[Pipet Devel] from Justin

J.W. Bizzaro bizzaro at bc.edu
Wed Jun 9 18:53:24 EDT 1999

This was originally sent to me...Jeff

I'm going to work a little late tongiht and start on the first
implementation of the underlying loci infrastructure. Here's my plan:

1. simple command-line digest program. feed it a peptide sequence (1
   letter abreviations), and a digestion enzyme selected from a few
   hardcoded in the program.

2. python wrapper from paos object to 1 and back, merged with paos server

3. merged paos server and client, combined with a mini tool address book.

4. paos client with simple text interface to allow entering a peptide 
   sequence and an enzyme name, as well as outputing a list of digested

2 and 3 will then run on their own ports as daemons.

a user starts up 4, types in the seq/enzyme.
4 makes an object with entered data, and connected to 3
3 accepts object from 4, and looks at destination/tool property.
if dest/tool prop. is a specific network address, have the client aspect
of 3 contact 2. if a generic tool, consult address book to find
appropriate address, then contact 2
2 accepts the object from 3, formats the data so 1 can use it.
run 1, and 2 takes output, stores in object.
2 then updates 3, and 3 then updates 4.
4 outputs the data.

I already have a number of things I want to change, but I'll just build
that first. Then, we have to decide how the network layer will work,
and how to abstract objects (particularly XML) and how they are

I actually have quite a bit of free-time now with school out, so once I
have a home network connection again, I hope to get a lot of the lowlevel
loci done this summer. I'm on the xml-mol list, which is also rather
silent. Hopefully we can hash out the DTD's for our various datatypes


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