

Our Open Science project is looking for a dev - emeltzer
http://openprotocols.net/hiring/

======
zdw
Design the data format (API) first, then the user interface later. You have
the cart in front of the horse.

Rather than decide how it looks and works, decide how you want the data
structured then come up with a format to represent it. This sounds like
unstructured to minimally structured document centric data - something like a
Markdown with additional tagging or an XML format would probably be ideal.

This way, eventually when your design changes or someone wants to shift the
data into another format (say mobile use, or transformed into LaTeX for
publication), it's a matter of writing a fairly simple converter, rather than
trying to scrape the site or do other PITA stuff.

~~~
Cixelyn
I think it would be even better if the protocols were stored in some sort of
machine parse-able format rather than just human readable text.

This solves two problems a) the big problem of reproducibility in fields like
biology, and b) if it's machine-readable, you can just toss the file onto a
robot and have the whole procedure done for you.

Check out Biocoder for an example of a language for describing protocols:
[http://research.microsoft.com/en-
us/um/india/projects/biocod...](http://research.microsoft.com/en-
us/um/india/projects/biocoder/)

Format conversion and outputting versions for publication also follow quite
easily once a strict protocol language is defined.

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djacobs
I work in a lab and also code. I was _just_ thinking about implementing a
prototype site with this functionality _this week_. I have coded for a while
but have no coding resume, so I don't know if I qualify for your position. But
here are a couple of ideas I had, if you'd like them:

\- Create protocol versioning backed by something like Git - changes made to
protocols are tracked according to the user, and it should be simple to refer
to any version of the protocol (which will usually be versioned with words
instead of numbers)

\- Allow users to upload raw protocols and attempt to parse them for the key
sections - maybe have an assisted parsing, where the user can edit the final
interpretation

\- Make elements as semantic as possible (for example, catalog numbers,
repeatable steps, timepoints, notes/advisories)

\- Have protocols that are "certified" as being proofread or accepted by
multiple, reliable sources or contributors - especially protocols describing
reagent recipes

\- Make protocols as abstract as possible such that you can change variables
(volumes, number of reads, timing) at the top of the protocol, and the rest of
the protocol changes accordingly

\- Allow a rough graphing option of active/inactive time during the protocol,
so that the experimenter can generally gauge how to manage his time

\- Allow automatic creation of flow charts if protocol is formatted correctly

I have loads of experience with the pain points of protocols in science, so
I'd love to see a good, standard solution emerge in this space.

~~~
emeltzer
Many of these ideas are things we are either planning to implement or have
discussed in the past--great minds think alike :)

We'd absolutely love to talk more about this stuff with someone else who's as
interested in the problem as we are! Please do get in touch--email in the ad.

~~~
djacobs
Excellent, will send an e-mail tomorrow. I'm really excited about making an
integral part of my day as up-to-date as the rest of my workflow.

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kanzure
Git-revisioned protocols and sharing is nice, and is one step up from the
current situation in sharing and developing lab protocols. DIYbio as a group
has been eyeballing more programmatic ways of specifying protocols, either
through structured document formats (like XML) or parsed languages like in
Microsoft's Biocoder project:

[http://research.microsoft.com/en-
us/um/india/projects/biocod...](http://research.microsoft.com/en-
us/um/india/projects/biocoder/) or xml: <http://diyhpl.us/~bryan/irc/pcr.xml>

Still, I think this isn't a solved problem. The API for Biocoder feels all
wrong for numerous reasons; on top of that, nobody is going to learn a new
API, library or programming language just to write down a protocol, unless
they are being paid, or there's some really compelling reason to do so (which,
there isn't). Without something changing here, you just end up with a giant
corpus of protocols like we presently have, without metadata and basically
useless unless you already know what you want or need, or have the time to
manually check and double check everything in each protocol you might be
using.

One of the advantages of machine parsable protocols is being able to query
against your lab inventory...
[http://diyhpl.us/cgit/skdb/plain/doc/BOMs/diybio-
equipment.y...](http://diyhpl.us/cgit/skdb/plain/doc/BOMs/diybio-
equipment.yaml)

I should also point out that Jonathan Cline was working on parsing plaintext
protocols a while back:

Don’t Train the Biology Robot: Have the Machine Read the Protocol and Automate
Itself <http://88proof.com/synthetic_biology/blog/archives/290>

So it's just unclear how you plan to fix or assist in some of these dynamics,
at this point, or which specific problems you're solving.

I also posted this to the diybio people:
[http://groups.google.com/group/diybio/browse_thread/thread/1...](http://groups.google.com/group/diybio/browse_thread/thread/19df187ef1014735)

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possibilistic
One problem you might face is that there are already more than a few wikis for
this. For the last few experiments I've run, I used sites like these.

That said, you could easily distinguish yourselves. A website that could
recalculate concentrations, etc. based on your setup would be neat. To make it
even more accessible to newcomers, you should try to one day host a collection
of "open" review articles.

If I weren't so bogged down I'd love to work on something like this. Good
luck!

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jergason
This looks really neat. I am doing web development for a lab that is pretty
obsessed with open source, open protocols, ect, so I will for sure keep an eye
out on this. Wish I wasn't so swamped with work, because this looks like it
would be lots of fun.

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ylem
Do you want to run this as an open source project? Also, are you going for
standard lab protocols (of say the pharma variety), or reproducible
statistical analysis as well?

~~~
emeltzer
It'll be open source (like most projects in the open science space are, see
PLOS's open journal effort for a good example) because there is no reason for
it not to be :)

As for the type of protocol, since the site is oriented around user-moderated
groups, we're absolutely down with any kinds of protocol our users are
interested in.

------
emeltzer
Any critique of our ad or design spec are also very very welcome!

~~~
ajray
I am a research scientist but not a web developer. Is there anyway/anywhere I
can sign my email up to be notified when an Alpha/Beta is available? I'd love
to contribute if possible!

~~~
emeltzer
Absolutely. Should have linked this off the bat, but here is our signup page:
<http://openprotocols.net/>

~~~
ajray
Why does the subscription tell me I've subscribed to SynBioWorld?

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duportet
when do you plan to launch?

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georgieporgie
> That said, if you have the chops

Is 'chops' the 'ninja' of 2011? It seems to be making a comeback.

