[emboss-dev] Task Update

Thu Jul 2 04:20:09 EDT 2009

Dear Sir,

I have created the database design for the task of running the tasks of
Emboss in parallel.
As this is to be monitored from any place, I thought of making it web-based.
Java/Servets/JSP/Beans is my choice as I am confortablw with these.

Now, I will need an IP address of another machine , located in a distant
place , having Emboss running on it.

The first interface would be the master interface, tracking all the
activities, This should be easy, provided I have all the IP addresses and
program details.

Next, this is what will happen. I have Jemboss installed on my PC ( with
internet ) . Next I get the first task, say try creating a sequence or any
simple input function.

This interface will need some input from (another Jemboss interface ) at
machine in another location. The details are sent to this machine via
internet as this is the widest network available.

I am using Servlets / JSP with MySQL support.

Note:- In above scenario, to send an input from one interface,  I will need
a button or a menu item in the main interface of Jemboss, this will send the
details on the click event.

For receving part, when the user receives via email, a Jemboss receiving
interface  will listen for such mails, get the details from reading this
email (All this is done in the background) and thus is the details are sent
to this interface.

This is a little difficult but worth implementing. Once done, this would
mean that a person can execute an interface of Jemboss in India while he
sends the result to a Jemboss interface in UK , which in turn processes
details to some other place.

All this will be controlled and decided by the Monitor interface. This can
be controlled by the user, but a degree of automation in scheduling is
provided.

Any feedback is most welcome. I have started writing. Any experts in Java
RMI and related areas, please help.

I request your reply.

Regards,
Jitesh

Thanks & Regards,
Jitesh Dundas
Phone:- +91-9860925706
http://jiteshbdundas.blogspot.com

---------- Forwarded message ----------
From: jitesh dundas <jbdundas at gmail.com>
Date: Wed, Jun 24, 2009 at 8:31 PM
Subject: Fwd: [emboss-dev] (no subject)
To: Peter Rice <pmr at ebi.ac.uk>
Cc: emboss-dev at lists.open-bio.org

Dear Sir,

This is the logic that I intend to implement:-
1) I have emboss on my laptop(India) installed. I will need another
machine(say in UK) with EMBOSS installed in it. When I run one interface
on my machine, the output will be sent to the machine to the UK machine.
The UK machine will have another interface thread waiting for this
input(from India). Please note that this information will be sent via
internet/intranet (in encrypted form). Thus the execution will continue on
UK machine. IN the same way, the execution for India machine will continue
till it needs some input from UK machine.

2) The decision to allot the tasks/input and output will be done by an
independent monitoring master interface. This will track continuously the
progress of both the machines for each inteface.

3) The information about each interface will have to be sent to a database
for storage. For e.g.) a table with the fields interface no, actuvity start
time, duration, timestamp,allowed time to execution, input needed, output to
be sent, etc. This will be continuously used by the monitor interface.

I wanted to implement one of my methods for managing these projects in
parallel processing. Based on the results obtained , a paper with the
results can be published.

Sir, this is my basic idea, which I intend to build on. I will need another
machine that I can use for executing this idea. However, it will be needed
after 1-2 weeks by which I intend to finish the prior needed parts.

TECHINICAL POINTS:-
1) RMI (Remote Method Invocation) will be needed.
2) Internet access / network connection will be needed.
3) MySQL Db.

 I request your feedback.

Thanks & Regards,
Jitesh Dundas
---------- Forwarded message ----------
From: jitesh dundas <jbdundas at gmail.com>
Date: Tue, Jun 16, 2009 at 1:42 PM
Subject: Re: [emboss-dev] (no subject)
To: Peter Rice <pmr at ebi.ac.uk>

Dear Sir

I have installed BOINC on my PC and currently I am studying the code and it
could take me some time in getting my grip on it. I assure you though that I
will get the task done soon.

I will update you about progress every 2 days.

Regards,
Jitesh

---------- Forwarded message ----------
From: emboss-dev-request at lists.open-bio.org <
emboss-dev-request at lists.open-bio.org>
Date: Jun 15, 2009 10:30 PM
Subject: emboss-dev Digest, Vol 10, Issue 3
To: emboss-dev at lists.open-bio.org

Send emboss-dev mailing list submissions to
       emboss-dev at lists.open-bio.org

To subscribe or unsubscribe via the World Wide Web, visit
       http://lists.open-bio.org/mailman/listinfo/emboss-dev
or, via email, send a message with subject or body 'help' to
       emboss-dev-request at lists.open-bio.org

You can reach the person managing the list at
       emboss-dev-owner at lists.open-bio.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of emboss-dev digest..."

Today's Topics:

  1. Re: (no subject) (jitesh dundas)

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

Message: 1
Date: Thu, 11 Jun 2009 20:59:45 +0530
From: jitesh dundas <jbdundas at gmail.com>
Subject: Re: [emboss-dev] (no subject)
To: Peter Rice <pmr at ebi.ac.uk>
Cc: emboss-dev at lists.open-bio.org
Message-ID:
       <326ea8620906110829p472a1b06x1e1f38a277c57959 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear Sir,

I hope my previous email gave you a clear idea of my plan on this task.

I will begin working on the code now. I will keep you posted every 2
days with my progress.

Please let me know if you need anthing else from my side.

Regards,
Jitesh Dundas

On 6/10/09, jitesh dundas <jbdundas at gmail.com> wrote:
> Dear Sir,
>
> Thank you for your reply. PLEASE FIND MY COMMENTS IN BLOCK LETTERS BELOW.
>
> On 6/9/09, Peter Rice <pmr at ebi.ac.uk> wrote:
>> Dear Jitesh,
>>
>>> I need to know the priority on which any script/ application in EMBOSS
>>> is executed.
>>
>> Currently, all EMBOSS applications simply execute.
>>
>> When they terminate, if EMBOSS_LOGFILE is defined they can write a
>> single record the the logfile.
>>
>> However, we can extend this is that is what you are suggesting.
>>
>> All EMBOSS (and EMBASSY) applications start with a call to ajAcdInit
>> (often via embInitP or ajGraphInit)
>>
>> All EMBOSS applications end with a call to ajExit on success. Failed
>> applications should call ajExitBad or ajExitAbort ... unless they crash
>> with a segmentation fault or are otherwise terminated.
>>
>> So we have places to put in additional monitoring code.
>
> I NEED THE CENTRAL LOCATION FROM WHERE THIS MONITORING SCRIPT CAN BE
> ACCESSED. AN INTERFACE THAT WILL BE AT THE HEART OF EMBOSS. THIS WILL
> BE A COMMON SCRIPT AND THUS, IT MUST HAVE ACCESS TO ALL  SCRIPTS.
>
>>> If applications in Emboss are to be executed, they need to be assigned
>>> a priority or an impact , besides the following:-
>>>
>>> 1) A master database or a table that stores list of applications
>>> running. These will be updated by a scheduled script running
>>> continuously in the background.
>>
>> This script, could, for example, check the list of known running
>> applications and remove any that appear to have crashed.
>>
>>> 2) the front-end GUI needs to showing a chart of applications running
>>> and parameters like progress, time consumed etc.
>>>
>>> Measuring progress needs some breakpoints. Their status will be
>>> pending,WIP or completed.
>>
>> We have no breakpoints in EMBOSS at present. Can you give examples of
>> what you have in mind?
>
> FOR E.G.) there are 5 stages/applications running in parallel. EACH
> STAGE WILL BE DIVIDED INTO PARTS,WHERE  EACH PART'S END-POINT ACTING
> AS  A COMPLETION SUB_TARGET.
>
> THE ENTRY IN DATABASE TABLE WILL HAVE A  PROCESS,SUB-PROCESS,STATUS
> FIELDS. DETAILS OF EACH FIELD ARE ENTERED HERE.
> tHE SCRIPT OR THE INTERFACE WILL RUN AND MONITOR THE EXECUTION
> PROGRESS OF EACH STAGE. REGULARLY, IT WILL UPDATE THE DATABASE TABLE.
>
>>> I will send further details in 1-2 days. Meanwhile, i request your
>>> feedback.
>>
>> Hope this helps.
>>
>> Peter Rice
>>
>
> PLEASE LET ME KNOW IF YOU NEED ANYTHING ELSE FROM MY SIDE.
>
> --
> Thanks & Regards,
> Jitesh Dundas
>
> Scientist, Edencore Technologies(www.edencore.net)
> Web Developer, JR Technologies, India
>
> Phone:- +91-9860925706
>
> http://jiteshbdundas.blogspot.com
>
> "NO IDEA IS STUPID,EITHER IT IS TOO GOOD TO BE TRUE OR IT IS WAY AHEAD
> OF ITS FUTURE "- GEORGE BERNARD SHAW.
>