Fwd: Here's the general plan... (proteins)

[Nadim Shaikli <shaikli at yahoo dot com>]

I'm forwarding this email from "Anson David Parker" to the
'general' list since I think there is alot more being talked
about than shear translation type of issues (a bit outside
the scope of the 'doc' list).  The initial post/reply can be
found here,

  http://lists.arabeyes.org/archives/doc/2003/March/msg00137.html

Let's please keep things on the 'general' list (and not mail
privately) as there might be others interested and willing
to help (if you are not subscribed to 'general' please do so).

Salam.

 - Nadim

--- Nadim Shaikli <shaikli yahoo.com> wrote:
> --- Anson David Parker <adp6j cms.mail.virginia.edu> wrote:
> > Howdy, my name is Anson Parker, I am the director of the
> > RAD Lab, located at the University of Virginia in
> > Charlottesville, Virginia, USA.
> 
> Let me the first to welcome ya - lurkers are always welcome 
> :-)
 
Thanks!
 
> > The Arabic department was impressed too.
> 
> Is there anyone at that department that would be willing to 
> engage with us to see how best we can work things out (in
> general initially with specifics to follow) ?
 
That's the idea. There are two men in particular who chowed 
particular interest.  Neither are too tech savvy and so the 
RAD Lab has volunteered to prepare their web sites so that 
you can check out their bio's
 
> > I have been working on creating tutorials on 3D protein 
> > modeling for the last couple months, I am using XTAL and
> > Pymol (both open source) for most of the work, and some
> > other freeware, it's actually a pretty long list... but
> > that's not the point - I want to put the Arabic Department
> > here to work translating as many of these tools as possible.
> 
> Out of shear curiosity, why Arabic and protein modeling ? 
> I mean its not like Arabic countries are full of protein 
> scientists; I certainly don't mean that the Arab world is 
> ignorant (far from it), but most won't equate protein 
> modeling with Arabs.  Don't get me wrong - I salute you on 
> your thoughts, efforts, plans and direction but I'm just 
> wondering if there is indeed a possible Arabic country or 
> university that is getting into this wonderful field 
> (again, just curious).

well if they aren't they will be soon - very soon.  this 
stuff is pretty daggone simple, and supremely powerful. 
The computational end of it, moreover, although rigorous in 
some senses, is largely theoretical.  Arabs & Math = 
Algebra...  Moreover There are many "soft computational" 
methods which we can explore at length such as neural 
networks, genetic algorithms, etc that are as much a matter 
of trial and error as a rigorous math...

> > 6) Are any of arabeyes.org actually in Iraq now?  How can
> > we communicate with people there? There is so much apathy
> > here, people need to understand how close we all are.
> 
> Few come and go, but we try to keep this forum apolitical 
> as we have plenty of things we need to work on and 
> accomplish.  Rehashing the past and speculating on the 
> future ought to be left to those sitting in cafe's 
> contemplating "philosophical" questions :-)  In short, we 
> rather work and show results instead of whine and complain.
 
Amen!  AMEN! Let me state that this isn't political, this 
is public relations.  The RAD Lab is highly goal oriented. 
We drink our coffee out of boiling pots (turkish style), 
and we aim to make a real impact...  by aligning ourselves 
to arabeyes.org we hope to strengthen both efforts, yours 
which intimately ties the language and ours which ties the 
technology in to one heck of a "digital care package" which 
we have named digitAla.  When all the dust has settled we 
want to be there to provide tech support to the youth of 
Iraq, and so we need to start by meeting Iraqi students, 
teachers etc... this is summarily important.  We at RAD Lab 
must demonstrate to our people (the community, the 
university etc...) our genuine interest in making this 
project work. With this we can attract the student unions. 
Then we may iron out the details.  It is the RAD Lab's firm 
belief that it is time to put all of these gadgets to the 
test and make it happen, no governments, no politics, just 
students and dreamers makin ends meet.

> > 7) I want to start importing data in an arabic font into
> > mysql - has anyone done this? This database began this
> > afternoon after meeting with the arabic department.  It 
> > was suggested that perhaps the students could do their 
> > homework by putting english in one side and arabic in on
> > the other online... it isn't running yet, but it should be
> > by tomorrow... we sincerely would appreciate your input on
> > this end... hopefully you guys have a better idea.
> 
> That is all possible - make sure to look at the QaMoose 
> project
> 
>   http://www.arabeyes.org/project.php?proj=QaMoose
> 
> it might be very helpful in getting you the structure you 
> require.
> 
> Mr. Parker, we look forward to hearing more from you and 
> the Arabic department in hopes of forging closer ties between
> the two of us. As I'm sure you've come to learn, we are rather 
> short-handed and so we can certainly use all the help we can
> (on all fronts - and again we'd love to hear from that Arabic
> department :-)
 
**We will touch base with the arabic dept and include these 
transmissions as signs of interest on the part of 
arabeyes.org in collaborations**  We firmly believe that 
our goals have significant overlap, we will do everything 
we can to publicly support arabeyes.org.

No prob - we likewise greatly appreciate your efforts, 
thank you for your personal reply, we at the RAD Lab will 
be working likewise short-handed, with contact with Iraq 
established we believe our public relations coup will be a 
smashing success, we will put ourselves in charge of 
contacting the newspapers to announce the efforts.  There 
are certain members of the RAD Lab with relatively 
lucrative previous careers in PR who are willing to go the 
distance on this one,

There are many strings being pulled together, and that
makes it easy to trip up.  The significance of the 
protein prediction is in its own right something of a 
mystery, to that end the math department has been notified 
of these efforts.  The protocol was developed last year and 
makes a broad step in the next history of biomedical 
sciences, essentially the next step to the human genome 
project...  I'm putting these Q & A's up today to better 
explain the importance of developing protein structure 
prediction.  The beauty is that these technologies stand to 
substantially lessen the dependence on highly expensive 
machinary and allow pseudo-novices / programming fans to 
play a role in biomedical sciences (Linux meets Biotech). 
We are really sincere about having personal direct contact 
with someone over in Iraq - we need a leg to stand on.  Do 
you have anyone at all you could put us in touch with ? 
just an email address or something, a website, anything.... 
we are building a case over here and this is a crucial 
link.

sincerely & rock on,
The RAD Lab


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