Mailman 3 September 1999 - Python-announce-list

Biopython.org (Call for Participation)
by Jeffrey Chang Sept. 23, 1999

Sept. 23, 1999

The Biopython Project (http://www.biopython.org/) is a new open collaborative effort to develop freely available Python libraries and applications that address the needs of current and future work in bioinformatics, including sequence analysis, structural biology, pathways, expression data, etc. When available, the source code will be released as open source (http://www.biopython.org/License.shtml) under terms similar to Python. This is a Call for Participation for interested people to join … [View More]

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Loci Project - for distributing bioinformatics programs and databases
by Markus Fleck Sept. 23, 1999

Sept. 23, 1999

http://theopenlab.uml.edu/loci/ The Open Lab Presents... The Loci Project Introduction Loci is an extremely modular and extensible system of clients and servers for distributing bioinformatics programs and databases. We are first of all concentrating on making GUI wrappers for command-line programs and databases that run on UNIX-type systems, of which a countless number exist. We are using the highly object-oriented scripting language Python as the base language. Despite the fact that we … [View More]are using platform-independent tools such as XML and Python, we are not concerned with making a platform-independent application. This may bother people who have traditionally developed on Windows systems, but we see an enormous void that needs to be filled: There is no highly graphical, comprehensive suite of bioinformatics tools native to UNIX. And there certainly isn't one that is free. Programs like DNAStar and MacVector are very nice commercial applications, but they are only for Windows and Macs. We say, let's take advantage of the power of UNIX, the status it has in Universities where so many command-line driven bioinformatics tools are written, and let's provide something that doesn't exist anywhere else. Below is an early production screenshot from June 19, 1999. Loci/locuses are represented by boxes connected with lines, forming a "work flow diagram". Double-clicking on a box will show or hide the actual GUI of each locus. A popup menu (from a right mouse button click) can be seen over one of the loci (bottom right). A windowlet (from a left mouse button double-click) can be seen below another (top right). Everything can be dragged and dropped, and loci can be merged to form higher level loci. [Image] Features * A system of servers and clients. * Communicates with other systems across an intra/Internet. * Allows for bioinformatics collaboratories across an intra/Internet. * Gives command-line programs and databases a consistent look and feel. * Has built-in support for sequence and structure analyses of macromolecules. * Provides native support for phylogenetics and systematics. * Includes a library of basic analysis tools. * Produces 2D vector-drawn schematics. * Treats biological data as scientific illustrations. * Provides drawing tools and a materials library for figure construction. * Tracks the system's work path with a flow chart. * Automatically logs activity to an electronic notebook. * Seamlessly integrates utilities for building applications and extending the system. * Free software! As far as graphics are concerned, the idea is to define vector graphics so that custom made schematics can be generated by the plug-in, and the plug-in developer can choose some high-level representations...sort of like graphical widgets. How is Loci developed? This project is under heavy development, and we are in need of assistance. If you are interested in contributing to Loci, please visit the Development page for more information. We are also collaborating with other free-software, bioinformatics projects: AMMP and tacg(and EMBOSS more or less). It is our desire that all projects compatible with the GNU LGPL license will become at least interoperable and hopefully combined. Modified on 21-Jun-99. Copyright (c) 1999 by The Open Lab. <A HREF="http://theopenlab.uml.edu/loci/">The Loci Project</A> - a modular and extensible system of clients and servers for distributing bioinformatics programs and databases; written in Python. (10-Sep-99) -- ----------- comp.lang.python.announce (moderated) ---------- Article Submission Address: python-announce(a)python.org Python Language Home Page: http://www.python.org/ Python Quick Help Index: http://www.python.org/Help.html ------------------------------------------------------------ [View Less]

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Pyfort Version 2 now available
by Paul F. Dubois Sept. 23, 1999

Sept. 23, 1999

Version 2 of Pyfort, a tool that lets you extend Python with Fortran, is now available. See http://xfiles.llnl.gov/python.htm. To use Pyfort, you construct an input file in a Fortran-90 like syntax. This input file contains interfaces for the functions in Fortran that are to be called. Pyfort then constructs a C-language extension module that contains the "glue" to turn Python calls into the calls to your Fortran. Example: Fortran: function sum (n, x) ! return sum of elements … [View More]of x integer n real x(n) real sum ....implementation... end function sum Pyfort input: module modsum function sum (n, x) ! return sum of elements of x integer n = size(x) real x(n) real sum end function sum end module modsum Calling sum in Python: from modsum import sum x = [1., 2., 3.] # or a Numeric array print sum(x) print sum.__doc__ #prints "return sum of elements of x" pyfort -c compiler modsum.pyf produces modsummodule.c and modsum.txt; the former is used to construct the Python extension and the latter documents the Python calling sequence. If no comment is given, the doc string is the calling sequence. Users can declare output quantities by using the intent attribute: real, intent(out):: y(n) Such an argument becomes an output of the function. If there are multiple return values, a tuple is returned. Intent "temporary" requests that an array be constructed and passed to the Fortran as a work array. Persons wanting a "raw" interface that is exactly like the Fortran routine and which does as little as possible can achieve this by declaring any array arguments or scalar outputs as intent(inout). New for version 2: Module attributes NONE, TRANSPOSE (default), MIRROR control behavior of multiple dimension intent(in) and intent(output) arrays. NONE -- pass argument as is; return array has transposed strides to "look right" in Python. TRANSPOSE -- transpose the data area on input; return array has transposed strides. A returned array subsequently used in another call as input will not in fact ever be transposed. MIRROR -- the Fortran has been written with all the dimensions reversed; check shapes backward and create output arrays with a backward shape. No data movement ever required. Method set_pyfort_option available to set the default option. Each generated wrapper can take an optional extra argument of one of these three attributes to override the default. Scalar input arguments can be given an initial value as an expression involving constants, the Fortran 90 size operator, other scalar input arguments that were not given an initial value, and scalar input arguments that occur earlier in the argument list. See argument "n" above, for example. The size operator can be size(a) or size(a, dimensionnumber) (Fortran style, 1-based). Example: subroutine doit (n, m, x, k, y, z) integer n = size(x, 1), m = size(x, 2) , k = n * m real x(n, m) real, intent(out):: y(k) complex, intent(temporary):: z(n, m) Python call: y = doit(x) The purpose of this facility is to enable the construction of "nice" interfaces without needing an additional Python layer in many cases. Pyfort has been tested under Linux using the Portland Group (-c pgf77) and g77 (-c g77) compilers, under Solaris (choose -c solaris) and SGI (-c solaris works). Potential users should note that both a Fortran and C compiler are needed. Pyfort has not yet been heavily used and bugs are possible. Documentation is in the file pyfort.pdf that comes with the package. Pyfort has been released for free redistribution. See Legal.htm. Questions to support(a)pcmdi.llnl.gov Paul F. Dubois Program for Climate Model Diagnosis and Intercomparison Lawrence Livermore National Laboratory <A HREF="http://xfiles.llnl.gov/python.htm">Pyfort 2</A> - Python/FORTRAN connection tool. (10-Sep-99) -- ----------- comp.lang.python.announce (moderated) ---------- Article Submission Address: python-announce(a)python.org Python Language Home Page: http://www.python.org/ Python Quick Help Index: http://www.python.org/Help.html ------------------------------------------------------------ [View Less]

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North Colorado UG meets Oct 19th, 1999
by Evelyn Mitchell Sept. 23, 1999

Sept. 23, 1999

http://www.lwn.net/1999/0909/a/frpythoneers.html Date: Wed, 8 Sep 1999 02:16:33 -0600 From: Evelyn Mitchell <efm(a)tummy.com> To: lwn(a)lwn.net Subject: Python UG To all: Uche Ogbuji and I were talking at the Fort Collins Linux User's Group tonight, and we thought that the time was ripe for forming a Python Group in Northern Colorado. Tell your friends, and bring good suggestions for a name. First Meeting will be October 19th at Healthy Habits Restaurant, 4760 Baseline Road, Boulder … [View More]CO (map at http://yp.yahoo.com/py/ypMap.py?Pyt=Typ&YY=20335&city=Boulder&state=CO&coun… 303-494-9177 >From the North take Foothills Parkway to Baseline, right (west) on Baseline. Healthy Habits is at the first? light on the South West corner. >From the South or East, take 36 to Boulder, turn off on Foothills Parkway, north to Baseline, left (west) on Baseline. Healthy Habits is at the first? light on the South West corner. ----- Forwarded message from Uche Ogbuji <uche.ogbuji(a)fourthought.com> ----- Date: Tue, 07 Sep 1999 22:04:22 -0600 From: Uche Ogbuji <uche.ogbuji(a)fourthought.com> Organization: FourThought LLC X-Accept-Language: en To: Evelyn Mitchell <efm(a)tummy.com> Subject: Re: Python UG Evelyn Mitchell wrote: > Well, the biggest barrier to forming a Python Users Group is > finding a good place to meet. Healthy Habits on Baseline in > Boulder has a great meeting room that is private, and a huge > selection of food. They don't charge extra for the room. > > When do you want to have the first meeting? We should give about > a month's notice, and the 3rd week of the month is best for > us (no LUGs that week). What say October 19th? Should be enough notice, and it's the 3rd week. I'm wondering what to call it. A few ideas: PURe (Python Users of the Rockies) Front Range Pythoneers (FRaP?) PUNC (Python Users of Northern Colorado) Or just the Northern Colorado Python Association, no acro necessary. I'll also think of a few ideas for first meeting topics/features to hopefully attract a decent inaugural crowd. == Uche Ogbuji FourThought LLC, IT Consultants uche.ogbuji(a)fourthought.com (970)481-0805 Software engineering, project management, Intranets and Extranets http://FourThought.com http://OpenTechnology.org ----- End forwarded message ----- -- http://www.tummy.com/ Consulting and Software for Linux and Unix XVScan - Scanning software for Linux, HP-UX, Solaris, FreeBSD and BSD/OS Northern Colorado Python Users Group. The first meeting will be on October 19th at Healthy Habits Restaurant, 4760 Baseline Road, Boulder CO. (08-Sep-99) -- ----------- comp.lang.python.announce (moderated) ---------- Article Submission Address: python-announce(a)python.org Python Language Home Page: http://www.python.org/ Python Quick Help Index: http://www.python.org/Help.html ------------------------------------------------------------ [View Less]

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COMMERCIAL: Zeus for Windows Programmer's Editor
by Jussi Jumppanen Sept. 23, 1999

Sept. 23, 1999

Zeus for Windows Version 3.00 Now Released ------------------------------------------ The Zeus for Windows programmer's editor has been totally re-developed and the results of this full re-write are now ready for use. The Programmer's is designed to run on the Windows 95, Windows 98 or NT platforms. So what is new: 1) New syntax highlighting engine should now support almost any language. 2) Comes with pre-configured syntax highlighting for: C/C++, Java, Perl,… [View More]

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Python snippets site has moved!
by Hans Nowak Sept. 23, 1999

Sept. 23, 1999

Due to problems with my previous host (hvision.nl), which has proven to be more than a little unstable, I deciced to move my snippets site. The new URL is http://tor.dhs.org/~zephyrfalcon/snippets/ Thanks to Blake Winton for offering me the account and the web space. (Lots of people suggested the Python Starship as the new snippet home, but I am not a PSA member. :-/ ) I will remove the HTML from the old address as soon as possible. By the way, I haven't been able to add any new … [View More]

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New Czech Python Web Site
by Tomas Kouba Sept. 23, 1999

Sept. 23, 1999

New web site in Czech about Python: http://www.python.cz ------------------------------ Tomas Kouba mailto:tomas@neo.cz <A HREF="http://www.python.cz">Czech Python Web Site</A> - new web site in Czech about Python. (07-Sep-99) -- ----------- comp.lang.python.announce (moderated) ---------- Article Submission Address: python-announce(a)python.org Python Language Home Page: http://www.python.org/ Python Quick Help Index: http://www.python.org/Help.html ------------------------------------------------------------

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LORAX -- new Red Hat installation procedure written in Python
by Patrick Phalen Sept. 23, 1999

Sept. 23, 1999

---------- Forwarded Message ---------- Subject: LORAX: Red Hat Linux Beta Release Date: Mon, 6 Sep 1999 18:08:56 -0400 (EDT) From: Cristian Gafton <gafton(a)redhat.com> For the brave... the reckless... the foolish... those with extra hard disks... those with too much free time... those who miss fixing their own bugs... people who want to hack device drivers... people who need to see exceptions... and people who think Linux has gotten too easy... … [View More]

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CVS Access to source code for Python for Windows Extensions
by Mark Hammond Sept. 23, 1999

Sept. 23, 1999

All source code for the Python for Windows extensions are now being managed by CVS. Anyone can use anonymous access to ensure they always have the most recent sources available. There is also a "checkins" mailing list provided, so you can be informed of all CVS checkins made into this repository as they happen (or daily if you use the digest mode!) All the gory details can be found via http://starship.python.net/crew/mhammond/cvs.html Many thanks to the Python Pros (http://www.pythonpros.… [View More]

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COMMERCIAL: GRiNS 1.0 (Multimedia authoring software in Python) available
by Sjoerd Mullender Sept. 23, 1999

Sept. 23, 1999

This is a commercial announcement. Oratrix Development BV is proud to announce the release of version 1.0 of the GRiNS Editor and Player for SMIL. The GRiNS Editor for SMIL is a tool to create, edit, and preview multimedia presentations for Web delivery. The free GRiNS Player for SMIL allows you to preview the presentations. Presentations created with GRiNS can be played with the Real Networks RealPlayer G2. GRiNS uses the Synchronized Multimedia Interchange Language (SMIL -- see http://… [View More]

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