Comment by sveme | Hacker News Reader

Comment by sveme | Hacker News Reader

Years ago, when I hadn't yet completed the switch from the lab to computers, I used 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 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...

>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.

There are many ex-companies that tried to push for an electronic lab notebook (ELN). There are several other ELN companies today that seem to have gotten nowhere. That's due to a panel of reasons, most important of which - they are competing with a paper notebook. May not be digital, but getting information into the paper one is trivial. Getting it into all the others a huge barrier.

Some free protocols, but most are not/are available on a subscription basis, but http://www.springerprotocols.com/ could be a much suitable alternative. However, I'm sceptical that your company hasn't heard of them, perhaps it's an issue of available funds for it unfortunately.

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