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Bopper and Internet biosequence analsyses

An Internet method of using "child apps" is now available with SeqPup. This allows one to run external analyses programs on a remote computer, yet interface with SeqPup's editor platform transparently, as for the local child apps. This is made possible with a new network protocol, called BOP (Biocomputing Office Protocol; obviously the acronym came first). It is based directly on the POP (Post Office Protocol) used for reading Internet mail, and also shares features with SMTP for sending Internet mail.

One popular use for this BOP interface may be to offer a simple-to-use client for Genetics Computing Group (GCG) command-line software. The current releas of SeqPup includes forms to interact with several GCG applications. Many other command-line programs, including versions of Clustal, FastA, BLAST, the Phylip series, fastDNAml, etc., can be added as BOP services fairly simply.

The implementation is very similar to use of local child apps on the user-interface. Additions that the user deals with include specifying a remote host, port, username and password.

Make available new BOP client-services, one must follow these steps:

-- Install Bopper, a network server daemon for Unix computers. This provides the interface from Internet port to command-line programs, and handles data file transfer and process status checking.

-- Configure bopper to add new command-line programs

-- Add SeqPup HTML forms for the new programs

To install and configure Bopper, see the distribution software, as <ftp://iubio.bio.indiana.edu/ util/dclap/source/bopper.tar.gz>

To add new SeqPup forms, follow these steps (see also the section on Child Apps):

- create a new form in HTML format, e.g., fasta.html

- use this style for the form call

<FORM

METHOD=bop

ACTION="bop://$bophost:$bopport/map

myseq -OUT=myseq.map -MEN=$menu

$three $silent $perfect $all $six $once

$?mismatch:$mismatch=$misval:

$?open:$open=$opval:

$?mincuts:$mincuts=$mcval:

$othercmd

">

where METHOD=bop, and

ACTION="bop://host:port/bop-path input-file output-file(s) other-commands"


The following variables are currently understood and substituted by SeqPup

bophost, bopport

currently defined host computer and Internet port# for BOP usage (see Bop setup dialog).

As HTML "<INPUT TYPE=hidden>" values, you may set these variables that SeqPup interprets:

infile, <INPUT TYPE=hidden NAME=infile VALUE="myseq">

the input data for the child or bop application, taken from the currently selected sequence data.

seqformat, <INPUT TYPE=hidden NAME=seqformat VALUE="gcg">

the format which infile should be created in. Values are any possible Readseq format types.

minseq, <INPUT TYPE=hidden NAME=minseq VALUE="1">

maxseq, <INPUT TYPE=hidden NAME=maxseq VALUE="1">

minimum and maximum number of sequences in selection to run application

outfile#, <INPUT TYPE=hidden NAME=outfile1 VALUE="myseq.map text/plain">

output file name(s) which application produces. Value includes name produced by application, and format type, in pseudo-mime syntax.


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