From kikimaeda at gmail.com  Tue Sep  1 05:36:09 2009
From: kikimaeda at gmail.com (daniel maeda)
Date: Tue, 1 Sep 2009 11:36:09 +0200
Subject: [BiO BB] How to Order cDNAs or plasmids for Viral proteins
Message-ID: <e84a9b430909010236q3f982967w4032ffcf0cb23166@mail.gmail.com>

Hi everyone,

I would like to order a cDNA clone or plasmid containing the Kaposis Sarcoma
associated Herpes Virus (KSHV) vGPCR (g Protein Coupled Receptor) protein
preferably from a sequence repository. May someone please give me links to
sequence repositories that could have it since I have only managed to find
sequence repositories for animal genomes and some other model organisms but
not KSHV. Thanks for your time.

Yours Sincerely,

-- 
Daniel


From JATP at Lundbeck.com  Wed Sep 16 08:00:35 2009
From: JATP at Lundbeck.com (Jan Torleif Pedersen)
Date: Wed, 16 Sep 2009 14:00:35 +0200
Subject: [BiO BB] What are the alternatives to Rosetta Biosoftware,
 Resolver and Syllego systems
Message-ID: <0BE5E2912653804CA2B37F5D7E7519C42624082E20@EMEAEXMBX03.hlu.corp.lundbeck.com>


Greetings all,

I am looking for a general database plaform for omics-data, analysis and frontend capability like what was provided in the Rosetta biosoftware suite. Unfortunately this is being de-supported within the next 24 month. So I am trying to make a quick survey of alternatives. Any input is appreciated.

Thanks -- Jan

Dr Jan Torleif Pedersen
Head, Bioinformatics
Chair, Alzheimers disease team
Discovery Biology Research
H. Lundbeck A/S
jatp at lundbeck.com




From dan.bolser at gmail.com  Wed Sep 16 10:10:15 2009
From: dan.bolser at gmail.com (Dan Bolser)
Date: Wed, 16 Sep 2009 15:10:15 +0100
Subject: [BiO BB] What are the alternatives to Rosetta Biosoftware,
	Resolver and Syllego systems
In-Reply-To: <0BE5E2912653804CA2B37F5D7E7519C42624082E20@EMEAEXMBX03.hlu.corp.lundbeck.com>
References: <0BE5E2912653804CA2B37F5D7E7519C42624082E20@EMEAEXMBX03.hlu.corp.lundbeck.com>
Message-ID: <2c8757af0909160710h9237beet460a98e233192c74@mail.gmail.com>

2009/9/16 Jan Torleif Pedersen <JATP at lundbeck.com>:
>
> Greetings all,
>
> I am looking for a general database plaform for omics-data, analysis and frontend capability like what was provided in the Rosetta biosoftware suite. Unfortunately this is being de-supported within the next 24 month. So I am trying to make a quick survey of alternatives. Any input is appreciated.
>
> Thanks -- Jan

Hi Jan,

Sorry, but could you briefly describe what the Rosetta biosoftware
suite does and what your requirements are? I'm not familiar with that
package, and it could be that some other package better suits your
exact requirements.


Cheers,
Dan.



> Dr Jan Torleif Pedersen
> Head, Bioinformatics
> Chair, Alzheimers disease team
> Discovery Biology Research
> H. Lundbeck A/S
> jatp at lundbeck.com
>
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>



From randalls at bioinfo.wsu.edu  Wed Sep 16 11:42:20 2009
From: randalls at bioinfo.wsu.edu (randalls at bioinfo.wsu.edu)
Date: Wed, 16 Sep 2009 08:42:20 -0700 (PDT)
Subject: [BiO BB] What are the alternatives to Rosetta Biosoftware,
	Resolver and Syllego systems
In-Reply-To: <2c8757af0909160710h9237beet460a98e233192c74@mail.gmail.com>
Message-ID: <1059798123.1111253115740411.JavaMail.root@mail>

Here is the website

http://www.rosettabio.com/products/resolver#more_information

Sorry for the double post.  

Randall Svancara
Systems Administrator/DBA/Developer
Main Bioinformatics Laboratory



----- Original Message -----
From: "Dan Bolser" <dan.bolser at gmail.com>
To: "General Forum at Bioinformatics.Org" <bbb at bioinformatics.org>
Sent: Wednesday, September 16, 2009 7:10:15 AM
Subject: Re: [BiO BB] What are the alternatives to Rosetta Biosoftware,	Resolver and Syllego systems

2009/9/16 Jan Torleif Pedersen <JATP at lundbeck.com>:
>
> Greetings all,
>
> I am looking for a general database plaform for omics-data, analysis and frontend capability like what was provided in the Rosetta biosoftware suite. Unfortunately this is being de-supported within the next 24 month. So I am trying to make a quick survey of alternatives. Any input is appreciated.
>
> Thanks -- Jan

Hi Jan,

Sorry, but could you briefly describe what the Rosetta biosoftware
suite does and what your requirements are? I'm not familiar with that
package, and it could be that some other package better suits your
exact requirements.


Cheers,
Dan.



> Dr Jan Torleif Pedersen
> Head, Bioinformatics
> Chair, Alzheimers disease team
> Discovery Biology Research
> H. Lundbeck A/S
> jatp at lundbeck.com
>
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>

_______________________________________________
BBB mailing list
BBB at bioinformatics.org
http://www.bioinformatics.org/mailman/listinfo/bbb



From kiekyon.huang at gmail.com  Wed Sep 16 11:43:57 2009
From: kiekyon.huang at gmail.com (Kie Kyon Huang)
Date: Wed, 16 Sep 2009 23:43:57 +0800
Subject: [BiO BB] EST mapping
Message-ID: <a54400840909160843k52a656fai7182c076d1e3fc14@mail.gmail.com>

Hi all,

I need to map my EST data to a fungal genome.  The goal here is to
evaluate the accuracy of the gene prediction data.

At the moment, all I have is fasta file containing the entire genome,
the ESTs, and the predicted genes respectively.

Can anyone point me to the correct tools/softwares to achieve this?

Thanks a lot.

Huang



From JATP at Lundbeck.com  Wed Sep 16 15:34:11 2009
From: JATP at Lundbeck.com (Jan Torleif Pedersen)
Date: Wed, 16 Sep 2009 21:34:11 +0200
Subject: [BiO BB] What are the alternatives to Rosetta Biosoftware,
 Resolver and Syllego systems
Message-ID: <0BE5E2912653804CA2B37F5D7E7519C42624082F66@EMEAEXMBX03.hlu.corp.lundbeck.com>

The rosetta software is no longer supported and sold as I understand it. Microsoft has bought the company and is planning to build the software into their Life Sciences platform. So I need to find an alternative database/analysis platform for omics- data.

So I will pose my question again - this time read carefully:

I am looking for a general database plaform for omics-data, analysis and frontend capability like what was provided in the Rosetta biosoftware suite. Unfortunately this is being de-supported within the next 24 month. So I am trying to make a quick survey of alternatives. Any input is appreciated.

Thanks Jan



From golharam at umdnj.edu  Wed Sep 16 16:00:35 2009
From: golharam at umdnj.edu (Ryan Golhar)
Date: Wed, 16 Sep 2009 16:00:35 -0400
Subject: [BiO BB] What are the alternatives to Rosetta Biosoftware,
 Resolver and Syllego systems
In-Reply-To: <0BE5E2912653804CA2B37F5D7E7519C42624082F66@EMEAEXMBX03.hlu.corp.lundbeck.com>
References: <0BE5E2912653804CA2B37F5D7E7519C42624082F66@EMEAEXMBX03.hlu.corp.lundbeck.com>
Message-ID: <4AB143E3.6070900@umdnj.edu>

Can you give more details as to what features in Rosetta you are looking 
for?

The link you posted isn't loading for me.

Jan Torleif Pedersen wrote:
> The rosetta software is no longer supported and sold as I understand
> it. Microsoft has bought the company and is planning to build the
> software into their Life Sciences platform. So I need to find an
> alternative database/analysis platform for omics- data.
> 
> So I will pose my question again - this time read carefully:
> 
> I am looking for a general database plaform for omics-data, analysis
> and frontend capability like what was provided in the Rosetta
> biosoftware suite. Unfortunately this is being de-supported within
> the next 24 month. So I am trying to make a quick survey of
> alternatives. Any input is appreciated.
> 
> Thanks Jan
> 
> _______________________________________________ BBB mailing list 
> BBB at bioinformatics.org 
> http://www.bioinformatics.org/mailman/listinfo/bbb
> 



From marty.gollery at gmail.com  Wed Sep 16 16:00:58 2009
From: marty.gollery at gmail.com (Martin Gollery)
Date: Wed, 16 Sep 2009 13:00:58 -0700
Subject: [BiO BB] What are the alternatives to Rosetta Biosoftware,
	Resolver and Syllego systems
In-Reply-To: <0BE5E2912653804CA2B37F5D7E7519C42624082F66@EMEAEXMBX03.hlu.corp.lundbeck.com>
References: <0BE5E2912653804CA2B37F5D7E7519C42624082F66@EMEAEXMBX03.hlu.corp.lundbeck.com>
Message-ID: <bdd10c2a0909161300x64c6de7dlcf4e120f9f43a59c@mail.gmail.com>

Hi Jan,
Take a look at GeneData's Expressionist product, or Geospiza's Genesifter.
I believe that they may be able to fill your needs.

Best,
Marty

On Wed, Sep 16, 2009 at 12:34 PM, Jan Torleif Pedersen <JATP at lundbeck.com>wrote:

> The rosetta software is no longer supported and sold as I understand it.
> Microsoft has bought the company and is planning to build the software into
> their Life Sciences platform. So I need to find an alternative
> database/analysis platform for omics- data.
>
> So I will pose my question again - this time read carefully:
>
> I am looking for a general database plaform for omics-data, analysis and
> frontend capability like what was provided in the Rosetta biosoftware suite.
> Unfortunately this is being de-supported within the next 24 month. So I am
> trying to make a quick survey of alternatives. Any input is appreciated.
>
> Thanks Jan
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>



-- 
-- 
Martin Gollery
Senior Bioinformatics Scientist
Tahoe Informatics
www.bioinformaticist.biz
www.hiddenmarkovmodels.com


From jeff at bioinformatics.org  Wed Sep 16 16:02:19 2009
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Wed, 16 Sep 2009 16:02:19 -0400
Subject: [BiO BB] What are the alternatives to Rosetta Biosoftware,
 Resolver and Syllego systems
In-Reply-To: <2c8757af0909160710h9237beet460a98e233192c74@mail.gmail.com>
References: <0BE5E2912653804CA2B37F5D7E7519C42624082E20@EMEAEXMBX03.hlu.corp.lundbeck.com>
	<2c8757af0909160710h9237beet460a98e233192c74@mail.gmail.com>
Message-ID: <4AB1444B.9080704@bioinformatics.org>

Information on Rosetta's product line has been taken down.  Here's what Archive.org has:

  http://web.archive.org/web/20071223181048/www.rosettabio.com/products/default.htm

Here's the press release:

"Microsoft Signs Agreement With Merck & Co. Inc. to Acquire Assets of Rosetta Biosoftware, Strengthening Position in Life Science

"REDMOND, Wash. - Microsoft Corp. today announced that it has signed an agreement with Merck & Co. Inc. to acquire certain assets of Rosetta Biosoftware, a business unit of Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck & Co. Inc. The deal allows Microsoft to incorporate genetic, genomic, metabolomic and proteomics data management software into the Microsoft Amalga Life Sciences platform for enhanced translational research capabilities. In addition, Microsoft will establish a strategic relationship with Merck to enhance the Amalga Life Sciences platform to meet emerging pharmaceutical research needs.

"Under the terms of the agreement, Merck will become a customer of the Microsoft Amalga Life Sciences 2009 platform and also will provide strategic input to Microsoft on the direction and evolution of new solutions incorporating Rosetta Biosoftware technologies. The software platform will help drive improvements in Merck?s already advanced research capabilities."

http://www.rosettabio.com/company/news/rosetta_microsoft

Cheers,
Jeff

Dan Bolser wrote:
> Sorry, but could you briefly describe what the Rosetta biosoftware
> suite does and what your requirements are? I'm not familiar with that
> package, and it could be that some other package better suits your
> exact requirements.



-- 
J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 978 621 8258
--



From dan.bolser at gmail.com  Wed Sep 16 17:39:23 2009
From: dan.bolser at gmail.com (Dan Bolser)
Date: Wed, 16 Sep 2009 22:39:23 +0100
Subject: [BiO BB] EST mapping
In-Reply-To: <a54400840909160843k52a656fai7182c076d1e3fc14@mail.gmail.com>
References: <a54400840909160843k52a656fai7182c076d1e3fc14@mail.gmail.com>
Message-ID: <2c8757af0909161439u6579ab33j56c023ecd48a12b8@mail.gmail.com>

2009/9/16 Kie Kyon Huang <kiekyon.huang at gmail.com>:
> Hi all,
>
> I need to map my EST data to a fungal genome. ?The goal here is to
> evaluate the accuracy of the gene prediction data.
>
> At the moment, all I have is fasta file containing the entire genome,
> the ESTs, and the predicted genes respectively.
>
> Can anyone point me to the correct tools/softwares to achieve this?

First you need a tool to align the ESTs to the genome. Many tools will
do this. I'd suggest Blast or MUMmer, but their are others.

Next you need software to compare your gene predictions to the
alignments to check that they coincide (and to measure the degree of
coincidence). Off hand I don't know of any specific tool to do this
(although I'd be surprised if there wasn't something that you could
use).

However, given the specifics of the problem, you may be best off just
processing the data yourself, and measuring your own 'coincidence
statistic'. To do this you could use something like BioPerl, BioPython
or BioJava, etc. These libraries will make processing the data a
little easier, but at the expense of learning the overall library
design.

HTH,
Dan.



> Thanks a lot.
>
> Huang
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>



From nevan.ml at gmail.com  Wed Sep 16 23:51:15 2009
From: nevan.ml at gmail.com (Nevan King)
Date: Thu, 17 Sep 2009 12:51:15 +0900
Subject: [BiO BB] Find common regions in 3 organisms
Message-ID: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>

Hi,

This question has probably been asked, but I'm not sure what search
terms to use to find answers. This is a question from one of the
researchers in my lab.

I want to find common regions of sequences in 3 organisms. The first
organism (P. gingivalis) has been fully sequenced and described. It
has around 2000 genes. The other two are similar to P. gingivalis.

I've set up all three organisms in Blast, but comparing the genes one
by one would be a big task. What's the best way to automate this? I
understand that you can enter a list of fastas into blast and it will
compare each one to all the genes in its database. Is there a way to
do this with 3 organisms? Is Blast the best tool to use for this job?

Sorry if this is short on details, I don't fully understand the topic.

Thanks

Nevan.



From dan.bolser at gmail.com  Thu Sep 17 06:25:58 2009
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 17 Sep 2009 11:25:58 +0100
Subject: [BiO BB] Find common regions in 3 organisms
In-Reply-To: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
References: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
Message-ID: <2c8757af0909170325n2589750fg86657ed46feb9f13@mail.gmail.com>

2009/9/17 Nevan King <nevan.ml at gmail.com>:
> Hi,
>
> This question has probably been asked, but I'm not sure what search
> terms to use to find answers. This is a question from one of the
> researchers in my lab.
>
> I want to find common regions of sequences in 3 organisms. The first
> organism (P. gingivalis) has been fully sequenced and described. It
> has around 2000 genes. The other two are similar to P. gingivalis.
>
> I've set up all three organisms in Blast, but comparing the genes one
> by one would be a big task. What's the best way to automate this? I
> understand that you can enter a list of fastas into blast and it will
> compare each one to all the genes in its database. Is there a way to
> do this with 3 organisms? Is Blast the best tool to use for this job?
>
> Sorry if this is short on details, I don't fully understand the topic.

Often the answer to this sort of question is 'there is more than one
way to do it', and the way that you use usually depends on what you
want to see...

I would suggest something like this:

1) blast all genes of organism A against organism B and vice verse
(as described above).

2) Pick 'orthologues' using the 'reciprocal best hits' method (i.e. if
gene Ax' and gene Bx'' both find each other as the 'top blast hit' in
the respective organisms gene list, call them an orthologus pair.

3) Repeat step 1 and 2, but use organism A and C instead of A and B.

4) Pick 'orthologues' when Ax' and Bx'' are an orthologus pair AND Ax'
and Cx''' are an orthologus pair.

5) er... do you need to do B vs. C?


> Thanks
>
> Nevan.

Once you get the above blast results (A vs. B, A vs. C, B vs. C and
vice verse) into a database, you will have more than enough data to
play with. You can then define orthologues however you like.


That is just one idea to get you going.

HTH
Dan.


> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>



From marchywka at hotmail.com  Thu Sep 17 07:09:01 2009
From: marchywka at hotmail.com (Mike Marchywka)
Date: Thu, 17 Sep 2009 07:09:01 -0400
Subject: [BiO BB] Find common regions in 3 organisms
In-Reply-To: <2c8757af0909170325n2589750fg86657ed46feb9f13@mail.gmail.com>
References: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
	<2c8757af0909170325n2589750fg86657ed46feb9f13@mail.gmail.com>
Message-ID: <BLU113-W21DA7ABD65115E63829D7BBEE10@phx.gbl>









----------------------------------------
> Date: Thu, 17 Sep 2009 11:25:58 +0100
> From:
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] Find common regions in 3 organisms
>
> 2009/9/17 Nevan King :
>> Hi,
>>
>> This question has probably been asked, but I'm not sure what search
>> terms to use to find answers. This is a question from one of the
>> researchers in my lab.
>>
>> I want to find common regions of sequences in 3 organisms. The first
>> organism (P. gingivalis) has been fully sequenced and described. It
>> has around 2000 genes. The other two are similar to P. gingivalis.
>>
>> I've set up all three organisms in Blast, but comparing the genes one
>> by one would be a big task. What's the best way to automate this? I
>> understand that you can enter a list of fastas into blast and it will
>> compare each one to all the genes in its database. Is there a way to
>> do this with 3 organisms? Is Blast the best tool to use for this job?
>>
>> Sorry if this is short on details, I don't fully understand the topic.
>
> Often the answer to this sort of question is 'there is more than one
> way to do it', and the way that you use usually depends on what you
> want to see...
>
> I would suggest something like this:
>
> 1) blast all genes of organism A against organism B and vice verse
> (as described above).
>
> 2) Pick 'orthologues' using the 'reciprocal best hits' method (i.e. if
> gene Ax' and gene Bx'' both find each other as the 'top blast hit' in
> the respective organisms gene list, call them an orthologus pair.
>
> 3) Repeat step 1 and 2, but use organism A and C instead of A and B.
>
> 4) Pick 'orthologues' when Ax' and Bx'' are an orthologus pair AND Ax'
> and Cx''' are an orthologus pair.
>
> 5) er... do you need to do B vs. C?
>
>
>> Thanks
>>
>> Nevan.
>
> Once you get the above blast results (A vs. B, A vs. C, B vs. C and
> vice verse) into a database, you will have more than enough data to
> play with. You can then define orthologues however you like.
>

I guess if you need speed and have limited comparisons like this, it may
make more sense to index the 3 genomes and work from there. I don't remember exactly how BLAST works but indexing like this is a common
approach to speeding things up and gives you a lot of flexibility for
tweaking. If there are interesting exact matches in distant places you can find them more easily this way. I think this
approach has been mentioned here before with terms like "string matching"
or exact strings or something. I wrote something like this that I tested
on strains of IIRC e coli and while not production it seemed to find 
regions of difference and SNP's pretty fast. Once you have string 
index tables, you can decide which keys are "low complexity" or uninteresting etc.
 
Besides algorithmic order issues ( NxM ) there are also issues with 
memory access patterns. If you know apriori how you will access the
data and have finite memory ( even with multi-Gig RAM the cache size 
can be limited) you stand to make things a lot faster. So, if this
will be a recurring thing you may want to write or get some short c++
string utilities with data structs designed for your needs. 
 
Of course you can put arbitrary sequences into clustalw too...
 
 
Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165
415-264-8477 (w)<- use this
404-788-1216 (C)<- leave message
989-348-4796 (P)<- emergency only
marchywka at hotmail.com
Note: If I am asking for free stuff, I normally use for hobby/non-profit
information but may use in investment forums, public and private.
Please indicate any concerns if applicable.
Note: hotmail is censoring incoming mail using random criteria beyond my control and often hangs my browser
but all my subscriptions are here..., try also marchywka at yahoo.com

 
_________________________________________________________________
Your E-mail and More On-the-Go. Get Windows Live Hotmail Free.
http://clk.atdmt.com/GBL/go/171222985/direct/01/


From lijo.skb at gmail.com  Thu Sep 17 02:11:23 2009
From: lijo.skb at gmail.com (Lijo)
Date: Wed, 16 Sep 2009 23:11:23 -0700
Subject: [BiO BB] Find common regions in 3 organisms
In-Reply-To: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
References: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
Message-ID: <a79c50f0909162311h4d974569w39e5150846567164@mail.gmail.com>

Neaven, I don't know you are talking about basic multiple alignment. if so,
you have plenty of tools to try with.
And if your input space is big you may download static version for clusters
and try.
Lijo

On Wed, Sep 16, 2009 at 8:51 PM, Nevan King <nevan.ml at gmail.com> wrote:

> Hi,
>
> This question has probably been asked, but I'm not sure what search
> terms to use to find answers. This is a question from one of the
> researchers in my lab.
>
> I want to find common regions of sequences in 3 organisms. The first
> organism (P. gingivalis) has been fully sequenced and described. It
> has around 2000 genes. The other two are similar to P. gingivalis.
>
> I've set up all three organisms in Blast, but comparing the genes one
> by one would be a big task. What's the best way to automate this? I
> understand that you can enter a list of fastas into blast and it will
> compare each one to all the genes in its database. Is there a way to
> do this with 3 organisms? Is Blast the best tool to use for this job?
>
> Sorry if this is short on details, I don't fully understand the topic.
>
> Thanks
>
> Nevan.
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>



-- 
Centre for Bioinformatics,
University of Kerala, India.
+91 9446515705


From jyotirusia at gmail.com  Thu Sep 17 02:22:13 2009
From: jyotirusia at gmail.com (jyoti gupta)
Date: Thu, 17 Sep 2009 11:52:13 +0530
Subject: [BiO BB] Find common regions in 3 organisms
In-Reply-To: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
References: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
Message-ID: <1a423b840909162322h1229bc2eua1b2b42b239a7bb7@mail.gmail.com>

Hi
Nevan

you can go for multiple sequence alignment for finding common regions in
more than two sequences..

try this link

http://www.ebi.ac.uk/Tools/clustalw2/index.html

and use clustal W for aligning more than two sequences.

thanks



On Thu, Sep 17, 2009 at 9:21 AM, Nevan King <nevan.ml at gmail.com> wrote:

> Hi,
>
> This question has probably been asked, but I'm not sure what search
> terms to use to find answers. This is a question from one of the
> researchers in my lab.
>
> I want to find common regions of sequences in 3 organisms. The first
> organism (P. gingivalis) has been fully sequenced and described. It
> has around 2000 genes. The other two are similar to P. gingivalis.
>
> I've set up all three organisms in Blast, but comparing the genes one
> by one would be a big task. What's the best way to automate this? I
> understand that you can enter a list of fastas into blast and it will
> compare each one to all the genes in its database. Is there a way to
> do this with 3 organisms? Is Blast the best tool to use for this job?
>
> Sorry if this is short on details, I don't fully understand the topic.
>
> Thanks
>
> Nevan.
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>



-- 
Regards,

  Jyoti Rusia Gupta


The greatest gift you can give to someone is your time because when you give
someone your time, you have given them a portion of your life that you'll
never get back" .


From kiekyon.huang at gmail.com  Thu Sep 17 07:03:57 2009
From: kiekyon.huang at gmail.com (Kie Kyon Huang)
Date: Thu, 17 Sep 2009 19:03:57 +0800
Subject: [BiO BB] Find common regions in 3 organisms
In-Reply-To: <2c8757af0909170325n2589750fg86657ed46feb9f13@mail.gmail.com>
References: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
	<2c8757af0909170325n2589750fg86657ed46feb9f13@mail.gmail.com>
Message-ID: <a54400840909170403m66a0092as2c5c242969b90a0f@mail.gmail.com>

it is actually possible to find orthologous relationship using the
Inparanoid software among 3 organisms.

On Thu, Sep 17, 2009 at 6:25 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
> 2009/9/17 Nevan King <nevan.ml at gmail.com>:
>> Hi,
>>
>> This question has probably been asked, but I'm not sure what search
>> terms to use to find answers. This is a question from one of the
>> researchers in my lab.
>>
>> I want to find common regions of sequences in 3 organisms. The first
>> organism (P. gingivalis) has been fully sequenced and described. It
>> has around 2000 genes. The other two are similar to P. gingivalis.
>>
>> I've set up all three organisms in Blast, but comparing the genes one
>> by one would be a big task. What's the best way to automate this? I
>> understand that you can enter a list of fastas into blast and it will
>> compare each one to all the genes in its database. Is there a way to
>> do this with 3 organisms? Is Blast the best tool to use for this job?
>>
>> Sorry if this is short on details, I don't fully understand the topic.
>
> Often the answer to this sort of question is 'there is more than one
> way to do it', and the way that you use usually depends on what you
> want to see...
>
> I would suggest something like this:
>
> 1) blast all genes of organism A against organism B and vice verse
> (as described above).
>
> 2) Pick 'orthologues' using the 'reciprocal best hits' method (i.e. if
> gene Ax' and gene Bx'' both find each other as the 'top blast hit' in
> the respective organisms gene list, call them an orthologus pair.
>
> 3) Repeat step 1 and 2, but use organism A and C instead of A and B.
>
> 4) Pick 'orthologues' when Ax' and Bx'' are an orthologus pair AND Ax'
> and Cx''' are an orthologus pair.
>
> 5) er... do you need to do B vs. C?
>
>
>> Thanks
>>
>> Nevan.
>
> Once you get the above blast results (A vs. B, A vs. C, B vs. C and
> vice verse) into a database, you will have more than enough data to
> play with. You can then define orthologues however you like.
>
>
> That is just one idea to get you going.
>
> HTH
> Dan.
>
>
>> _______________________________________________
>> BBB mailing list
>> BBB at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/bbb
>>
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>


From jeff at bioinformatics.org  Thu Sep 17 10:06:09 2009
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Thu, 17 Sep 2009 10:06:09 -0400
Subject: [BiO BB] Apologies: A little gift - Anil
In-Reply-To: <20090917124040.B6E741F0808@skoismta03.skoost.com>
References: <20090917124040.B6E741F0808@skoismta03.skoost.com>
Message-ID: <4AB24251.9080801@bioinformatics.org>

Since all posts are held for moderation, even my own, it must be some bug or hole in Mailman.  Sorry.

Jeff
-- 
J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 978 621 8258
--





From marchywka at hotmail.com  Thu Sep 17 10:16:54 2009
From: marchywka at hotmail.com (Mike Marchywka)
Date: Thu, 17 Sep 2009 10:16:54 -0400
Subject: [BiO BB] Find common regions in 3 organisms
In-Reply-To: <1a423b840909162322h1229bc2eua1b2b42b239a7bb7@mail.gmail.com>
References: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
	<1a423b840909162322h1229bc2eua1b2b42b239a7bb7@mail.gmail.com>
Message-ID: <BLU113-W9554EAEE0A533A571D987BEE10@phx.gbl>










----------------------------------------
> Date: Thu, 17 Sep 2009 11:52:13 +0530
> From: jyotirusia at gmail.com
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] Find common regions in 3 organisms
>
> Hi
> Nevan
>
> you can go for multiple sequence alignment for finding common regions in
> more than two sequences..
>
> try this link
>
> http://www.ebi.ac.uk/Tools/clustalw2/index.html
>
> and use clustal W for aligning more than two sequences.
>
> thanks

 
The only reason I mentioned this in passing after a long spiel on
the string matching approach was I didn't think it would work in
reasonable time for the initial objective nor find genes that are in different locations etc.
If you just want to align different strains and have a very very fast
computer, it might be possible. If you are looking for orthologues that 
could be anywhere it probably won't work. If you have blast hits 
and want to look at these, then, sure it is a tool. 
 
Personally I found that making ad hoc or app specific indexes is quite helpful and flexible  and can be very fast if you are just asking "where are these things similar?" Since your index tells you how many entries there are for a given key, you can make some reasonable guess about a given key being an interesting match or a piece of low complexity filler. 
If you start finding things that only occur once in each input genome, those would presumably be most interesting.
If you expect to use the same approach many times, it may be worth the effort. 
 
 
 
 
 
>
>
>
> On Thu, Sep 17, 2009 at 9:21 AM, Nevan King wrote:
>
>> Hi,
>>
>> This question has probably been asked, but I'm not sure what search
>> terms to use to find answers. This is a question from one of the
>> researchers in my lab.
>>
>> I want to find common regions of sequences in 3 organisms. The first
>> organism (P. gingivalis) has been fully sequenced and described. It
>> has around 2000 genes. The other two are similar to P. gingivalis.
>>
>> I've set up all three organisms in Blast, but comparing the genes one
>> by one would be a big task. What's the best way to automate this? I
>> understand that you can enter a list of fastas into blast and it will
>> compare each one to all the genes in its database. Is there a way to
>> do this with 3 organisms? Is Blast the best tool to use for this job?
>>
>> Sorry if this is short on details, I don't fully understand the topic.
>>
>> Thanks
>>
>> Nevan.
>>
>> _______________________________________________
>> BBB mailing list
>> BBB at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/bbb
>>
>
>
>
> --
> Regards,
>
> Jyoti Rusia Gupta
>
>
> The greatest gift you can give to someone is your time because when you give
> someone your time, you have given them a portion of your life that you'll
> never get back" .
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
_________________________________________________________________
Hotmail: Free, trusted and rich email service.
http://clk.atdmt.com/GBL/go/171222984/direct/01/


From lijo.skb at gmail.com  Thu Sep 17 10:34:52 2009
From: lijo.skb at gmail.com (Lijo)
Date: Thu, 17 Sep 2009 20:04:52 +0530
Subject: [BiO BB] Apologies: A little gift - Anil
In-Reply-To: <4AB24251.9080801@bioinformatics.org>
References: <20090917124040.B6E741F0808@skoismta03.skoost.com>
	<4AB24251.9080801@bioinformatics.org>
Message-ID: <a79c50f0909170734h664d6f12r6577f8b10ca77a2b@mail.gmail.com>

dear Jeff,

i really wonderd how do you do moderation for all those mails exchanged in
the group(?) i don't believe its a manual validation.

lijo
Centre for Bioinformatics,
University of Kerala, India.
+91 9446515705

On Thu, Sep 17, 2009 at 7:36 PM, J.W. Bizzaro <jeff at bioinformatics.org>wrote:

> Since all posts are held for moderation, even my own, it must be some bug
> or hole in Mailman.  Sorry.
>
> Jeff
> --
> J.W. Bizzaro
> Bioinformatics Organization, Inc. (Bioinformatics.Org)
> E-mail: jeff at bioinformatics.org
> Phone:  +1 978 621 8258
> --
>
>
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>



--


From jeff at bioinformatics.org  Thu Sep 17 11:01:35 2009
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Thu, 17 Sep 2009 11:01:35 -0400
Subject: [BiO BB] Apologies: A little gift - Anil
In-Reply-To: <a79c50f0909170734h664d6f12r6577f8b10ca77a2b@mail.gmail.com>
References: <20090917124040.B6E741F0808@skoismta03.skoost.com>	<4AB24251.9080801@bioinformatics.org>
	<a79c50f0909170734h664d6f12r6577f8b10ca77a2b@mail.gmail.com>
Message-ID: <4AB24F4F.4010305@bioinformatics.org>

Moderation is indeed done manually, by Gary and myself.  We also invite frequent contributers/posters to become moderators and help shorten the time that messages are held.  If anyone is interested, let me know.

Cheers,
Jeff


Lijo wrote:
> dear Jeff,
> 
> i really wonderd how do you do moderation for all those mails exchanged in
> the group(?) i don't believe its a manual validation.
> 
> lijo
> Centre for Bioinformatics,
> University of Kerala, India.
> +91 9446515705
> 
> On Thu, Sep 17, 2009 at 7:36 PM, J.W. Bizzaro <jeff at bioinformatics.org>wrote:
> 
>> Since all posts are held for moderation, even my own, it must be some bug
>> or hole in Mailman.  Sorry.
>>
>> Jeff


-- 
J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 978 621 8258
--




From andrea.splendiani at bbsrc.ac.uk  Thu Sep 17 11:28:05 2009
From: andrea.splendiani at bbsrc.ac.uk (Andrea Splendiani)
Date: Thu, 17 Sep 2009 16:28:05 +0100
Subject: [BiO BB] SWAT4LS Cfp updates: new deadlines and journal supplement
Message-ID: <3A8058EF-45A7-4D36-BB8F-379E66FA63C3@bbsrc.ac.uk>

SWAT4LS Semantic Web Applications and Tools for Life Sciences

*** apologies for multiple postings ***

--- updates ---

We are glad to announce that there will be a special issue of the BMC  
Journal of Biomedical Semantics dedicated to the SWAT4LS workshop.  
This is a new open access journal published by BMC and we are  
confident that the supplement will benefit from the additional  
exposure and promotion associated with its launch (more information on  
this journal can be found at http://www.jbiomedsem.com/).

The call for this special issue will be open to all the contributors  
to the SWAT4LS workshop (accepted papers, posters and demos). Authors  
will be invited to submit an extended version of their work,  
elaborated in the light of the discussion held at the workshop.  
Workshop proceedings will be published on CEUR.

In order to facilitate submissions, we have extended submission  
deadlines as follows:

intention to submit (abstract only):     October 5th
submission of papers:                        October 12
submission of posters and demos:      October 15
communication of acceptance:            October 28
camera ready:                                   November 13

Due to the limited time for reviews, we would ask you to submit an  
abstract of your paper by October 5th, in order to facilitate  
assignment of reviews.

The lenght of contributions to the workshop as been revised to offer  
more flexibility:
      * Submissions for Oral communications should be between 8 and 15  
pages.
      * Posters submissions should be between 2 and 4 pages.
      * Software demo proposals should also be between 2 and 4 pages.

Finally, we would like to announce that the special issue BMC  
Bioinformatics dedicated to SWAT4LS-2008 will be published on October  
1st (BMC Bioinformatics, Vol 10, Supp 10)


--- call for papers ---

***Location and date
Amsterdam, Science Park, November 20th 2009
(http://swat4ls.org/2009/)


***Rationale

The adoption of semantic-enabled applications and collaborative social  
environments is ever more common in the Life Sciences. The Semantic  
Web provides a set of technologies and standards that are key to  
support semantic markup, ontology development, distributed information  
resources and collaborative social environments. Altogether the  
adoption of the Semantic Web in the Life Sciences has potential impact  
on the future of publishing, biological research and medecine. This  
workshop will provide a venue to present and discuss benefits and  
limits of the adoption of these technologies and tools in biomedical  
informatics and computational biology. It will showcase experiences,  
information resources, tools development and applications. It will  
bring together researchers, both developers and users, from the  
various fields of Biology, Bioinformatics and Computer Science, to  
discuss goals, current limits and some real use cases for Semantic Web  
technologies in Life Sciences.


***Topics

Topics of interest include, but are not limited to:

      * Standards, Technologies, Tools for the Semantic Web
            o Semantic Web standards and new proposals (RDF, OWL,  
SKOS,... )
            o Biomedical Ontologies and related tools
            o Formal approaches to large biomedical knowledge bases
      * Systems for a Semantic Web for Bioinformatics
            o RDF stores, Reasoners, query and visualization systems  
for life sciences
            o Semantic biomedical Web Services
            o Semantics aware Biological Data Integration Systems
      * Existing and prospective applications of the Semantic Web for  
Bioinformatics
            o Semantics aware application tools
            o Semantic collaborative research environments
            o Case studies, use cases, and scenarios

***Scientific Program

The workshop will be interactive and include keynotes, oral  
presentations, panel discussion and a poster and demo session.

The keynote speakers of this edition will be:
       * Barend Mons (http://www.biosemantics.org/index.php?page=barend-mons 
)
       * Michael Schroeder (http://www.biotec.tu-dresden.de/schroeder)
       * Alan Ruttenberg (http://sciencecommons.org/about/whoweare/ruttenberg/ 
)

***Scientific Committee (committed so far:)

      * Christopher J. O. Baker, Department of Computer Science and  
Applied Statistics, University of Brunswick, Canada
      * Pedro Barahona, Department of Informatics, New University of  
Lisboa, Lisboa, Portugal
      * Liliana Barrio-Alvers, Transinsight GmbH, Dresden, Germany
      * Olivier Bodenreider, National Library of Medicine, Bethesda,  
MD, United States of America
      * Matt-Mouley Bouamrane, School of Computer Science, University  
of Machester, manchester, United Kingdom
      * Werner Ceusters, NY CoE in Bioinformatics and Life Sciences,  
University at Buffalo, Buffalo, NY, United States of America
      * Kei Cheung, Center for Medical Informatics, Yale University  
School of Medicine, New Haven, United States of America
      * Tim Clark, Massachusetts General Hospital and Harvard Medical  
School, Boston MA, United States of America
      * Marie-Dominique Devignes, LORIA, Vandoeuvre les Nancy, France
      * Olivier Dameron, INSERM U936, University of Rennes 1, France
      * Michel Dumontier, Carleton University, Ottawa, Ontario, Canada
      * Huajun Chen, Zhejiang University, China
      * Duncan Hull, School of Chemistry, University of Manchester, UK
      * C. Maria Keet, Faculty of Computer Science, Free University of  
Bozen-Bolzano, Bolzano, Italy
      * Graham Kemp, Chalmers University of Technology, Sweden
      * Jacob Tilman Koehler, Department of Molecular Biotechnology,  
Institute of Medical Biology, University of Troms?, Troms?, Norway
      * Michael Krauthammer, Department of Pathology, Yale University  
School of Medicine, United States of America
      * Martin Kuiper, Department of Pathology, Systems Biology group,  
Department of Biology, Norwegian University of Science and Technology,  
Trondheim, Norway
      * Patrick Lambrix, Department of Computer and Information  
Science, Link?ping University, Link?ping, Sweden
      * Phillip Lord, School of Computing Science, Newcastle  
University, Newcastle-upon-Tyne, United Kingdom
      * M. Scott Marshall, Leiden University Medical Center /  
University of Amsterdam, The Netherlands
      * Chris Mungall, Lawrence Berkeley National Laboratories, United  
States of America
      * Stephan Philippi, Institute for Software Technology,  
University of Koblenz-Landau, Koblenz, Germany
      * Marco Roos, Instituut voor Informatica, University of  
Amsterdam, Netherlands
      * Alan Ruttenberg, Science Commons, Cambridge, MA, United States  
of America
      * Matthias Samwald, DERI, Galway, Ireland, and Konrad Lorenz  
Institute for Evolution and Cognition Research, Altenberg, Austria
      * Nigam Shah, Center for Biomedical Informatics Research,  
Stanford, United States of America
      * Michael Schr?der, Biotechnology Centre, TU Dresden, Dresden,  
Germany
      * Robert Stevens, School of Computer Science, University of  
Manchester, Manchester, United Kingdom
      * Tetsuro Toyoda, Genomic Sciences Center, RIKEN, Yokohama, Japan
      * Mark D. Wilkinson, iCAPTURE Center, St. Paul Hospital,  
Vancouver, Canada

and the organizers


***Type of contributions

The following possible contributions are sought:

      * Oral communications (regular papers)
      * Posters
      * Software demos


***Proceedings

All accepted oral communications and posters will be published with  
the CEUR-WS.org Workshop Proceedings service (see http://ceur-ws.org/).
We are finalizing the agreement to have a dedicated special issue on  
the 2009 edition of swat4ls in an international scientific journal of  
the BMC group (open access, pubmed indexed).
To this end, a special Call will be launched shortly after the  
workshop, for extended and revised versions of contributions submitted  
to the workshop and accepted either as oral communication or poster.


***New Deadlines

      * Intention to submit (abstract only):     October 5th
      * Submission of papers:                        October 12
      * Submission of posters and demos:      October 15
      * Communication of acceptance:            October 28
      * Camera ready:                                   November 13



***Instructions

All papers and posters must be in English and must be submitted  
through the EasyChair review system at
http://www.easychair.org/conferences/?conf=swat4ls-09 .
Please upload all submissions as PDF files in LNCS format (http://www.springer.de/comp/lncs/authors.html 
).
To ensure high quality, submitted papers will be carefully peer- 
reviewed by at least three members of the Scientific Committee.
      * Submissions for Oral communications should be between 8 and 15  
pages.
      * Posters submissions should be between 2 and 4 pages.
      * Software demo proposals should also be between 2 and 4 pages.


***Organization

      * M. Scott Marshall, Leiden University Medical Center /  
University of Amsterdam, The Netherlands
      * Albert Burger, School of Mathematical and Computer Sciences,  
Heriot-Watt University, and Human Genetics Unit, Medical Research  
Council, Edinburgh, Scotland, United Kingdom
      * Adrian Paschke, Corporate Semantic Web, Freie Universitaet  
Berlin, Germany
      * Paolo Romano, Bioinformatics, National Cancer Research  
Institute, Genova, Italy
      * Andrea Splendiani, Biomathematics and Bioinformatics dept.,  
Rothamsted Research, UK

***More information
    * http://www.swat4ls.org/2009/
    * http://swat4ls.blogspot.com
    * info at swat4ls.org
---
Andrea Splendiani
Senior Bioinformatics Scientist
Rothamsted Research, Harpenden, UK
andrea.splendiani at bbsrc.ac.uk
+44(0)1582 763133 ext 2004




From harry.mangalam at uci.edu  Thu Sep 17 12:27:04 2009
From: harry.mangalam at uci.edu (Harry Mangalam)
Date: Thu, 17 Sep 2009 09:27:04 -0700
Subject: [BiO BB] Find common regions in 3 organisms
In-Reply-To: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
References: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
Message-ID: <200909170927.04390.harry.mangalam@uci.edu>

Based on the question & follow-ups, it sounds like you want is a complete 
genome similarity comparison.  Have you looked at Vista (no relation to MS)?

http://genome.lbl.gov/vista/index.shtml

That's what it does (among an increasing list of other things)...

hjm

On Wednesday 16 September 2009 20:51:15 Nevan King wrote:
> Hi,
>
> This question has probably been asked, but I'm not sure what search
> terms to use to find answers. This is a question from one of the
> researchers in my lab.
>
> I want to find common regions of sequences in 3 organisms. The first
> organism (P. gingivalis) has been fully sequenced and described. It
> has around 2000 genes. The other two are similar to P. gingivalis.
>
> I've set up all three organisms in Blast, but comparing the genes one
> by one would be a big task. What's the best way to automate this? I
> understand that you can enter a list of fastas into blast and it will
> compare each one to all the genes in its database. Is there a way to
> do this with 3 organisms? Is Blast the best tool to use for this job?
>
> Sorry if this is short on details, I don't fully understand the topic.
>
> Thanks
>
> Nevan.
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb



-- 
Harry Mangalam - Research Computing, NACS, Rm 225 MSTB, UC Irvine
[ZOT 2225] / 92697  949 824-0084(o), 949 285-4487(c)
MSTB=Bldg 415 (G-5 on <http://today.uci.edu/pdf/UCI_09_map_campus.pdf>
---
It is better to be roughly right than precisely wrong.
Keynes



From marty.gollery at gmail.com  Thu Sep 17 11:46:23 2009
From: marty.gollery at gmail.com (Martin Gollery)
Date: Thu, 17 Sep 2009 08:46:23 -0700
Subject: [BiO BB] Find common regions in 3 organisms
In-Reply-To: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
References: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
Message-ID: <bdd10c2a0909170846m3ad9431ek32e087675a170ec4@mail.gmail.com>

If they are similar enough and you have complete genomes, you may use
ClustalW or some other similar MSA. If they have genome rearrangements then
you will have to use BLAST as others have noted. ClustalW does not work well
when the order of the genes is shifted.

Marty

On Wed, Sep 16, 2009 at 8:51 PM, Nevan King <nevan.ml at gmail.com> wrote:

> Hi,
>
> This question has probably been asked, but I'm not sure what search
> terms to use to find answers. This is a question from one of the
> researchers in my lab.
>
> I want to find common regions of sequences in 3 organisms. The first
> organism (P. gingivalis) has been fully sequenced and described. It
> has around 2000 genes. The other two are similar to P. gingivalis.
>
> I've set up all three organisms in Blast, but comparing the genes one
> by one would be a big task. What's the best way to automate this? I
> understand that you can enter a list of fastas into blast and it will
> compare each one to all the genes in its database. Is there a way to
> do this with 3 organisms? Is Blast the best tool to use for this job?
>
> Sorry if this is short on details, I don't fully understand the topic.
>
> Thanks
>
> Nevan.
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>



-- 
-- 
Martin Gollery
Senior Bioinformatics Scientist
Tahoe Informatics
www.bioinformaticist.biz
www.hiddenmarkovmodels.com


From marchywka at hotmail.com  Fri Sep 18 20:16:23 2009
From: marchywka at hotmail.com (Mike Marchywka)
Date: Fri, 18 Sep 2009 20:16:23 -0400
Subject: [BiO BB] Find common regions in 3 organisms
In-Reply-To: <bdd10c2a0909170846m3ad9431ek32e087675a170ec4@mail.gmail.com>
References: <84095720909162051n4f6e26c1sc0a5278d209bd5c7@mail.gmail.com>
	<bdd10c2a0909170846m3ad9431ek32e087675a170ec4@mail.gmail.com>
Message-ID: <BLU113-W160055CB31310373E9CD74BEDF0@phx.gbl>






----------------------------------------
> Date: Thu, 17 Sep 2009 08:46:23 -0700
> From: marty.gollery at gmail.com
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] Find common regions in 3 organisms
>
> If they are similar enough and you have complete genomes, you may use
> ClustalW or some other similar MSA. If they have genome rearrangements then
> you will have to use BLAST as others have noted. ClustalW does not work well
> when the order of the genes is shifted.

It works fine for what it is supposed to do - multi sequence alignment. 
These things don't know a lot about likely operations that have been performed to generate one set of features from another source.
If you did this with text and wanted to diff versions of a file that may be fine when files are nominally similar. If you are trying to find similar sentences or paragraphs in texts with no assumed apriori similarity, you can eeither do some kind of NxM exhaustive search or 
build and use various indexes with lower order algorithms. I guess
I'd be curious if there are even "general purpose" string indexers
around that let you operate on the indicies etc. 
 
 
>
> Marty
>
> On Wed, Sep 16, 2009 at 8:51 PM, Nevan King wrote:
>
>> Hi,
>>
>> This question has probably been asked, but I'm not sure what search
>> terms to use to find answers. This is a question from one of the
>> researchers in my lab.
>>
>> I want to find common regions of sequences in 3 organisms. The first
>> organism (P. gingivalis) has been fully sequenced and described. It
>> has around 2000 genes. The other two are similar to P. gingivalis.
>>
>> I've set up all three organisms in Blast, but comparing the genes one
>> by one would be a big task. What's the best way to automate this? I
>> understand that you can enter a list of fastas into blast and it will
>> compare each one to all the genes in its database. Is there a way to
>> do this with 3 organisms? Is Blast the best tool to use for this job?
>>
>> Sorry if this is short on details, I don't fully understand the topic.
>>
>> Thanks
>>
>> Nevan.
>>
>> _______________________________________________
>> BBB mailing list
>> BBB at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/bbb
>>
>
>
>
> --
> --
> Martin Gollery
> Senior Bioinformatics Scientist
> Tahoe Informatics
> www.bioinformaticist.biz
> www.hiddenmarkovmodels.com
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
_________________________________________________________________
Ready for Fall shows? Use Bing to find helpful ratings and reviews on digital tv's.
http://www.bing.com/shopping/search?q=digital+tv's&form=MSHNCB&publ=WLHMTAG&crea=TEXT_MSHNCB_Vertical_Shopping_DigitalTVs_1x1


From Robin.Haw at oicr.on.ca  Tue Sep 22 16:44:16 2009
From: Robin.Haw at oicr.on.ca (Robin Haw)
Date: Tue, 22 Sep 2009 16:44:16 -0400
Subject: [BiO BB] Reactome Pathway Database User Survey
Message-ID: <C6DEAF60.14DE%robin.haw@oicr.on.ca>

Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools.  With this in mind, we are actively soliciting comments from the research community in order to assess community needs.  We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools.

You can access the survey at: http://tinyurl.com/l48zzq

Thank you for taking part.

Robin Haw
Manager of Reactome Outreach
Outreach [at] reactome.org
http://www.reactome.org


From karen.morris at bbsrc.ac.uk  Thu Sep 24 09:45:11 2009
From: karen.morris at bbsrc.ac.uk (karen morris (RRes-Roth))
Date: Thu, 24 Sep 2009 14:45:11 +0100
Subject: [BiO BB] IB2010 - Integrative Bioinformatics Symposium - Cambridge
 UK March 2010
Message-ID: <F3D21FDC7F93274D8AF904D6E31398080CE941816D@rothexch1.rothamsted.bbsrc.ac.uk>

CALL FOR PAPERS

The Integrative Bioinformatics Symposium
is being held on 22nd to 24th March 2010
in Cambridge, United Kingdom.

web site:
http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib2010

This sixth meeting on Integrative Bioinformatics will be of interest to
Bioinformaticians, Computer Scientists and others working in, or
interested in finding out more about, the developing area of integrative
bioinformatics. There will be opportunities to present and discuss methods,
theoretical approaches, and their practical applications.

We are now inviting submission of manuscripts to be considered for
presentation at IB2010.

The deadline for online submissions is 1st December 2009.

Accepted papers will appear in a special issue of the Journal of
Integrative Bioinformatics (http://journal.imbio.de) which will be available as the
printed conference proceedings.

To submit a paper, please visit the symposium web site where further
details can be found.

Topics of interest include:
Data integration and knowledge management
Errors and inconsistencies in biological databases
Combined dry- and wet-lab studies
Prediction and integration of metabolic and regulatory networks
Genotype-phenotype linkage
Protein-protein interactions
Integrative microarray modelling and analyses
Integrative approaches for drug design
Virtual cell modelling
Tool integration and workflow systems
Computational systems biology
Integrative modelling and simulation frameworks
Integrative data and text mining approaches
Network analysis
Data visualisation and visual analytics

Further information can be obtained from
Paul Verrier (paul.verrier at bbsrc.ac.uk)
or
Chris Rawlings (chris.rawlings at bbsrc.ac.uk)



From manuscripts.jcbbr at gmail.com  Fri Sep 25 04:16:09 2009
From: manuscripts.jcbbr at gmail.com (JCBBR Journals)
Date: Fri, 25 Sep 2009 09:16:09 +0100
Subject: [BiO BB] =?windows-1252?q?Introducing_=91=91Journal_of_Computatio?=
	=?windows-1252?q?nal_Biology_and_Bioinformatics_Research=91=91?=
Message-ID: <b1d225690909250116q218bfb79t184d2702ab96cea4@mail.gmail.com>

*Journal of Computational Biology and Bioinformatics Research*

www.academicjournals.org/JCBBR <http://www.academicjournals.org/JMGG>






* *

Dear Colleague,



The *Journal of Computational Biology and Bioinformatics Research
(JCBBR)*is a multidisciplinary peer-reviewed journal published monthly
by Academic
Journals (www.academicjournals.org/JCBBR<http://www.academicjournals.org/JMGG>
). *JCBBR* is dedicated to increasing the depth of research across all areas
of this subject.



*Editors and reviewers*



JCBBR* *is seeking qualified researchers to join its editorial team as
editors, subeditors or reviewers. Kindly send your resume to *
jcbbr.journal at gmail.com <jasd.journal at gmail.com>*.



*Call for Papers*



JCBBR welcomes the submission of manuscripts that meet the general criteria
of significance and scientific excellence in this subject area, and will
publish:**



?       Original articles in basic and applied research

?       Case studies

?       Critical reviews, surveys, opinions, commentaries and essays



We invite you to submit your manuscript(s) to
*jcbbr.journal at gmail.com<ijppb.journal at gmail.com>
* for publication in the Maiden Issue (October 2009). Our objective is to
inform authors of the decision on their manuscript(s) within four weeks of
submission. Following acceptance, a paper will normally be published in the
next issue. Instruction for authors and other details are available on our
website; http://www.academicjournals.org/JCBBR/Instruction.htm<http://www.academicjournals.org/IJPPB/Instruction.htm>


*JCBBR   *is an Open Access Journal

One key request of researchers across the world is unrestricted access to
research publications. Open access gives a worldwide audience larger than
that of any subscription-based journal ad thus increases the visibility and
impact of published work. It also enhances indexing, retrieval power and
eliminates the need for permissions to reproduce and distribute content.
JCBBR is fully committed to the Open Access Initiative and will provide free
access to all articles as soon as they are published.



Best regards,



*Oyo Excel*

Editorial Assistant

Journal of Computational Biology and Bioinformatics Research(JCBBR)

E-mail: *jcbbr.journal at gmail.com <ijppb.journal at gmail.com>*

www.academicjournals.org/*JCBBR* <http://www.academicjournals.org/JMGG>


From bioinfo.robert at gmail.com  Fri Sep 25 12:08:54 2009
From: bioinfo.robert at gmail.com (Robert lzw)
Date: Fri, 25 Sep 2009 12:08:54 -0400
Subject: [BiO BB] [Portal Web Design for Bioinformatics] How to start and
	cross platform issues
Message-ID: <30811a2b0909250908s6a5922eese98465951d3d9c92@mail.gmail.com>

Hi there,

I am a newbie to web design for bioinformatics and going to design a portal
web page similar to the following link:
http://www.eh3.uc.edu:8080/GenomicsPortals/

It looks that the above portal was designed on Unix/Linux using JavaScript
and Microsoft FrontPage 5.0 processing datasets in MySQL database. As I only
have MS Visual Studio 2008 Prof software, I plan to go with ASP.NET and
ADO.NET to do it for processing datasets in SQL databases.

Does anybody know if this will work? Can the portal web pages designed based
on Windows .NET framework be browsed without any problem on Linux/Unix.
i.e., other platforms than the Windows? Regardless, any suggestions on how
to start designing such a portal web page (books, online resources,
framework and tools) would be highly appreciated. I need a general, correct
direction to follow. Thank you very much in advance.

Robert


From marchywka at hotmail.com  Fri Sep 25 13:57:49 2009
From: marchywka at hotmail.com (Mike Marchywka)
Date: Fri, 25 Sep 2009 13:57:49 -0400
Subject: [BiO BB] [Portal Web Design for Bioinformatics] How to start
 and	cross platform issues
In-Reply-To: <30811a2b0909250908s6a5922eese98465951d3d9c92@mail.gmail.com>
References: <30811a2b0909250908s6a5922eese98465951d3d9c92@mail.gmail.com>
Message-ID: <BLU113-W127E192F9F1DAC93AD5C4EBED90@phx.gbl>









----------------------------------------
> Date: Fri, 25 Sep 2009 12:08:54 -0400
> From: bioinfo.robert at gmail.com
> To: bbb at bioinformatics.org
> Subject: [BiO BB] [Portal Web Design for Bioinformatics] How to start and cross platform issues
>
> Hi there,
>
> I am a newbie to web design for bioinformatics and going to design a portal
> web page similar to the following link:
> http://www.eh3.uc.edu:8080/GenomicsPortals/
>
> It looks that the above portal was designed on Unix/Linux using JavaScript
> and Microsoft FrontPage 5.0 processing datasets in MySQL database. As I only
> have MS Visual Studio 2008 Prof software, I plan to go with ASP.NET and
> ADO.NET to do it for processing datasets in SQL databases.
>
> Does anybody know if this will work? Can the portal web pages designed based
> on Windows .NET framework be browsed without any problem on Linux/Unix.
> i.e., other platforms than the Windows? Regardless, any suggestions on how
> to start designing such a portal web page (books, online resources,
> framework and tools) would be highly appreciated. I need a general, correct
> direction to follow. Thank you very much in advance.
>

I guess suggesting that you worry about an API first and design around
that wouldn't help? This is a prior debate we had here when someone
asked a similar question. You want to support the casual user and have
demo's for management but generally this data is best made available with
a programatic interface, not just something that requires human interaction-
remember, computers should automate data processing not just produce
pictures.



 		 	   		  
_________________________________________________________________
Insert movie times and more without leaving Hotmail?.
http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_QuickAdd_062009


From randalls at bioinfo.wsu.edu  Fri Sep 25 14:11:02 2009
From: randalls at bioinfo.wsu.edu (randalls at bioinfo.wsu.edu)
Date: Fri, 25 Sep 2009 11:11:02 -0700 (PDT)
Subject: [BiO BB] [Portal Web Design for Bioinformatics] How to start
 and	cross platform issues
In-Reply-To: <701425996.3961253902137951.JavaMail.root@mail>
Message-ID: <342409280.3981253902262429.JavaMail.root@mail>

Yes, you can build web pages in .net that are accessible or browseable using the plethora of browsers available for Linux, like Firefox.  Just make sure you stay away from things like activex controls, which are a Microsoft Proprietary plugin for Internet Explorer based on COM (pure evil).  

However, you can develop anything you wish in .net, which is a good platform for development, but most of the BioInformatics software that we work with is either written in Java (BioJava) or Perl (BioPerl).  I have not seen at this point any strong development camps for Bioinformatics focused around the .net frame work (yet..but this will/or is changing). 

The site: http://www.eh3.uc.edu:8080/GenomicsPortals/ uses java (not to be confused with javascript) and a servlet engine (most likely tomcat) to render the dynamic content you see.  They may have used frontpage to design the layout, and then embedded <%jsp %> tags into the page to hook into the dynamic pieces.  

To start development of such a site I would begin with a fundamental understanding of HTML. Even though there are lot of HTML generators, like FrontPage or Dreamweaver, you have to possess a fundemental understanding of things like creating web forms using tags like <form></form> or the differences between a get and post request and when to use them.  Once you understand basic things like HTML, then move forward with dynamically generating content using .net or whatever you choose to use.  It is really an evolution every web application developer must go through.  

It can take years to master these skills, so be patient.  As far as online resources, there are plenty on the internet and google will be your most valuable resource.

Good luck.


Randall Svancara
Systems Administrator/DBA/Developer
Main Bioinformatics Laboratory



----- Original Message -----
From: "Robert lzw" <bioinfo.robert at gmail.com>
To: bbb at bioinformatics.org
Sent: Friday, September 25, 2009 9:08:54 AM
Subject: [BiO BB] [Portal Web Design for Bioinformatics] How to start and	cross platform issues

Hi there,

I am a newbie to web design for bioinformatics and going to design a portal
web page similar to the following link:
http://www.eh3.uc.edu:8080/GenomicsPortals/

It looks that the above portal was designed on Unix/Linux using JavaScript
and Microsoft FrontPage 5.0 processing datasets in MySQL database. As I only
have MS Visual Studio 2008 Prof software, I plan to go with ASP.NET and
ADO.NET to do it for processing datasets in SQL databases.

Does anybody know if this will work? Can the portal web pages designed based
on Windows .NET framework be browsed without any problem on Linux/Unix.
i.e., other platforms than the Windows? Regardless, any suggestions on how
to start designing such a portal web page (books, online resources,
framework and tools) would be highly appreciated. I need a general, correct
direction to follow. Thank you very much in advance.

Robert
_______________________________________________
BBB mailing list
BBB at bioinformatics.org
http://www.bioinformatics.org/mailman/listinfo/bbb



From jeff at bioinformatics.org  Fri Sep 25 14:34:47 2009
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri, 25 Sep 2009 14:34:47 -0400
Subject: [BiO BB] [Portal Web Design for Bioinformatics] How to start
 and cross platform issues
In-Reply-To: <30811a2b0909250908s6a5922eese98465951d3d9c92@mail.gmail.com>
References: <30811a2b0909250908s6a5922eese98465951d3d9c92@mail.gmail.com>
Message-ID: <4ABD0D47.7090208@bioinformatics.org>

Hi Robert,

The separation of server-side software (e.g., PHP, ASP, etc.) from client-side software (browser and plugin) is an aspect of the Web that has made it so flexible and successful.  As long as the software that you choose to run on the client-side (e.g., JavaScript and plugins such as Flash, etc.) is widely supported on multiple platforms, it doesn't matter what you choose to run on the server-side.

So, you can set up a server that runs on Windows, Mac OS, Linux, Commodore 64, or whatever, and people can access your site on any platform that supports the client software that you use, if you even use anything beyond HTML.

Technically speaking, many bioinformatics portals work on the "model-view-controller" (MVC) paradigm, intentionally or not.  Here's some more information on the topic:

  http://en.wikipedia.org/wiki/Model-view-controller

Applied to the Web, the model resides on the server (e.g., in MySQL), while the view and controller reside on the client (e.g., browser and plugin).

If you choose to use a plugin and not just JavaScript, be sure that it is supported on multiple platforms.  Microsoft solutions are always best supported on Windows computers, including plugins.  Mac OS is a second-class citizen to Microsoft, and Linux barely exists.  For Linux, it is often left up to a third-party developer (e.g., Novell) to develop clones of Microsoft applications (e.g., Novell Mono attempts to bring .NET to Linux).  ActiveX and Silverlight are two examples of where Microsoft doesn't make their own plugins for Linux (AFAIK).

Cheers,
Jeff

Robert lzw wrote:
> Hi there,
> 
> I am a newbie to web design for bioinformatics and going to design a portal
> web page similar to the following link:
> http://www.eh3.uc.edu:8080/GenomicsPortals/
> 
> It looks that the above portal was designed on Unix/Linux using JavaScript
> and Microsoft FrontPage 5.0 processing datasets in MySQL database. As I only
> have MS Visual Studio 2008 Prof software, I plan to go with ASP.NET and
> ADO.NET to do it for processing datasets in SQL databases.
> 
> Does anybody know if this will work? Can the portal web pages designed based
> on Windows .NET framework be browsed without any problem on Linux/Unix.
> i.e., other platforms than the Windows? Regardless, any suggestions on how
> to start designing such a portal web page (books, online resources,
> framework and tools) would be highly appreciated. I need a general, correct
> direction to follow. Thank you very much in advance.
> 

-- 
J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 978 621 8258
--




From cupton at uvic.ca  Fri Sep 25 15:00:38 2009
From: cupton at uvic.ca (Chris Upton)
Date: Fri, 25 Sep 2009 12:00:38 -0700
Subject: [BiO BB] [Portal Web Design for Bioinformatics] How to start
 and cross platform issues
In-Reply-To: <4ABD0D47.7090208@bioinformatics.org>
Message-ID: <C6E26166.223DB%cupton@uvic.ca>

And remember, large numbers in the life sciences and in bioinformatics use Mac OS X.

Chris


On 9/25/09 11:34 AM, "J.W. Bizzaro" <jeff at bioinformatics.org> wrote:

Hi Robert,

The separation of server-side software (e.g., PHP, ASP, etc.) from client-side software (browser and plugin) is an aspect of the Web that has made it so flexible and successful.  As long as the software that you choose to run on the client-side (e.g., JavaScript and plugins such as Flash, etc.) is widely supported on multiple platforms, it doesn't matter what you choose to run on the server-side.

So, you can set up a server that runs on Windows, Mac OS, Linux, Commodore 64, or whatever, and people can access your site on any platform that supports the client software that you use, if you even use anything beyond HTML.

Technically speaking, many bioinformatics portals work on the "model-view-controller" (MVC) paradigm, intentionally or not.  Here's some more information on the topic:

  http://en.wikipedia.org/wiki/Model-view-controller

Applied to the Web, the model resides on the server (e.g., in MySQL), while the view and controller reside on the client (e.g., browser and plugin).

If you choose to use a plugin and not just JavaScript, be sure that it is supported on multiple platforms.  Microsoft solutions are always best supported on Windows computers, including plugins.  Mac OS is a second-class citizen to Microsoft, and Linux barely exists.  For Linux, it is often left up to a third-party developer (e.g., Novell) to develop clones of Microsoft applications (e.g., Novell Mono attempts to bring .NET to Linux).  ActiveX and Silverlight are two examples of where Microsoft doesn't make their own plugins for Linux (AFAIK).

Cheers,
Jeff

Robert lzw wrote:
> Hi there,
>
> I am a newbie to web design for bioinformatics and going to design a portal
> web page similar to the following link:
> http://www.eh3.uc.edu:8080/GenomicsPortals/
>
> It looks that the above portal was designed on Unix/Linux using JavaScript
> and Microsoft FrontPage 5.0 processing datasets in MySQL database. As I only
> have MS Visual Studio 2008 Prof software, I plan to go with ASP.NET and
> ADO.NET to do it for processing datasets in SQL databases.
>
> Does anybody know if this will work? Can the portal web pages designed based
> on Windows .NET framework be browsed without any problem on Linux/Unix.
> i.e., other platforms than the Windows? Regardless, any suggestions on how
> to start designing such a portal web page (books, online resources,
> framework and tools) would be highly appreciated. I need a general, correct
> direction to follow. Thank you very much in advance.
>

--
J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 978 621 8258
--


_______________________________________________
BBB mailing list
BBB at bioinformatics.org
http://www.bioinformatics.org/mailman/listinfo/bbb



From bioinfo.robert at gmail.com  Fri Sep 25 15:38:21 2009
From: bioinfo.robert at gmail.com (Robert lzw)
Date: Fri, 25 Sep 2009 15:38:21 -0400
Subject: [BiO BB] [Portal Web Design for Bioinformatics] How to start
	and cross platform issues
In-Reply-To: <C6E26166.223DB%cupton@uvic.ca>
References: <4ABD0D47.7090208@bioinformatics.org>
	<C6E26166.223DB%cupton@uvic.ca>
Message-ID: <30811a2b0909251238u1eeec166re9db3dffc5b451da@mail.gmail.com>

Thanks a lot, guys, for the detailed messages, which is very helpful. Now I
know where to start at least.

My understanding is that platform decides which tools / frameworks would be
available to you. So that is a big decision for a starter...

Robert

On Fri, Sep 25, 2009 at 3:00 PM, Chris Upton <cupton at uvic.ca> wrote:

> And remember, large numbers in the life sciences and in bioinformatics use
> Mac OS X.
>
> Chris
>
>
> On 9/25/09 11:34 AM, "J.W. Bizzaro" <jeff at bioinformatics.org> wrote:
>
> Hi Robert,
>
> The separation of server-side software (e.g., PHP, ASP, etc.) from
> client-side software (browser and plugin) is an aspect of the Web that has
> made it so flexible and successful.  As long as the software that you choose
> to run on the client-side (e.g., JavaScript and plugins such as Flash, etc.)
> is widely supported on multiple platforms, it doesn't matter what you choose
> to run on the server-side.
>
> So, you can set up a server that runs on Windows, Mac OS, Linux, Commodore
> 64, or whatever, and people can access your site on any platform that
> supports the client software that you use, if you even use anything beyond
> HTML.
>
> Technically speaking, many bioinformatics portals work on the
> "model-view-controller" (MVC) paradigm, intentionally or not.  Here's some
> more information on the topic:
>
>  http://en.wikipedia.org/wiki/Model-view-controller
>
> Applied to the Web, the model resides on the server (e.g., in MySQL), while
> the view and controller reside on the client (e.g., browser and plugin).
>
> If you choose to use a plugin and not just JavaScript, be sure that it is
> supported on multiple platforms.  Microsoft solutions are always best
> supported on Windows computers, including plugins.  Mac OS is a second-class
> citizen to Microsoft, and Linux barely exists.  For Linux, it is often left
> up to a third-party developer (e.g., Novell) to develop clones of Microsoft
> applications (e.g., Novell Mono attempts to bring .NET to Linux).  ActiveX
> and Silverlight are two examples of where Microsoft doesn't make their own
> plugins for Linux (AFAIK).
>
> Cheers,
> Jeff
>
> Robert lzw wrote:
> > Hi there,
> >
> > I am a newbie to web design for bioinformatics and going to design a
> portal
> > web page similar to the following link:
> > http://www.eh3.uc.edu:8080/GenomicsPortals/
> >
> > It looks that the above portal was designed on Unix/Linux using
> JavaScript
> > and Microsoft FrontPage 5.0 processing datasets in MySQL database. As I
> only
> > have MS Visual Studio 2008 Prof software, I plan to go with ASP.NET and
> > ADO.NET to do it for processing datasets in SQL databases.
> >
> > Does anybody know if this will work? Can the portal web pages designed
> based
> > on Windows .NET framework be browsed without any problem on Linux/Unix.
> > i.e., other platforms than the Windows? Regardless, any suggestions on
> how
> > to start designing such a portal web page (books, online resources,
> > framework and tools) would be highly appreciated. I need a general,
> correct
> > direction to follow. Thank you very much in advance.
> >
>
> --
> J.W. Bizzaro
> Bioinformatics Organization, Inc. (Bioinformatics.Org)
> E-mail: jeff at bioinformatics.org
> Phone:  +1 978 621 8258
> --
>
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>


From marchywka at hotmail.com  Sat Sep 26 07:33:58 2009
From: marchywka at hotmail.com (Mike Marchywka)
Date: Sat, 26 Sep 2009 07:33:58 -0400
Subject: [BiO BB] [Portal Web Design for Bioinformatics] How to
	start	and cross platform issues
In-Reply-To: <30811a2b0909251238u1eeec166re9db3dffc5b451da@mail.gmail.com>
References: <4ABD0D47.7090208@bioinformatics.org>
	<C6E26166.223DB%cupton@uvic.ca>
Message-ID: <BLU113-W272CD655D3CA8B22E37A5BBED80@phx.gbl>



[ this is a trimmed down version of message I sent earlier that
was too big for distro. Note also that hotmail is trying to encode
the special chars so it reads poorly, I'm going to gmail... ]
>
>>
>> Thanks a lot=2C guys=2C for the detailed messages=2C which is very helpfu=
> l. Now I
>> know where to start at least.
>>
>> My understanding is that platform decides which tools / frameworks would =
> be
>> available to you. So that is a big decision for a starter...
>
>
?I really depends on what you mean by tools and models versus views.
?And API is more concerned with the information part rather than
?the human viewing thing. If you provide that the tools are generally
?available everywhere and much more versatile. If you provide vendor-specifi=
?c
?pictures or human readable views only=2C you reduce the ability of the user
?to process your data in an automated ad hoc manner. Without knowing specifi=
?cally what you are doing but assuming it has something to do
?with information=2C I would try to consider an information-providing API
?early on rather than jump into more constraining view formats.=20

?Certainly the first question would be something like=2C "is my information
?a dead end or would people want to integrate it with other data and
?processing methods?" If it isn't a dead end data set=2C you really help
?make it available with an API not just a Flash app.=20
>
>
>>
>> Robert
>>
>> On Fri=2C Sep 25=2C 2009 at 3:00 PM=2C Chris Upton wrote:
>>
>>> And remember=2C large numbers in the life sciences and in bioinformatics=
> use
>>> Mac OS X.
>>>
>>> Chris
>>>
>>>
>>> On 9/25/09 11:34 AM=2C "J.W. Bizzaro" wrote:
>>>
>>> Hi Robert=2C
>>>
>>> The separation of server-side software (e.g.=2C PHP=2C ASP=2C etc.) from
>>> client-side software (browser and plugin) is an aspect of the Web that h=
> as
>>> made it so flexible and successful. As long as the software that you cho=
> ose
>>> to run on the client-side (e.g.=2C JavaScript and plugins such as Flash=
> =2C etc.)
>>> is widely supported on multiple platforms=2C it doesn't matter what you =
> choose
>>> to run on the server-side.
>>>
>>> So=2C you can set up a server that runs on Windows=2C Mac OS=2C Linux=2C=
> Commodore
>>> 64=2C or whatever=2C and people can access your site on any platform tha=
> t
>>> supports the client software that you use=2C if you even use anything be=
> yond
>>> HTML.
>>>
>>> Technically speaking=2C many bioinformatics portals work on the
>>> "model-view-controller" (MVC) paradigm=2C intentionally or not. Here's s=
> ome
>>> more information on the topic:
>>>
>>> http://en.wikipedia.org/wiki/Model-view-controller
>>>
>>> Applied to the Web=2C the model resides on the server (e.g.=2C in MySQL)=
> =2C while
>>> the view and controller reside on the client (e.g.=2C browser and plugin=
> ).

 		 	   		  
_________________________________________________________________
Hotmail? has ever-growing storage! Don?t worry about storage limits.
http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutorial_Storage_062009


From sgoetz at cipf.es  Sat Sep 26 06:33:17 2009
From: sgoetz at cipf.es (Stefan Goetz)
Date: Sat, 26 Sep 2009 12:33:17 +0200
Subject: [BiO BB] [Portal Web Design for Bioinformatics] How to start
 and cross platform issues
In-Reply-To: <30811a2b0909251238u1eeec166re9db3dffc5b451da@mail.gmail.com>
References: <4ABD0D47.7090208@bioinformatics.org>	<C6E26166.223DB%cupton@uvic.ca>
	<30811a2b0909251238u1eeec166re9db3dffc5b451da@mail.gmail.com>
Message-ID: <4ABDEDED.7080104@cipf.es>

Hi Robert.
for such an approach and in case you are planing to create something big 
and long-lasting, I would go for Java Technology (Servlets,Struts, JSPs, 
JSF (or even Wicket or GWT)) in combination with an application server 
(Tomcat or similar). On the client side plain html+css and 
javascript/ajax. With Java you are platform independent, you have a big 
user community (and biojava) and find wrappers to connect to other 
programing languages important to bioinformatics like R, Python, Perl etc.
As a development platform I would recommend you Eclipse with SVN/Git and 
Ant or Maven.
Good luck,
Stefan


Robert lzw wrote:
> Thanks a lot, guys, for the detailed messages, which is very helpful. Now I
> know where to start at least.
>
> My understanding is that platform decides which tools / frameworks would be
> available to you. So that is a big decision for a starter...
>
> Robert
>
> On Fri, Sep 25, 2009 at 3:00 PM, Chris Upton <cupton at uvic.ca> wrote:
>
>   
>> And remember, large numbers in the life sciences and in bioinformatics use
>> Mac OS X.
>>
>> Chris
>>
>>
>> On 9/25/09 11:34 AM, "J.W. Bizzaro" <jeff at bioinformatics.org> wrote:
>>
>> Hi Robert,
>>
>> The separation of server-side software (e.g., PHP, ASP, etc.) from
>> client-side software (browser and plugin) is an aspect of the Web that has
>> made it so flexible and successful.  As long as the software that you choose
>> to run on the client-side (e.g., JavaScript and plugins such as Flash, etc.)
>> is widely supported on multiple platforms, it doesn't matter what you choose
>> to run on the server-side.
>>
>> So, you can set up a server that runs on Windows, Mac OS, Linux, Commodore
>> 64, or whatever, and people can access your site on any platform that
>> supports the client software that you use, if you even use anything beyond
>> HTML.
>>
>> Technically speaking, many bioinformatics portals work on the
>> "model-view-controller" (MVC) paradigm, intentionally or not.  Here's some
>> more information on the topic:
>>
>>  http://en.wikipedia.org/wiki/Model-view-controller
>>
>> Applied to the Web, the model resides on the server (e.g., in MySQL), while
>> the view and controller reside on the client (e.g., browser and plugin).
>>
>> If you choose to use a plugin and not just JavaScript, be sure that it is
>> supported on multiple platforms.  Microsoft solutions are always best
>> supported on Windows computers, including plugins.  Mac OS is a second-class
>> citizen to Microsoft, and Linux barely exists.  For Linux, it is often left
>> up to a third-party developer (e.g., Novell) to develop clones of Microsoft
>> applications (e.g., Novell Mono attempts to bring .NET to Linux).  ActiveX
>> and Silverlight are two examples of where Microsoft doesn't make their own
>> plugins for Linux (AFAIK).
>>
>> Cheers,
>> Jeff
>>
>> Robert lzw wrote:
>>     
>>> Hi there,
>>>
>>> I am a newbie to web design for bioinformatics and going to design a
>>>       
>> portal
>>     
>>> web page similar to the following link:
>>> http://www.eh3.uc.edu:8080/GenomicsPortals/
>>>
>>> It looks that the above portal was designed on Unix/Linux using
>>>       
>> JavaScript
>>     
>>> and Microsoft FrontPage 5.0 processing datasets in MySQL database. As I
>>>       
>> only
>>     
>>> have MS Visual Studio 2008 Prof software, I plan to go with ASP.NET and
>>> ADO.NET to do it for processing datasets in SQL databases.
>>>
>>> Does anybody know if this will work? Can the portal web pages designed
>>>       
>> based
>>     
>>> on Windows .NET framework be browsed without any problem on Linux/Unix.
>>> i.e., other platforms than the Windows? Regardless, any suggestions on
>>>       
>> how
>>     
>>> to start designing such a portal web page (books, online resources,
>>> framework and tools) would be highly appreciated. I need a general,
>>>       
>> correct
>>     
>>> direction to follow. Thank you very much in advance.
>>>
>>>       
>> --
>> J.W. Bizzaro
>> Bioinformatics Organization, Inc. (Bioinformatics.Org)
>> E-mail: jeff at bioinformatics.org
>> Phone:  +1 978 621 8258
>> --
>>
>>
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>>
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>>
>>     
> _______________________________________________
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>   


-- 

--------------------------------------------
Stefan G?tz
Bioinformatics Department
Centro de Investigaci?n Pr?ncipe Felipe (CIPF)
C/E.P. Avda. Autopista del Saler, 16-3 
(junto Oceanogr?fico)
46013 Valencia, Spain
Tel: +34 963289680 Ext. 1011
Fax: +34 963289574
E-Mail: sgoetz at cipf.es
http://bioinfo.cipf.es
--------------------------------------------

FIRST INTERNATIONAL COURSE IN AUTOMATED 
FUNCTIONAL ANNOTATION AND DATA MINING
VALENCIA/ORLANDO September-October 2009
http://bioinfo.cipf.es/blast2gocourse
============================================