year-end SENS research fundraising

[Reason]

This isn't quite DIYbio, but I though that this group might be
interested from the perspective of following the evolution of
fundraising efforts in a related space, the SENS project.

SENS research programs aim to build the foundation technologies needed
to repair the cellular and molecular damage that causes aging - under
the mainstream model of aging that sees it as the consequence of
stochastic damage. The lines of research running under the auspices of
the SENS Research Foundation include a range of really interesting
molecular biology, and are entirely funded by philanthropic donations at
this point, from the grassroots community (25% perhaps) and from figures
such as Jason Hope, Peter Thiel, and Aubrey de Grey (75% perhaps). The
SENS Research Foundation is an excellent model to look over when it
comes to fundraising for specific research goals in human life sciences
that are not viewed favorably by the establishment - especially since so
much of the history of the organization and its funding is open. It
demonstrates very well the need to raise comparatively small amounts
from lots of people in order to open the door to raise large amounts
from high net work individuals.

But you really should look at the Foundation's research reports. There
is a lot of interesting stuff in there.

In any case, a collection of us are running a matching fund for
charitable donations made to SENS research until the end of the year.
This is an ad-hoc initiative that just sort of happened to fall together
over the last week or so as various people said "sure, that's a good plan."

So the details: Fight Aging!, philanthropist Jason Hope (who helped fund
the SENS Cambridge lab and ongoing AGE-breaker work with glucosepane),
and Methuselah Foundation are each putting up $15,000 to match the next
$15,000 donated to the SENS Research Foundation before 12/31/2013.

Donations are tax deductible and will be matched 3:1 - every $1 donated
pulls an additional $3 from the matching funds. With the help of the
community we hope to raise $60,000 over the next few weeks to help
expand SENS research programs in the coming year.

See:

https://www.fightaging.org/archives/2013/11/fight-aging-provides-15000-matching-fund-for-rejuvenation-research-donations.php

https://www.fightaging.org/archives/2013/12/jason-hope-partners-with-fight-aging-to-match-sens-rejuvenation-research-donations-in-december.php

https://www.fightaging.org/archives/2013/12/methuselah-foundation-expands-the-year-end-sens-rejuvenation-research-donation-match.php

If you are so inclined, you can do your part by donating at the SENS
Research Foundation site:

http://sens.org/donate

Reason

[Stephanie]

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...

[leaking pen]

hmm, I personally dont have any VERY diy bio program ideas at the moment (that i can afford the hardware to use for testing) but I do have a few human potential program ideas, such as one to try and teach perfect pitch that I have a design doc for, if you'd be interested.

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[Brian Degger]

Have you tried looking on sourceforge at the different (not specifically diybio) synthetic biology projects like tinkercad and genocad?  

Maybe they have open tickets you could contribute too!

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAFaFt-TGYN_SLXT571%3D1O%2BacbFhfWn_9reKVk9mcO6rOhTP5LA%40mail.gmail.com.

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Brian Degger

twitter: @drbrian

http://makerspace.org.uk

http://transitlab.org

----------------------------------------

[Stephanie]

Sure, send them over!

 

From: leaking pen

Sent: Wednesday, December 04, 2013 11:31 PM

To: diy...@googlegroups.com

Subject: Re: [DIYbio] programmer/web developer available

 

hmm, I personally dont have any VERY diy bio program ideas at the moment (that i can afford the hardware to use for testing) but I do have a few human potential program ideas, such as one to try and teach perfect pitch that I have a design doc for, if you'd be interested.

On Wed, Dec 4, 2013 at 9:07 PM, Stephanie <st...@photofischer.net> 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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[Jonathan Cline]

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
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

[Matthew Harbowy]

It's worth looking into BIKALIMS (open source) for this.

Matt

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[Cathal Garvey]

Hey Stephanie!
If you're bored, a webapp interface to PySplicer (my codon
optimisation engine using Vienna and Python) would probably make it
useful to people otherwise unable to use it (because they're
terminal-averse..)! :)
https://gitorious.org/pysplicer