[Bioperl-l] Revising and updating the bioperl tutorial

[Peter Schattner]

Hello all-

I am working on revising  and updating the bioperl tutorial  (in
preparation for the 1.0 release) .

The prinicipal additions & modifications to the tutorial:I am envisioning
include:

1. Modify description  and tutorial scriptroutine  for bl2seq parser  to
describe syntax change required to enable reading multiple HSP's.

2.  Add descriptions and routines in the tutorial script to describe
newly added functions in SimpleAlign.pm

3.  Add a section to the descriptions and to the tutorial script to
describe  Remoteblast.pm

4.  Add a section on Location objects (simple, split, fuzzy etc)

5.  I am trying to decide whether it is useful to keep  "Appendix 1" in
the tutorial.  This appendix lists all the methods for (almost) all of the
bioperl objects  indicating from which object the method is inherited.
This infromation is useful for tracking down the correct documentation.
However the appendix is quite long and the user can obtain the same
information for any object by running the bptutorial.pl  script  ( with
option "100") as described in the tutorial.
Any thoughts one-way-or-the-other as to whether this appendix should be
eliminated in the next revision??

6.  I would be glad to add a section on the use of the bioperl-gui, if it
is anticipated that it will be relatively-easily usable by the time of the
bioperl 1.0 release.
Will it be ready by 1.0?  - or isit perhaps already usable and I just need
to be pointed in the direction of a little documentation and a sample
script ?

7.  I would be glad to add a section on the use of the bioperl-db, if it
is anticipated that it will be relatively-easily usable by the time of the
release.
Will it be ready by 1.0?  - or isit perhaps already usable and I just need
to be pointed in the direction of a little documentation and a sample
script ?

8.  I would be glad to add a section on the interface to EMBOSS if it will
be available as part of release 1.0.
Will it be ready by 1.0?  - or isit perhaps already usable and I just need
to be pointed in the direction of a little documentation and a sample
script ?

**** Are there any other new or significantly modified features planned
for bioperl1.0 that were not in bioperl 0.7 that should be included in the
revised tutorial??
If so, please let me know and I'll make sure they are included.

Thanks in advance for the input.

Peter