[emboss-dev] emboss-dev Digest, Vol 10, Issue 1

Tue Jun 9 01:20:39 UTC 2009

Dear  Lapointe Sir,

I got your reply in the digest just now. It is strange that i did not
receive your mail earlier. Please excuse for the inconvenience. Do you
need my help in anything?

I wanted to know if any work on distributed computing is still being
done. Have all your issues been resolved?

For updation of all the nodes, a centralized repository needs to be
created which is updated every time you press an update button or it
may be scheduled periodically.

May i suggest writing a script to perform this funtionality. I would
love to work on this. I request your consent.

It would be nice to know what is expected from the new applictions on
Emboss. Are we open to suggestions/ideas on them ? Can i contribute.

I can check my mail daily once atleast so keeping updated will not be
an problem.

Regards,
Jitesh Dundas
http://jiteshbdundas.blogspot.com

On 6/8/09, emboss-dev-request at lists.open-bio.org
<emboss-dev-request at lists.open-bio.org> wrote:
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> Today's Topics:
>
>    1. Re: Fwd: Request For Work (Lapointe, David)
>    2. Re: Fwd: Request For Work (jitesh dundas)
>    3. density (Sebastien Moretti)
>    4. USA syntax and `%' character in sequence file names (Nicolas Joly)
>    5. Re: USA syntax and `%' character in sequence file names
>       (ajb at ebi.ac.uk)
>    6. Re: USA syntax and `%' character in sequence file names
>       (Nicolas Joly)
>    7. Re: USA syntax and `%' character in sequence file names
>       (Peter Rice)
>    8. Re: USA syntax and `%' character in sequence file names
>       (Nicolas Joly)
>    9. EMBOSS Funding and New developments (Peter Rice)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 13 Aug 2008 10:46:31 -0400
> From: "Lapointe, David" <David.Lapointe at umassmed.edu>
> Subject: Re: [emboss-dev] Fwd: Request For Work
> Cc: emboss-dev at lists.open-bio.org
> Message-ID:
>  <5ECA525B88314B48870E4AC72E3B9AF202469E86 at EDUNIVMAIL05.ad.umassmed.edu>
>
> Content-Type: text/plain; charset=us-ascii
>
> We are running Rocks (4.3) on our cluster currently and the Bio roll has
> EMBOSS installed (4.1.0). One peculiarity is that
> EMBOSS is installed on every node locally so that updating databases (
> rebase, tfsites, etc) must be done on every node. Other than that there
> could some creative work with distributed computing ( distinct from mpi
> which would also be interesting ).  Having a mechanism to share the data
> would be a plus.
>
> David
>
> -----Original Message-----
> From: emboss-dev-bounces at lists.open-bio.org
> [mailto:emboss-dev-bounces at lists.open-bio.org] On Behalf Of Peter Rice
> Sent: Wednesday, August 13, 2008 10:22 AM
> To: jitesh dundas
> Cc: emboss-dev at lists.open-bio.org
> Subject: Re: [emboss-dev] Fwd: Request For Work
>
> Dear jitesh,
>
>> Thank you for your reply. Please excuse me for the delay in replying
>> as I was out of town.
>> I am looking at working on this issue in 2 ways:-
>> 1) I wish to parallelize the phases of different softwares( if they
>> are in develpment stage).
>> 2) Next, if there is a connection or dependency between two or more
>> projects( or applications), then we can try to give the output that is
>
>> needed based on the current status of the output-supplying
> application.
>
> Aha ... so you are looking at running several EMBOSS applications in
> parallel? That is a very interesting issue for us.
>
>> I will need to know if there is any relationship identified between
>> any of the applications defined in the  EMBOSS project. If there are
>> any relations already present between the applications, it will become
>
>> easier to get a handle to move the execution from one point to
> another.
>
> The inputs and outputs of all EMBOSS applications are marked up in the
> .acd files with a "knowntype" that identifies common outputs that could,
> for example, be combined and visuallised together - and also which
> ooutput could be used as inputs by other applications. For sequences,
> features, alignments and reports this includes whether the type is
> nucleotide or protein.
>
>> Also, Running applications in parallel will require a change in the
>> way we make our applications. We need to define a master relationship
>> between all the apllications, so as to relate all the applications
> with each other.
>
> We are also looking at adding definitions for the algorithm used by an
> applications, and a standard way to represent the transformations of
> inputs into outputs.
>
> Any feedback on these issues would be very welcome.
>
> We are also interested in looking at executing EMBOSS code in parallel
> is anyone is looking at that.
>
>
> regards,
>
> Peter Rice
> _______________________________________________
> emboss-dev mailing list
> emboss-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss-dev
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 14 Oct 2008 19:40:32 +0530
> From: "jitesh dundas" <jbdundas at gmail.com>
> Subject: Re: [emboss-dev] Fwd: Request For Work
> To: "Peter Rice" <pmr at ebi.ac.uk>
> Cc: emboss-dev at lists.open-bio.org
> Message-ID:
>  <326ea8620810140710m355d3c6cydaad03bafe2dbf12 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Sir,
>
> I apologize for dissappearing from the activity after assuring to work on
> this issue of trying to parallelize the EMBOSS project. I was not feeling
> well and have not been able to work for 1-2 months. I am fine now and will
> start working right now.
>
> By the way, I want to congratulate you for getting the funding from BBSRC( I
> saw on one of the science blogs).I hope we can continue to contribute on
> this wonderful project.
>
> I wanted to know the algorithm used in making the EMBOSS software. Maybe we
> can fine tune the algorithm to getting better and longer patterns...
>
> Any advise is most welcome.
>
> Regards,
> Jitesh Dundas
>
> On Wed, Aug 13, 2008 at 7:51 PM, Peter Rice <pmr at ebi.ac.uk> wrote:
>
>> Dear jitesh,
>>
>>  Thank you for your reply. Please excuse me for the delay in replying as I
>>> was out of town.
>>> I am looking at working on this issue in 2 ways:-
>>> 1) I wish to parallelize the phases of different softwares( if they are
>>> in
>>> develpment stage).
>>> 2) Next, if there is a connection or dependency between two or more
>>> projects( or applications), then we can try to give the output that is
>>> needed based on the current status of the output-supplying application.
>>>
>>
>> Aha ... so you are looking at running several EMBOSS applications in
>> parallel? That is a very interesting issue for us.
>>
>>  I will need to know if there is any relationship identified between any
>> of
>>> the applications defined in the  EMBOSS project. If there are any
>>> relations
>>> already present between the applications, it will become easier to get a
>>> handle to move the execution from one point to another.
>>>
>>
>> The inputs and outputs of all EMBOSS applications are marked up in the
>> .acd
>> files with a "knowntype" that identifies common outputs that could, for
>> example, be combined and visuallised together - and also which ooutput
>> could
>> be used as inputs by other applications. For sequences, features,
>> alignments
>> and reports this includes whether the type is nucleotide or protein.
>>
>>  Also, Running applications in parallel will require a change in the way
>> we
>>> make our applications. We need to define a master relationship between
>>> all
>>> the apllications, so as to relate all the applications with each other.
>>>
>>
>> We are also looking at adding definitions for the algorithm used by an
>> applications, and a standard way to represent the transformations of
>> inputs
>> into outputs.
>>
>> Any feedback on these issues would be very welcome.
>>
>> We are also interested in looking at executing EMBOSS code in parallel is
>> anyone is looking at that.
>>
>>
>> regards,
>>
>> Peter Rice

> ------------------------------
>
> Message: 9
> Date: Mon, 08 Jun 2009 14:41:19 +0100
> From: Peter Rice <pmr at ebi.ac.uk>
> Subject: [emboss-dev] EMBOSS Funding and New developments
> To: emboss <emboss at emboss.open-bio.org>,
>  emboss-dev at emboss.open-bio.org, emboss-announce at emboss.open-bio.org
> Message-ID: <4A2D14FF.9000109 at ebi.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear EMBOSS Users and Developers
>
> We bring you great news - EMBOSS is funded in full by the BBSRC
> "Bioinformatics and Biological Resources" Fund. We now have money for
> Alan Bleasby and 2 other positions (Jon Ison and Mahmut Uludag) from 1st
> May until the end of 2011.
>
> The core aims of the funding proposal were to continue support,
> maintenance and development of EMBOSS, and to provide extensive online
> training materials for users, developers and system administrators using
> text from a series of books to be published by Cambridge University Press.
>
> We are also explicitly targeting areas where we see EMBOSS can be
> expanded:
>
> * Richer data content in EMBOSS outputs leading to major improvements
>    in the integration and visualisation of results in browsers.
>
> * Processing many more data fields in EMBOSS inputs (taxonomy,
>    genes, GO terms, cross-references, keywords.
>
> * Extending and improving database access: better indexing, query
>    language support and combining searches across multiple databases,
>    support for non-sequence data resources and new data access methods
>
> * Scaling up the libraries and adding new applications to support the
>    data volumes generated by next-generation sequencing runs. We
>    anticipate many more users will be working with short read data
>    mapped to reference sequences over the next few years.
>
> * We aim to add at least 100 new applications in these 3 years.
>    Suggestions for new applications are very welcome.
>
> * Release 6.1.0 will appear, as usual, on 15th July.
>
> * Major work on new developments and new library code will start from
>    August.
>
> We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of
> this month, We will arrange a lunchtime "Birds of a Feather" session
> at ISMB to discuss the needs of users over the next 3 years.
>
> regards,
>
> Peter Rice
>
>
> ------------------------------
>
> _______________________________________________
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> emboss-dev at lists.open-bio.org
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>
>
> End of emboss-dev Digest, Vol 10, Issue 1
> *****************************************
>

-- 
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.