These are chat archives for chapmanb/obf-codefest

19th
Jan 2018
Denis Loginov
@dinvlad
Jan 19 00:42
Anyone interested in working on native Protobuf support in WDL tomorrow? This is an open protocol that Google uses internally for a lot of its services (if I'm not mistaken) and it enables very efficient message communication (faster than JSON in most benchmarks), strong typing, and
automatic code generation for most languages (so you spend less time coding and more time doing useful stuff :P). We have an idea on creating a read_proto() function similar to read_json() provided by Cromwell
Jeff Gentry
@geoffjentry
Jan 19 00:48
I was wondering who added that to the doc. I’m not sure I understand what you mean, can you explain further? I’ll not be there in the morning, but at the least try to grab @cjllanwarne to run the idea past him in general
Denis Loginov
@dinvlad
Jan 19 00:50
we'd like to pass protobufs as input to WDL, which would contain structured data (including filenames/paths) that could later be queried directly within WDL itself and within our tasks, without having to use any converters
this could make it more flexible towards structured data types passed in from external databases
rowlandm
@rowlandm
Jan 19 01:05
That looks very interesting!
Denis Loginov
@dinvlad
Jan 19 01:11
actually, has read_json() been implemented yet? In any case, we can brainstorm with @cjllanwarne in that direction
maybe even help with read_json() first as a more common use case
Aiden Lewis
@AyedynL_twitter
Jan 19 01:30
Hi all, I am a biomedical engineering student studying at Tufts, I was not able to attend the first day due to conflicts with classes, but I was interested in finding out more about open source bioinformatic programming. Is there somewhere I can start for learning the basics of what these programs generally seek to accomplish and what the goals are? Is there any value in me attending tomorrow?
rowlandm
@rowlandm
Jan 19 01:31
hey @AyedynL_twitter - it will be fun for you to see all the possibilities - so tomorrow would be great for you
Bioinformatic programming is a big field and you will have plenty to choose from :)
Aiden Lewis
@AyedynL_twitter
Jan 19 01:32
Alright, I think I will show up for the presentations and get a feel for what the field looks like today, even if I won't understand much.
rowlandm
@rowlandm
Jan 19 01:32
even if I won't understand much.
That is bioinformatic programming to a T ;)
You'll fit in great :D
Brad Chapman
@chapmanb
Jan 19 02:21
Aiden -- you're definitely welcome to come tomorrow and talk with folks at Codefest, we'd love to have you there. We'll have a summary of things people are working on in the morning at 9:30ish and then you'd have the chance to sit in on any group discussions or talk with folks about things they're working on. Hope that would be useful for you.
Brad Chapman
@chapmanb
Jan 19 11:39
Thanks to everyone for a great and productive day yesterday. I'm looking forward to seeing everyone this morning around 9 for more fun and science. Just a reminder that we're in a different location in the Longwood quad: Countway library. It's only a minute further walk at the back of the quad: https://www.open-bio.org/wiki/Codefest_Winter_2018#Logistics
Manabu ISHII
@manabuishii
Jan 19 12:08
@chapmanb Thanks for reminder :+1:
Today I'll do some stuff editor support for SublimeText (firstly syntax highlight ), after that completion .
If someone has interest about editor support let's discuss.
Peter Amstutz
@tetron
Jan 19 13:38
Hi everyone, when you get to the library take the North elevator or you'll be on the wrong side of the building
Brad Chapman
@chapmanb
Jan 19 14:16
The zoom room is up and going today for anyone joining remotely : https://zoom.us/j/492788307 We're still organizing ourselves here, maybe aiming for 9:45 ET for morning updates
Brad Chapman
@chapmanb
Jan 19 14:30
Also today we'll be working on updating our Google Doc with accomplishments and future goals for post-Codefest. Luda is coordinating this bug please help by adding things you worked on. Feel free to add extra sections as needed: https://docs.google.com/document/d/1RlDUWRFqMcy4V2vvkA1_ENsVo6TXge2wIO_Nf73Itk0/edit#heading=h.xmwxawo32s62
Brad Chapman
@chapmanb
Jan 19 14:40
Morning organization in 5 minutes
Pau Ruiz Safont
@psafont
Jan 19 15:13
sorry
I don't
Azza Ahmed
@zo0z
Jan 19 15:16
@chapmanb Are Spark discussions in the main Zoom room today?
Michael L Heuer
@heuermh
Jan 19 15:16
@zo0z re: Spark, I'll be mostly hacking by myself on CWL and WDL for Spark-based tools today, so perhaps chat here would be more useful than video on zoom. Or if you are interested in the UC Berkeley stack, we have our own gitter at https://gitter.im/bigdatagenomics/adam
Azza Ahmed
@zo0z
Jan 19 15:17
@heuermh Perfect! Cool!
Michael L Heuer
@heuermh
Jan 19 15:17
Great!
Brad Chapman
@chapmanb
Jan 19 15:18
The main zoom is open for discussions and just ping here if you want to chat to anyone in real time. Thank you to everyone participating remotely, let us know if there is anything we can do to make it easier.
Stian Soiland-Reyes
@stain
Jan 19 15:37
In case someone wants to go a bit old-skool I'm looking for reviews on this new URI scheme to identify files inside archives:
https://tools.ietf.org/id/draft-soilandreyes-app-03.html
made day before the codefest.. not sure if that counts!
Brad Chapman
@chapmanb
Jan 19 15:38
Did anyone take pictures of Codefest yesterday (or today) they could share?
Lorena Pantano
@lpantano
Jan 19 15:57
@cjfields, are you interesting to work in the miRNA project?
Farah Zaib Khan
@FarahZKhan
Jan 19 15:58
@chapmanb Michael shared some on twitter :)
Brad Chapman
@chapmanb
Jan 19 16:05
Awesome, thanks Farah. I missed those yesterday.
Michael R. Crusoe
@mr-c
Jan 19 16:18
@chapmanb see my Twitter
Chris Fields
@cjfields
Jan 19 16:27
@lpantano possibly
I'm splitting my time w/ the CWL side as well, but I'm def. interested in that
Lorena Pantano
@lpantano
Jan 19 16:28
@cjfields , well, maybe for today is too much, but if you want to know more, we can chat more here: https://gitter.im/mirtop/devel
Morgan Taschuk
@morgantaschuk
Jan 19 17:16
does anyone have a script to turn samtools flagstat into a JSON file?
Morgan Taschuk
@morgantaschuk
Jan 19 17:24
image.png
sorry/not sorry
Lorena Pantano
@lpantano
Jan 19 17:24
lol
Brad Chapman
@chapmanb
Jan 19 17:25
Would any remote (or local) people need a pre-lunch orientation discussion today? Debating not interrupting folks before lunch but can do if anyone could use an update.
I don't have any memes for that.
Hervé Ménager
@hmenager
Jan 19 19:52
@mr-c jmchilton/common-workflow-language#2
Brad Chapman
@chapmanb
Jan 19 21:38
We'll do Codefest wrap ups in 10 minutes, feel free to join online: https://zoom.us/j/492788307
rowlandm
@rowlandm
Jan 19 21:54
Who was the person who was talking about the miRNA pipeline?
@lpantano - do you have any more info around the miRNA project?
running stuff across mesos is cool
Brad Chapman
@chapmanb
Jan 19 22:10
Thank you to everyone for a brilliant Codefest. Please clear your calendars and think about joining us for A bioinformatics community conference with BOSC and GCC in Portland, Oregon in June: https://gccbosc2018.sched.com/
rowlandm
@rowlandm
Jan 19 23:16
Thanks for pulling this together @chapmanb !