[Pipet Devel] Required Reading: CORBA at EBI

J.W. Bizzaro bizzaro at bc.edu
Sat Oct 9 16:04:54 EDT 1999

Here are some messages I dug up from our archive about AppLab:

---from me, 11/21/98-----------------
The following are some Java-based packages, tools, and links to tools.
              AppLab Homepage 

---from Peter Rice, 12/11/98 (Loci list)---
>  (4) TULIP also uses XML.

We could do. There are some XML fans over here. The AppLab project
at the EBI for example.

---from Peter Rice, 3/19/99 (EMBOSS list)----
It sounds like you have most of the functionality already.
USA processing uses various other parts of the ACD interface:

o database names form the emboss.defaults file
o sequence formats from the emboss.defaults file and the command line
o debugging calls which are redirected through the ACD options

.. and of course applications look exactly like any other EMBOSS
application to end users, and can be integrated with any other
interface on top of EMBOSS (AppLab for example)

---from Peter Rice, 6/2/99 (EMBOSS list)-----
>1) Do you plan to make a "DNA Strider"-like application, with a GUI?

EMBOSS is command line driven with the specific aim of running it
under any GUI that can cope. Examples we are looking at, though
implementations are some way off, include AppLab from the EBI....

---from Peter Rice, 7/20/99 (Loci list)------
EMBOSS appears to be command line based, but internally it uses a
simple "AJAX command definition" file (the idea comes from VMS). These
"ACD" files can be converted to other GUI definitions, so that we hope
to automate implementing EMBOSS under most other GUIs in

There are many of these around the EMBnet community and
beyond. Examples are BioNavigator (eBioinformatics and EMBnet
Australia) AppLab (Martin Senger, EBI), W2H (Martin Senger and EMBnet
Germany), www2gcg (EMBnet Belgium), SRS applications (EBI and Lion),
ACEDB utilities (Sanger Centre and Montpelier), Staden (Rodger Staden,
Cambridge), SeqPup (Don Gilbert, Indiana)....

I'd put AppLab in the list of programs most like Loci.  Like a couple others,
AppLab's description could be mistaken for Loci's.  The major difference,
however, is Loci's Workspace, which provides a unique (if not intuitive)
approach to distributed data processing.  Of course, AppLab is Java-based, while
Loci is mostly Python/C-based.

Loci is trying for a high degree of language independence, which AppLab gives
too by wrapping command-line programs.  But the GUI components of Loci can also
be 'written' in any language.

AppLab has a 'copyright-only' license, which makes it essentially freeware.  The
good news for Loci is that we can learn a lot from the CORBA implementation and
command-line wrapping scheme they have used.

I'd like to know if anyone on this list has actually used AppLab, besides Peter
Rice :-)

                         |        J.W. Bizzaro        |
                         |  jeff at bioinformatics.org   |
                         |                            |
                         |        THE OPEN LAB        |
                         | Open Source Bioinformatics |
                         |                            |
                         | http://bioinformatics.org/ |

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