lunch and coffee available for everyone attending. The rough schedule for the two days is:

  • Thursday July 20th 9am: Meet at Brmlab, introductions and organization into projects, coffee (from Ouky Douky café), local fruits & pastries (from the farmers' market)
  • Thursday July 20th 10-1: Work in groups
  • Thursday July 20th 1pm: Provided Lunch at Brmlab (Pizza Letná] + post-lunch presentations on progress and organization
  • Thursday July 20th 2-6: Work in groups
  • Thursday July 20th 6pm: End of day presentations
  • Thursday July 20th 7pm: Pay-your-way group dinner in [www.crossclub.cz/en Cross Club]. SEE DIRECTIONS
  • Thursday July 20th late evening: Additional work at your discretion
  • Friday July 21st 9am: Meet at Brmlab, provide status updates and organize, coffee (from Ouky Douky café), local fruits & pastries (from the farmers' market)
  • Friday July 21st 10-1: Work
  • Friday July 21st 1pm: Provided lunch at Brmlab (Pizza Letná) + post-lunch presentations on progress
  • Friday July 21st 2-6: Work
  • Friday July 21st 6pm: Wrap up presentations + clean-up of Brmlab, and get ready for BOSC 2017
  • Friday July 21st 7.30pm: Pay-your-own-way group beer + optional pub food (not vegan) at Zlý Časy. SEE DIRECTIONS

This is completely flexible based on progress and needs of attendees. Some resources while the hackathon is ongoing:

Dinner

On the first evening, Thursday July 20th, we're having a group dinner in Cross Club at 7pm. Directions:

  • Option two: 20 minutes walk

Please try to be there before 7.30pm, otherwise we'll loose our table reservations.


Beer

On the second evening, Friday July 21st, we're having a group beer at Zlý Časy at 7.30pm. They have some traditional pub food, too (no vegan and no gastro but authentic). The vegetarian options are various cheese dishes. The vegan option is eating elsewhere beforehand or afterwards.

It's a walking distance from the red C line, exactly from the stop at the congress center (Vyšehrad). Coming from the ISMB/ECCB keynote|registration|reception is thus very possible! Directions:

  
Brmlab to Zlý Časy (optionally via ISMB)
  

Sponsors

Repositive Limited logo
   
Seven Bridges


We are grateful to and welcome Repositive Limited (connecting the genomics community with the data they need) and Seven Bridges (the Biomedical Data Analysis Platform) as new sponsors for the Codefest and BOSC 2017. We thank the gorgeous Brmlab and its members for providing us their great space, equipment, and help. We also thank the Institute of Organic Chemistry and Biochemistry for lending us additional equipment.

We're looking for sponsors interested in being involved with the open source community. Sponsorship money helps provide food and drink for the Codefest and Open Bioinformatics Foundation Travel Fellowships for BOSC and Codefest. If interested, please get in touch with Brad (Codefest) or the BOSC committee (general).

Organizers