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42 点作者 emeltzer超过 14 年前

9 条评论

zdw超过 14 年前
Design the data format (API) first, then the user interface later. You have the cart in front of the horse.<p>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.<p>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.
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djacobs超过 14 年前
I work in a lab and also code. I was <i>just</i> thinking about implementing a prototype site with this functionality <i>this week</i>. 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:<p>- 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)<p>- 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<p>- Make elements as semantic as possible (for example, catalog numbers, repeatable steps, timepoints, notes/advisories)<p>- Have protocols that are "certified" as being proofread or accepted by multiple, reliable sources or contributors - especially protocols describing reagent recipes<p>- 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<p>- Allow a rough graphing option of active/inactive time during the protocol, so that the experimenter can generally gauge how to manage his time<p>- Allow automatic creation of flow charts if protocol is formatted correctly<p>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.
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kanzure超过 14 年前
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:<p><a href="http://research.microsoft.com/en-us/um/india/projects/biocoder/" rel="nofollow">http://research.microsoft.com/en-us/um/india/projects/biocod...</a> or xml: <a href="http://diyhpl.us/~bryan/irc/pcr.xml" rel="nofollow">http://diyhpl.us/~bryan/irc/pcr.xml</a><p>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.<p>One of the advantages of machine parsable protocols is being able to query against your lab inventory... <a href="http://diyhpl.us/cgit/skdb/plain/doc/BOMs/diybio-equipment.yaml" rel="nofollow">http://diyhpl.us/cgit/skdb/plain/doc/BOMs/diybio-equipment.y...</a><p>I should also point out that Jonathan Cline was working on parsing plaintext protocols a while back:<p>Don’t Train the Biology Robot: Have the Machine Read the Protocol and Automate Itself <a href="http://88proof.com/synthetic_biology/blog/archives/290" rel="nofollow">http://88proof.com/synthetic_biology/blog/archives/290</a><p>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.<p>I also posted this to the diybio people: <a href="http://groups.google.com/group/diybio/browse_thread/thread/19df187ef1014735" rel="nofollow">http://groups.google.com/group/diybio/browse_thread/thread/1...</a>
possibilistic超过 14 年前
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.<p>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.<p>If I weren't so bogged down I'd love to work on something like this. Good luck!
jergason超过 14 年前
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.
ylem超过 14 年前
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?
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emeltzer超过 14 年前
Any critique of our ad or design spec are also very very welcome!
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duportet超过 14 年前
when do you plan to launch?
georgieporgie超过 14 年前
&#62; That said, if you have the chops<p>Is 'chops' the 'ninja' of 2011? It seems to be making a comeback.