An idea I am having that I want feedback on

[William Heath]

Hi All,

All my ideas on synthetic biology have been peculating in my head for years.  As a computer scientist I never understood how best to get into synthetic biology.  After years of studying this new engineering discipline I have made a decision:

I don't really care about lab work

I thought I did but once I got all the petri dishes, cell cultures, fume hoods etc... I realized I am just not a lab person.  What I really am is an ensilico lab person as Drew Endy put it when he came to my Diybio group at the Tech Shop.  He was desperate to get help with creating computer programs to automate lab like processes/research that could then later be tested in a real lab etc...  He said it is much quicker to do work with computer programs then raw lab work.  Here is what I have learned about synthetic biology computer programming needs:

*  Synbio has a great need to automate the research/hypothesis generation of optimized gene expression of proteins

*  Synbio has a great need to automate comparative analysis of existing genes/proteins/protein expression networks to create a desired protein (kind of like how the malaria drug was developed)

*  3d protein analysis etc...

Anyway my idea is to create a website where synthetic biologists can submit their programming needs and computer scientists can assist them.  I am curious about the best way to create such a website to make it easier for synthetic biologists to submit programming project requests/tasks.  What input fields would help synthetic biologists enter in their programming tasks/projects?  Do you feel such a site would as useful as I do?

-Tim BCSE, MSCS, MBA

[Stephanie]

As a programmer who currently lacks a background in DIY biology, but would really love to be a programming partner for various bio groups, I would love to see this.

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[leaking pen]

this idea has been brought up before, I think it would be awesome, but the small projects ive seen like it mostly seem to be very narrow solutions being requested, not an overall program with lots of features. 

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/B2A4B13E41F0494CAE37A6D0EAA84FE5%40maeagle.corp.

[Ravasz]

I'm a biologist who often runs into programming challenges while trying to do labwork - and I really can't solve those. I think your idea could go a long way.

[Tom Hodder]

On 10 October 2013 23:00, William Heath <wgh...@gmail.com> wrote:

All my ideas on synthetic biology have been peculating in my head for years.  As a computer scientist I never understood how best to get into synthetic biology.  After years of studying this new engineering discipline I have made a decision:

I don't really care about lab work

As a person with quite a few years of IT infrastructure, and systems management I was convinced that I would find a bunch of stuff that I could apply my skills to in bio-engineering, and hence make a seamless career transition from media-tech  to biotech in a reasonable time. (without getting my hands dirty .. in the wet lab)

However about half way through my Masters study I realised that a key difference between IT "Information technology" and the sort of  technology that I am working with now (Lab automation), is that there is a clear distinction between the types of technology and how abstracted they are from that actual underlying process that you are trying to automate.

I am referring to the difference between "mature" web application technologies, that have little actual interface with the real world, and the sort of tech that is required for programming, and automating molecular biology. For many years, other than scanners and printers, my main equipment and software was limited to a web browser, a web server, a database, and some scripting or OO language to move around chunks of information.

However automating PCR, microscopy, or electrophoresis etc, and then processing the results is a whole different ball game. Much of the tech is really embedded into the process itself, literally in the case of arduino, and other control and data capture electronics...

If you insisted on remaining purely "in silico", then I suspect that you would be relegating yourself to a purely support role, as I think it is much easier to generate hypothesises than test them... ;-)

[Nathan McCorkle]

I have an account on oDesk and have done some programming and
biotech-related work through there. I wish more bio/sci/engi
programming jobs were posted there (or somewhere like that).
Personally I'm against building another website, an oDesk clone, since
that would just be reinventing the wheel. Maybe you can figure out a
way to advertise oDesk to all these scientists who need programming
help. I'm a biotech major with a minor in bioinformatics and 15+ years
of linux and programming.

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-Nathan

[Stephanie]

I am on oDesk also, and would love to be able to find biotech jobs on it, or
any other freelance sites. I haven't seen one, though. Since there is so
much to sift through on those sites, one place that people can go to for
this specific purpose would be absolutely perfect.

https://groups.google.com/d/msgid/diybio/CA%2B82U9KP%3DKA-AinUY0viyvyKDk%3DFEa%2BMMaGYExXoiPk-Mt8jTg%40mail.gmail.com.

[Tom Hodder]

On 11 October 2013 14:54, Stephanie <st...@photofischer.net> wrote:

I am on oDesk also, and would love to be able to find biotech jobs on it, or any other freelance sites. I haven't seen one, though. Since there is so much to sift through on those sites, one place that people can go to for this specific purpose would be absolutely perfect.

In the UK, I've had quite a bit of success both buying and selling on peopleperhour.com, though everyone complains about their rates, and their site can be buggy. Also elance.com and freelancer.com have both been a source of sub-contractors when I've been in a pinch... ;-)

[William Heath]

Hi All,

Thanks for the feedback.  Anyway, this site will only cater to synthetic biology needs.  I am not interested in doing systems biology or lab automation in general but core synthetic biology programming needs.  It will be tightly focused and controlled in that aim.

-Tim

P.S.

Anyway, I will get to work on this :>

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[Stephanie]

Also, for those interested, I just found this full time offer with a company called Synthego on GroupTalent, for programmers with a background in Python:

 

https://grouptalent.com/listings/1305

 

It seems they are aiming to fully automate biological research.

 

 

From: Tom Hodder

Sent: Friday, October 11, 2013 10:21 AM

To: diy...@googlegroups.com

Subject: Re: [DIYbio] An idea I am having that I want feedback on

 

On 11 October 2013 14:54, Stephanie <st...@photofischer.net> wrote:

I am on oDesk also, and would love to be able to find biotech jobs on it, or any other freelance sites. I haven't seen one, though. Since there is so much to sift through on those sites, one place that people can go to for this specific purpose would be absolutely perfect.

 

In the UK, I've had quite a bit of success both buying and selling on peopleperhour.com, though everyone complains about their rates, and their site can be buggy. Also elance.com and freelancer.com have both been a source of sub-contractors when I've been in a pinch... ;-)

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[Matt Lawes]

Interesting and ambitious concept of fully automated experimental suite.

One wonders on the feasibility though. If biology would succumb to massive automation when it is a fuzzy nth dimensional science with gray logic at best, one would think software and hardware coding (simpler system, fewer variables and driven entirely by logic) would itself have been automated already....

Thoughts?

>matt

Sent from my Verizon Wireless 4G LTE DROID

Stephanie <st...@photofischer.net> wrote:

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/D5F0953BE75441318534CDC91430491B%40maeagle.corp.

[Cathal Garvey (Phone)]

Biology is trivially automatable if you have a practically infinite degree of parallelism. You know, like a cell.

Reminds me of the notion from SMBC that any object can be considered a perfect simulation of itself on single-purpose optimised hardware. :)

Matt Lawes <ma...@insysx.com> wrote:

Interesting and ambitious concept of fully automated experimental suite.

One wonders on the feasibility though. If biology would succumb to massive automation when it is a fuzzy nth dimensional science with gray logic at best, one would think software and hardware coding (simpler system, fewer variables and driven entirely by logic) would itself have been automated already....

Thoughts?

>matt

Sent from my Verizon Wireless 4G LTE DROID

Stephanie <st...@photofischer.net> wrote:

Also, for those interested, I just found this full time offer with a company called Synthego on GroupTalent, for programmers with a background in Python:

 

https://grouptalent.com/listings/1305

 

It seems they are aiming to fully automate biological research.

 

 

From: Tom Hodder

Sent: Friday, October 11, 2013 10:21 AM

To: diy...@googlegroups.com

Subject: Re: [DIYbio] An idea I am having that I want feedback on

 

On 11 October 2013 14:54, Stephanie <st...@photofischer.net> wrote:

I am on oDesk also, and would love to be able to find biotech jobs on it, or any other freelance sites. I haven't seen one, though. Since there is so much to sift through on those sites, one place that people can go to for this specific purpose would be absolutely perfect.

 

In the UK, I've had quite a bit of success both buying and selling on peopleperhour.com, though everyone complains about their rates, and their site can be buggy. Also elance.com and freelancer.com have both been a source of sub-contractors when I've been in a pinch... ;-)

--

Sent from my Android device with K-9 Mail. Please excuse my brevity.

[Matt Lawes]

True,

And a good example. However I remember data from the microarray revolution ... Garbage in / garbage out.

A lot of money is made from the unpredictability of biological responses, leading to the need for experimentalist approaches.

In my career I have led sales teams selling highly reproducible wide / parallel assay and gene expression screening tools. The limiting factor was the scientific customer's ability to comprehend a larger or 'bigger' question.

I think this is the flaw in Synthego's business model, but I'd be intrigued by answers  demolishing my strawman.

>matt

Sent from my Verizon Wireless 4G LTE DROID

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[Tom Hodder]

On 11 October 2013 22:50, William Heath <wgh...@gmail.com> wrote:

Anyway, I will get to work on this :>

"Computer chemists win Nobel prize"
http://www.bbc.co.uk/news/science-environment-24458534
 

Next up... computer biologists?