

Protocols.io – Life Sciences Protocol Repository - StandardFuture
https://www.kickstarter.com/projects/1881346585/protocolsio-life-sciences-protocol-repository

======
sveme
Years ago, when I hadn't yet completed the switch from the lab to computers, I
used [http://www.protocol-online.org/](http://www.protocol-online.org/) from
time to time, which is, in my understanding, a similar project. Though
checking it out just now indicates that not much has been going on there for
the last couple of years. irollboozers already mentioned
[http://openwetware.org/wiki/Main_Page](http://openwetware.org/wiki/Main_Page)
as an alternative project with a wiki-style interface. Those sites attracted
some participants but it seems they never really went mainstream - should ask
the wet lab people about this to confirm.

As I'm working in Next Generation Sequencing (NGS) now after a stint in the
software industry, I'm actually shocked by the lack of standardization and
documentation in the wet lab, which makes a thorough statistical data analysis
so much harder. Few use electronic lab books and even fewer associate those
with experimental data.

I think that is what is really missing, a push to easy-to-use electronic lab
books that use open, machine- and human-readable formats and a straightforward
way of associating these with the generated data. Upload these documented and
annotated raw data to a central repository and you create a computational
biologist's wet dream.

But that would require a huge amount of work to create the necessary
ontologies...

~~~
aroch
>I'm actually shocked by the lack of standardization and documentation in the
wet lab

There's actually quite a lot of both of these. Here's the thing, we all have
protocols specific to our labs or organisms. For many of us, our protocols are
based on a canonical source (Which are now usually found in _Nature 's_
Prootcols) but optimized around what we do. Working with organics is rarely as
easy as it might seem (especially if you're coming from the software side of
things, I somwhat did too). I've digitized most of our protocols (some dating
back to the 1950's) but for the most part we all refer to hardcopies of them.
Electronic protocols aren't nearly as useful as print ones, especially since
they're constantly tweaked. And most of us in academia freely share our
optimized protocols with eachother -- you only have to ask.

There are a couple of Lab-notebook-in-the-cloud options but I've never really
liked any of them. Instead I keep everything in Dropbox (for sharing with my
colleagues) with versioning handled in a private git repo. I can commit
experiment notes and checkin images. All of my notes are in markdown.

------
twic
There's a newsgroup (and gatewayed mailing list), running for god knows how
long but at least since 1993 [1], called Methods and Reagents:

[https://groups.google.com/forum/#!forum/bionet.molbio.methds...](https://groups.google.com/forum/#!forum/bionet.molbio.methds-
reagnts)

Which has been used to share protocols, just like this, since the dawn of the
web. It's a newsgroup, so hardly anyone uses it any more, of course. I guess
it doesn't have a flat UI and an iPhone app.

At some point, some of the users of the group set up a wiki to capture
protocols in a more permanent form:

[http://methodsandreagents.pbworks.com/w/page/20806945/FrontP...](http://methodsandreagents.pbworks.com/w/page/20806945/FrontPage)

But it never took off like we hoped.

As irollboozers notes in another comment, there is nothing new under the sun.
The selection criterion for any such effort is simply getting a critical mass
of people involved and contributing protocols.

[1]
[http://schneider.ncifcrf.gov/methods/TIBS/nov93.txt](http://schneider.ncifcrf.gov/methods/TIBS/nov93.txt)

------
cfontes
Not sure about if that will work.

Most of the time you can't change a thing in protocols if you want to have a
minimal level of acceptance.

You would only need such a thing if you are developing a new protocol for
something, which might happen a lot but I am not sure if it would be nice to
be sharing not ready protocols on the web. Even if it would, people would
still need to agree on a single one or something. Otherwise you will end up
with 200000x DNA extraction protocols with their tiny customizations(Every lab
technician has it's own way of doing every single step in some protocols...)

It would probably be nice as a in house access only system for universities
and research facilities thought.

~~~
pallandt
There's already Springer Protocols
([http://www.springerprotocols.com/](http://www.springerprotocols.com/)), not
free, but IMHO, universities and research facilities already have it better
than whatever free alternative may come up in the future. This is not the sort
of project that requires only upfront costs, this is why I unfortunately don't
think it will live for long, if it ever gets completely funded.

------
irollboozers
The crowdsourced part is where this could really have a big impact, otherwise
the technology is pretty standard. Crowdsourcing legitimate and replicable
protocols is something others have tried (OpenWetWare, etc) but not quite
scaled to Github like levels. Still, this seems to run into the same
challenges that others before it faced.

I'll gladly pitch in some funds!

~~~
newyorklenny
Indeed, the effort to create a central protocol repository is at least 20
years old. No one succeeded. The key part here is the crowdsourcing. Won't
happen without a crowd. And won't happen unless a busy geneticist can share
with a tap of a button. That's why for two years we have been focused on
giving amazing tools to researchers - build the user base. We did not even
begin building protocols.io and the checklist app right away because we know
how hard it is to get traction. Also, we may just be doing this at the right
time - on mobile. The protocol checklist app is the key ingredient that will
make this happen.

------
danialtz
I work in a lab that does high throughput screening, and I do develop internal
web-based toolsets. After several years of iterations I can say that so far
electronic lab notebooks never worked; there are even several commercial
software available.

There are several reasons behind it:

1) Protocols are not a fixed predefined setup. One of the most important part
of a protocol is the annotations on top. What went wrong, what did you change,
etc. Today I have a repository of hand-written protocols (see [2]) that people
print before going to the lab, write a date on it, and write comments on it. I
cannot imagine this process of taking notes will be disrupted in near future,
unless a very easy to use note taking system is there. IPad, LiveScribe (even
wrote an app for it) et al are not there.

2) Writing protocols for lab people is cumbersome. Especially in our lab that
has a protocol for every little process, to ensure reproducibility and
standards. Asking them to sit behind computers (or mobile phone) to write is
madness. The best that worked so far is I ask them to write and draw the
process. Scan it, store in db, and print it with a click before experiment.
They are happier than ever. Once done, I scan them back into db with date
attached, and use evernote to search inside in case. The drawback is th
editing part, but surprisingly they prefer to rewrite the whole thing rather
than edit it behind the computer.

3) Protocols are subject to change, unless they are standard protocols
(probably the market that this kickstarter is aiming). How should people store
the revisions of the protocols? which one was used in the last experiment? did
this modification work? think about a "git" system for protocols!

4) Lab people hate computers. They hate to use mobile phones to do anything
than checking mails and calls. They love paper. Anything touchable. Taking
mobiles into the lab is messy (google glass?). I have a feeling this can work
with a geeky lab person but majority will oppose strongly.

5) Try to enter a protocol inside the tool. It will take ages until I have a
smart protocol that may use non-standard agents inside. They need to work on a
smarter way of entering protocols. Forms are too rigid.

6) I did an A/B test for some time, and what I found out was that pictures and
text combination work great together, and minimized the common errors a lot.
Printing a protocol, taking with them and ticking steps added another level of
quality. So, adding hand-drawn / google images to the protocols may help
besides an option for printing the protocol in the mobile app.

7) I love the common repository idea. The share button will be easy enough for
even the laziest laborant.

I believe this is a good step toward the mess that is happening in the labs.
Still the solution above currently is a local one to me; good enough for
iteration 1 and will donate to push the idea forward.

~~~
newyorklenny
I just wrote a long answer to "Will scientists use mobile in the lab?"
[http://blog.pubchase.com/was-henry-ford-an-idiot-will-
scient...](http://blog.pubchase.com/was-henry-ford-an-idiot-will-scientists-
use-mobile-in-the-lab/)

