Re: [ccp4bb] CCP4 for iphones

[Xiaoguang Xue]

Hi,

Your idea is very cool, but i think it's difficult to run CCP4, Coot or
Phenix on iphone/itouch. Because the CPU of iphone/itouch is very slow and
the graphics engine is also not good enough for these programs.

But I think we can install an SSH client app on iphone/itouch/ipad, such as
iSSH, then we can control our server or workstation by iphone/itouch, and we
can run these 'big' software remotely. If this can be considered working on
an iphone, I think we can do that.

Nice weekend!

Xiaoguang



On Fri, Feb 25, 2011 at 8:54 PM, Jacob Keller <
j-kell...@fsm.northwestern.edu> wrote:

> Hello All,
>
> is there a ccp4 app for iphones yet? Has any structure been solved on
> an iphone? I know BR uses an iphone to drive his robots, but what
> about structures?
>
> (A question for Friday afternoon...)
>
> JPK
>
>
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> cel: 773.608.9185
> email: j-kell...@northwestern.edu
> ***
>



-- 
Xiaoguang Xue, PhD student
Utrecht University
Crystal & Structural Chemistry
Padualaan 8. Room N807
3584 CH Utrecht
The Netherlands
Tel. +31-30-253-2383

Re: [ccp4bb] CCP4 for iphones

[Xiaoguang Xue]

But I don't know what will happen if we make a cluster by hundreds and
thousands of iphones.

On Fri, Feb 25, 2011 at 9:25 PM, Xiaoguang Xue  wrote:

> Hi,
>
> Your idea is very cool, but i think it's difficult to run CCP4, Coot or
> Phenix on iphone/itouch. Because the CPU of iphone/itouch is very slow and
> the graphics engine is also not good enough for these programs.
>
> But I think we can install an SSH client app on iphone/itouch/ipad, such as
> iSSH, then we can control our server or workstation by iphone/itouch, and we
> can run these 'big' software remotely. If this can be considered working on
> an iphone, I think we can do that.
>
> Nice weekend!
>
> Xiaoguang
>
>
>
>
> On Fri, Feb 25, 2011 at 8:54 PM, Jacob Keller <
> j-kell...@fsm.northwestern.edu> wrote:
>
>> Hello All,
>>
>> is there a ccp4 app for iphones yet? Has any structure been solved on
>> an iphone? I know BR uses an iphone to drive his robots, but what
>> about structures?
>>
>> (A question for Friday afternoon...)
>>
>> JPK
>>
>>
>> ***
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> cel: <773.608.9185> <773.608.9185>773.608.9185
>> email: j-kell...@northwestern.edu
>> ***
>>
>
>
>
> --
> Xiaoguang Xue, PhD student
> Utrecht University
> Crystal & Structural Chemistry
> Padualaan 8. Room N807
> 3584 CH Utrecht
> The Netherlands
> Tel. <%2B31-30-253-2383>+31-30-253-2383
>



-- 
Xiaoguang Xue, PhD student
Utrecht University
Crystal & Structural Chemistry
Padualaan 8. Room N807
3584 CH Utrecht
The Netherlands
Tel. +31-30-253-2383

Re: [ccp4bb] CCP4 for iphones

[Tommi Kajander]

why, If we are lucky they will all just vaporize and disappear...   
(...sorry couldn't resist...)


tommi

On Feb 25, 2011, at 10:51 PM, Xiaoguang Xue wrote:

But I don't know what will happen if we make a cluster by hundreds  
and thousands of iphones.


On Fri, Feb 25, 2011 at 9:25 PM, Xiaoguang Xue   
wrote:

Hi,

Your idea is very cool, but i think it's difficult to run CCP4, Coot  
or Phenix on iphone/itouch. Because the CPU of iphone/itouch is very  
slow and the graphics engine is also not good enough for these  
programs.


But I think we can install an SSH client app on iphone/itouch/ipad,  
such as iSSH, then we can control our server or workstation by  
iphone/itouch, and we can run these 'big' software remotely. If this  
can be considered working on an iphone, I think we can do that.


Nice weekend!

Xiaoguang




On Fri, Feb 25, 2011 at 8:54 PM, Jacob Keller > wrote:

Hello All,

is there a ccp4 app for iphones yet? Has any structure been solved on
an iphone? I know BR uses an iphone to drive his robots, but what
about structures?

(A question for Friday afternoon...)

JPK


***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j-kell...@northwestern.edu
***



--
Xiaoguang Xue, PhD student
Utrecht University
Crystal & Structural Chemistry
Padualaan 8. Room N807
3584 CH Utrecht
The Netherlands
Tel. +31-30-253-2383



--
Xiaoguang Xue, PhD student
Utrecht University
Crystal & Structural Chemistry
Padualaan 8. Room N807
3584 CH Utrecht
The Netherlands
Tel. +31-30-253-2383


Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
tommi.kajan...@helsinki.fi

Re: [ccp4bb] CCP4 for iphones

[William Scott]

Until tcl/tk gets ported, this might tide you over:

http://www.readpixel.com/remotetap/index.html

It is a VNC display optimized for iPod/iPhone/iPad use.

-- Bill


-


On Feb 25, 2011, at 11:54 AM, Jacob Keller wrote:

> Hello All,
> 
> is there a ccp4 app for iphones yet? Has any structure been solved on
> an iphone? I know BR uses an iphone to drive his robots, but what
> about structures?
> 
> (A question for Friday afternoon...)
> 
> JPK
> 
> 
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> cel: 773.608.9185
> email: j-kell...@northwestern.edu
> ***

William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/

Re: [ccp4bb] CCP4 for iphones

[Xiaoguang Xue]

Well, maybe building a distributed computing network （Like Fold@Home) by
iphone is an improvement of the clusters. Let's think about a phenomenon,
the most common functions of our iphone are calling, playing music, and
maybe gaming, so most of the time the phone is idle. Why don't we try to use
these idle computing time to help us doing some more important and
interesting things, like determining the proteins structures?

I also noticed that there is some progress in grid computing on iphone and
PS3. So I think it's possible to apply this technique to structural biology.

http://www.sciencedaily.com/releases/2010/04/100413072040.htm

Xiaoguang


On Fri, Feb 25, 2011 at 10:01 PM, Tommi Kajander  wrote:

> why, If we are lucky they will all just vaporize and disappear...
>  (...sorry couldn't resist...)
>
> tommi
>
>
> On Feb 25, 2011, at 10:51 PM, Xiaoguang Xue wrote:
>
>  But I don't know what will happen if we make a cluster by hundreds and
>> thousands of iphones.
>>
>> On Fri, Feb 25, 2011 at 9:25 PM, Xiaoguang Xue  wrote:
>> Hi,
>>
>> Your idea is very cool, but i think it's difficult to run CCP4, Coot or
>> Phenix on iphone/itouch. Because the CPU of iphone/itouch is very slow and
>> the graphics engine is also not good enough for these programs.
>>
>> But I think we can install an SSH client app on iphone/itouch/ipad, such
>> as iSSH, then we can control our server or workstation by iphone/itouch, and
>> we can run these 'big' software remotely. If this can be considered working
>> on an iphone, I think we can do that.
>>
>> Nice weekend!
>>
>> Xiaoguang
>>
>>
>>
>>
>> On Fri, Feb 25, 2011 at 8:54 PM, Jacob Keller <
>> j-kell...@fsm.northwestern.edu> wrote:
>> Hello All,
>>
>> is there a ccp4 app for iphones yet? Has any structure been solved on
>> an iphone? I know BR uses an iphone to drive his robots, but what
>> about structures?
>>
>> (A question for Friday afternoon...)
>>
>> JPK
>>
>>
>> ***
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> cel: <773.608.9185>773.608.9185
>> email: j-kell...@northwestern.edu
>> ***
>>
>>
>>
>> --
>> Xiaoguang Xue, PhD student
>> Utrecht University
>> Crystal & Structural Chemistry
>> Padualaan 8. Room N807
>> 3584 CH Utrecht
>> The Netherlands
>> Tel. <%2B31-30-253-2383>+31-30-253-2383
>>
>>
>>
>> --
>> Xiaoguang Xue, PhD student
>> Utrecht University
>> Crystal & Structural Chemistry
>> Padualaan 8. Room N807
>> 3584 CH Utrecht
>> The Netherlands
>> Tel. <%2B31-30-253-2383>+31-30-253-2383
>>
>
> Tommi Kajander, Ph.D.
> Structural Biology and Biophysics
> Institute of Biotechnology
> University of Helsinki
> Viikinkaari 1
> (P.O. Box 65)
> 00014 Helsinki
> Finland
> p. <%2B358-9-19158903>+358-9-19158903
> tommi.kajan...@helsinki.fi
>



-- 
Xiaoguang Xue, PhD student
Utrecht University
Crystal & Structural Chemistry
Padualaan 8. Room N807
3584 CH Utrecht
The Netherlands
Tel. +31-30-253-2383

Re: [ccp4bb] CCP4 for iphones

[Sean Seaver]

I've been curious if there has been discussion about moving data processing and 
refinement to a software as a service (SaaS) deployment.  If programs were web 
accessible then it may save researchers time and trouble (maintaining and 
installing software).  In turn, one could then process data via their iphone.  

The computational demand would be enormous and personally have a hard time even 
doing a back of the envelope calculation.  The demand could be offset such as 
by limiting jobs or the number of users, etc...  It will be interesting to see 
how mobile plays a role in crystallography.

Take Care,

Sean

P212121
http://store.p212121.com/

Re: [ccp4bb] CCP4 for iphones

[Nat Echols]

On Fri, Feb 25, 2011 at 2:10 PM, Sean Seaver  wrote:

> I've been curious if there has been discussion about moving data processing
> and refinement to a software as a service (SaaS) deployment.  If programs
> were web accessible then it may save researchers time and trouble
> (maintaining and installing software).  In turn, one could then process data
> via their iphone.
>
> The computational demand would be enormous and personally have a hard time
> even doing a back of the envelope calculation.  The demand could be offset
> such as by limiting jobs or the number of users, etc...  It will be
> interesting to see how mobile plays a role in crystallography.
>

SBGrid has done something like this for massively parallel MR searches:

https://portal.nebiogrid.org/secure/apps/wsmr/

But that's a massively parallel and highly distributed calculation, which
isn't what crystallographers do most of the time.  Nor do they need to be
particularly mobile in an era of remote synchrotron data collection.  There
would be additional concerns about data privacy - pharmaceutical companies
probably aren't going to use such a service, and even some academics are
paranoid about letting anyone (including methods developers) see what
they're working on.

I have a lot of other objections to the idea of doing everything as a
webapp, but that's a separate rant.  I do, however, like the idea of using
multi-touch interfaces for model-building, but you need something at least
the size of an iPad for that to be more productive than using a traditional
computer with a mouse.

-Nat

Re: [ccp4bb] CCP4 for iphones

[Eugene Krissinel]

Is there a real need?

Eugene

On 25 Feb 2011, at 19:54, Jacob Keller wrote:

> Hello All,
> 
> is there a ccp4 app for iphones yet? Has any structure been solved on
> an iphone? I know BR uses an iphone to drive his robots, but what
> about structures?
> 
> (A question for Friday afternoon...)
> 
> JPK
> 
> 
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> cel: 773.608.9185
> email: j-kell...@northwestern.edu
> ***

Re: [ccp4bb] CCP4 for iphones

[Pete Meyer]

Xiaoguang Xue wrote:
[snip]

Why don't we try to use these idle computing time to help us doing some more 
important and interesting things, like determining the proteins structures?


Battery life.  If a phone is doing number crunching, it's not putting 
the processor into a low-power state.  The heat sinks might also get 
overloaded - I haven't yet seen a phone with a cooling fan.


Pete

Re: [ccp4bb] CCP4 for iphones

[Ian Stokes-Rees]

In a sentence, primarily due to cost and power constraints mobile
devices don't (currently) have the horsepower to do any serious
*generic* number crunching, as would be required for anything of
interest to this community.

On the topic of using otherwise-idle compute time, our group has a
publicly available service for doing molecular replacement which
accesses a federation of computing centers across the US (through Open
Science Grid):

https://portal.nebiogrid.org/secure/apps/wsmr/

We regularly secure 50-150,000 hours per day of computing time from
OSG.  We're in the process of improving this and adding in additional
services.  Watch this space.  For those with more of an interest on this
topic, you can read on below.

Regards,

Ian



This thread raises some interesting questions, but indicates a lack of
understanding of the difference between what a mobile device like an
iPhone, iPad, or Android can do compared to a rack-mounted server,
desktop computer, or even laptop.The number crunching mobile devices
are capable of is for specific sorts of data like audio and video codecs
which are offloaded to specialized hardware and which can't (currently)
be reused for other applications (like protein structure studies).  GPUs
are showing how this can change, but I wouldn't hold your breath.  I
think power and battery life will continue to be challenges for mobile
devices for a long time, so even if generic computing ability catches up
with "conventional" desktop/server capabilities, few people will want
their batteries drained by their device running continuously doing an MD
simulation or structure refinement.

On 2/25/11 5:01 PM, Xiaoguang Xue wrote:
> Well, maybe building a distributed computing network （Like Fold@Home)
> by iphone is an improvement of the clusters. Let's think about a
> phenomenon, the most common functions of our iphone are calling,
> playing music, and maybe gaming, so most of the time the phone is
> idle. Why don't we try to use these idle computing time to help us
> doing some more important and interesting things, like determining the
> proteins structures

US-based non-commercial researchers can access Open Science Grid
(http://www.opensciencegrid.org/), which consists of a federation of
about 80,000 compute cores, by registering for a certificate and joining
(or forming) a Virtual Organization.  We host a Virtual Organization in
OSG called "SBGrid" which is open to all SBGrid consortium members
(http://sbgrid.org/).  We regularly get 2000-4000 compute cores from OSG
for extended periods (12-96 hours), so it is a very powerful resource.

Another alternative for structural biologists who could benefit from
>1000s of compute cores is to get an allocation at a national
supercomputing center.  In the US, NERSC or TeraGrid are good routes for
this, and many options exist.  In Europe EGI and DEISA provide a similar
"one stop shop" for federated grid computing and supercomputing center
access.

http://www.nersc.gov/
https://www.teragrid.org/
http://www.egi.eu/
http://www.deisa.eu/

Finally, you can benefit from the millions of desktop computers out
there with super-powerful compute cores and GPUs that spend most of the
time (often >90%) completely idle using "screen saver computing".  Here
there is really only one option which is BOINC, developed by the group
that created SETI@Home.  Rosetta is (sort-of) available this way through
Rosetta@home, developed by the Baker Lab.

http://boinc.berkeley.edu/
http://boinc.bakerlab.org/

> I also noticed that there is some progress in grid computing on iphone
> and PS3. So I think it's possible to apply this technique to
> structural biology.
> http://www.sciencedaily.com/releases/2010/04/100413072040.htm

I think adding "iPhone" to the title of that article was just to attract
readers.  They are only using the standard web-browsing features
available on pretty much any smart phone or mobile device to view
web-portal views of computational infrastructure.  All the actual
computing was done on PS3s (and only 16 of them).  In other words, if
you consider browsing to EBI or RCSB to access some sequence alignment
program or view some protein structures, then you can say "I've used an
iPhone for grid computing".  Most people, however, would question the
accuracy of this association.

Re: [ccp4bb] CCP4 for iphones

[Ian Stokes-Rees]

  
  


On 2/25/11 5:41 PM, Nat Echols wrote:
On Fri, Feb 25, 2011 at 2:10 PM, Sean Seaver 
  wrote:
  

  I've been curious if there has been discussion about moving
  data processing and refinement to a software as a service
  (SaaS) deployment.  If programs were web accessible then it
  may save researchers time and trouble (maintaining and
  installing software).  In turn, one could then process data
  via their iphone.
  
  The computational demand would be enormous and personally have
  a hard time even doing a back of the envelope calculation.
   The demand could be offset such as by limiting jobs or the
  number of users, etc...  It will be interesting to see how
  mobile plays a role in crystallography.



SBGrid has done something like this for massively parallel
  MR searches:


https://portal.nebiogrid.org/secure/apps/wsmr/


But that's a massively parallel and highly distributed
  calculation, which isn't what crystallographers do most of the
  time.  Nor do they need to be particularly mobile in an era of
  remote synchrotron data collection.
  


Nat, thanks for commenting on this.  As the person who has developed
it, I'm glad someone has noticed the connection between the
web-based application (well, really just an application wrapper,
since it uses CCP4 software underneath) and what it is actually
doing behind the scenes.  It seems to us (within SBGrid) that there
are quite a few applications that can benefit from access to large
scale computational infrastructure.  Sometimes having that resource
available will allow people to ask new questions or pose old
questions in a new way.  We're always happy to talk to people who
have ideas for new computational workflows or applications that can
benefit from 10s of thousands of compute cores or that process TB of
data.  And of course the underlying resources are available to
others to access themselves (see another post I made on this same
thread about an hour ago).


  
I have a lot of other objections to the idea of doing
  everything as a webapp, but that's a separate rant.  I do,
  however, like the idea of using multi-touch interfaces for
  model-building, but you need something at least the size of an
  iPad for that to be more productive than using a traditional
  computer with a mouse.

  


I agree that not everything should be done as a web app.  When
high-functionality UI features are required, developing these with
CSS, jQuery, AJAX, HTML5, Java, etc. is super time consuming,
compared with conventional integrated UI toolkits (Tcl/TK, Qt,
Cocoa, .NET, etc.).  Similarly when significant "real-time" data
processing is required, or if multiple applications are interacting
with the same data, then the UI (graphical or otherwise) needs to be
"close" to the user data, and not stuck messing around with web
browsers (which can't really be scripted) and web forms.

I got a 21" HP multi-touch screen last year to explore improved
touch-based interfaces for structural biology applications, however
it doesn't work (properly) under OS X, and I'm not inclined to shift
to a Windows based environment to develop for it.  Hopefully some
standard USB interfaces/drivers/libraries (events) will appear soon
so the iPad and other tablets aren't the exclusive domain for
touch-based applications.

Ian