Re: [DIYbio] programmer/web developer available

In terms of database needs it would be great to have an open source LIMS which connects to robotics control software such as my Perl Robotics package, http://search.cpan.org/dist/Robotics/ or other robotics packages.

Here is the use case. 

The robot has it's application and protocol fully developed and ready to go.  The application needs to query a database, a LIMS, to see if there is reagant X or Y in the inventory, and if so, where it is located, so the robo-arm can go fetch it (or if it is not available, to alert the operator or re-order low stock).  After the reagents are accounted for, the robot app calculates the number of microplates needed for the run, and again queries the LIMS to see where the stacks are and/or which robo-column they are loaded into. 

As with any database, typically a lab creates a database in a hurry to get a specific project done, it's not scalable, and it rots after the project is completed.  It would be great to design a scalable set of tables for LIMS with both web front end and open backend usable across multiple branches of biotech.  In industry of course, the vendors use the proprietary LIMS to create lock-in, and the databases are not very scalable because each vendor is serving a particular product niche, not interested in portability of the data or formats outside their limited scope.

Here is a use case in the vein of 4-decades-away implementation: 

A researcher is following a particular topic of interest and finds a paper written by a colleague, with an experimental protocol given in the supplementary data.  The researcher has a bright idea and wants to re-run the experiment.  He opens the browser to his lab's server, imports the paper.  The lab's server analyses the supplementary data section and parses the experimental protocol directly, cross-compiling it for the researcher's robots (which are a different brand than those in the paper).  The server software tells the researcher he needs to buy 4 new reagents to support the protocol.  The researcher connects the protocol to through the LIMS and accounting system to check his funding budget and the software suggests cross-references to different reagents not available in his lab or at his budget, but which can act as stand-ins.  The researcher orders the reagents.  Now the researcher has the exact copy of the instructions which he can run in his own lab.  Four days later, the delivery house drops the reagents off in dry ice and they're logged into the system, so the server sends a notification to the researcher that all ingredients are ready.  The researcher starts the run of the protocol without modifications, as a control, and the robot will take 3 hours to complete and 22 hours to incubate.  In parallel, the researcher modifies the protocol based on his bright idea, and develops 3 new versions, which he also starts in parallel, with various times to completion.  3 days later the incubation is complete and the measurement data is sitting on the system for post-run analysis.   2 weeks later, the researcher has his result and begins to write his own paper, one-upping the results of his colleague.  ;-D    

There's a long list of standards, formats, communication protocols, user interfaces, databases, etc etc, which do not exist today, yet are pieces of what seems like a rather simple use case above.

## Jonathan Cline
## jcline@ieee.org
## Mobile: +1-805-617-0223
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On Wednesday, December 4, 2013 8:07:53 PM UTC-8, scylla wrote:

Hi all. I would like to help out if anyone has a need for some web development or general programming. Web development in a range of languages and systems has been my full time job for the past 13 years. It includes server side ASP, PHP, ColdFusion, Java, and client side HTML5, CSS3, JavaScript, jQuery, AJAX, JSON, etc.

As far as desktop programming, I have experience in the .NET framework, C#, and Java so far.

Database wise: relational- MSSQL, MySql. flat file- Universe.

I love to learn, so I am totally open to picking up anything I either don't know or don't know much of.

Really, my goal is to help out in the field, even in a small way. So if you are interested in finding out more about me or my skills, just let me know...

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