From owner-comp-bio@hgmp.mrc.ac.uk Wed Feb 14 19:01:26 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 85D7D17B72; Wed, 14 Feb 2001 19:01:24 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6023) id BC04B17AC6; Wed, 14 Feb 2001 19:01:21 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 849F317AF2; Wed, 14 Feb 2001 09:49:33 +0000 (GMT) Received: from mr1.ash.ops.us.uu.net (mr1.ash.ops.us.uu.net [198.5.241.86]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C23DC4161A for ; Wed, 14 Feb 2001 09:49:26 +0000 (GMT) Received: from mail.fu-berlin.de by mr1.ash.ops.us.uu.net with ESMTP (peer crosschecked as: mail.fu-berlin.de [160.45.11.165]) id QQkchz12205 for ; Wed, 14 Feb 2001 09:49:25 GMT Received: by mail.fu-berlin.de (Smail3.2.0.98) from Curry.ZEDAT.FU-Berlin.DE (160.45.10.36) with esmtp id ; Wed, 14 Feb 2001 10:49:24 +0100 (MET) Received: by Curry.ZEDAT.FU-Berlin.DE (Smail3.2.0.98) from news.fu-berlin.de with bsmtp id ; Wed, 14 Feb 2001 10:49:24 +0100 (MET) To: bionet-biology-computational@moderators.isc.org From: January Weiner Newsgroups: bionet.biology.computational Subject: Re: GP and Arka -- software for molecular biology Message-ID: <96dkb3$kivfs$2@fu-berlin.de> References: <9611l1$ja7gd$1@fu-berlin.de> <96aunu$4ej$1@niobium.hgmp.mrc.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-2 Content-Transfer-Encoding: 8bit X-Trace: fu-berlin.de 982144164 21593596 129.206.119.41 (16 1086 1089 1090) X-Organization: Klub Nieszkodliwych Manjakow X-KNM: http://www.knm.org.pl/ X-KF: http://www . rzuser.uni-heidelberg.de/~jweiner1/filter User-Agent: tin/pre-1.4-981002 ("Phobia") (UNIX) (AIX/4-2) Date: Wed, 14 Feb 2001 19:01:21 +0000 (GMT) Sender: owner-comp-bio@hgmp.mrc.ac.uk Precedence: bulk [ Gary Williams ] > I was very interested to hear of your bioinformatics package. > We are doing something very similar - EMBOSS > http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ Wow, seems like I was forcing an open door. I should have examined the SAL database more carefully. Why didn't you put your package into the freshmeat database? > EMBOSS is a collection of Open Source command line tools written in ANSI C. > You might like to join our project, or contribute some software to it? Well, we have compatible licenses, and it shouldn't be very hard. BTW, I see that Peter Rice is working at LION Bioscience, and our group has a collaboration with this company -- interesting. One thing about my programs is that I try to keep them as ANSI and lightweight as possible. I will definitely download your developer tree and look at the source. > We are always interested in GUIs for EMBOSS. > Could Arka be adapted to be an interface to EMBOSS? Why, yes, quite easily. Basically, it is a very simple thing: you have three windows -- stdin, stderr and stdout. You can save or modify them. Then, you have a sort of database holding information about my command-line tools programs: names, options, short descriptions of the programs and options etc. Right now it is hard-wired into the program, but the next version will just read a configuration file which will be much more flexible. You can run any program included in the "database" or issue an arbitrary command -- you have a command history (stored before exiting) and I plan to extend it to build little "macros" which will be in fact just /bin/bash scripts. Apart from that, there are two graphical utilities: one for showing simple GC content graphs (which I did for learning to program gtk+) and one for showing 3D graphs of arbitrary data (which I did because I needed to visualize DNA structures). Unfortunately, Arka is not portable. This is gtk+, and though there is gtk+ in Windows, there is also a lot of Unix-specific code in my program, so basically Arka is Linux-specific. Best regards, January -- ----)-\//-///-----------------------------------January-Weiner-3------- AG Herrmann, Zentrum für Molekulare Biologie, Universität Heidelberg Im Neuenheimer Feld 282, 69120 Heidelberg Tel. (+49 6221) 546828, Fax 545893 http://www.zmbh.uni-heidelberg.de/M_pneumoniae/ .