Free cdf software for linux

Bio::Affymetrix::CDF is a Perl module to parse Affymetrix CDF files.

SYNOPSIS

use Bio::Affymetrix::CDF;

# Parse the CDF file

my $cdf=new Bio::Affymetrix::CDF({"probemode"=>0});

$cdf->parse_from_file("foo.cdf");

# Find some fun facts about this chip type

print $cdf->rows().",".$cdf->cols()."n";

print $cdf->version()."n";

# Print out all of the probeset names on this chip type

foreach my $i (keys %{$chp->probesets}) { print $chp->probesets->{$i}->name()."n"; }

The Affymetrix microarray system produces files in a variety of formats. If this means nothing to you, these modules are probably not for you :). This module parses CDF files. Use this module if you want to find out about the design of an Affymetrix GeneChip, or you need the object for another one of the modules in this package.

All of the Bio::Affymetrix modules parse a file entirely into memory. You therefore need enough memory to hold these objects. For some applications, parsing as a stream may be more appropriate- hopefully the source to these modules will give enough clues to make this an easy task. This module in particular takes a lot of memory if probe information is also stored (about 150Mb). Memory usage is not too onorous (about 15Mb) if probe level information is omitted. You can.control this by setting probemode=>1 or probemode=>0 in the constructor.

You can also use these modules to write CDF files (using the write_to_filehandle method). See COMPATIBILITY for some important caveats.

rawdog is an RSS Aggregator Without Delusions Of Grandeur. Written in Python, it uses Mark Pilgrims feed parser to read RSS 0.9, 1.0, 2.0, CDF and Atom feeds.
rawdog project runs from cron, collects articles from a number of feeds, and generates a static HTML page listing the newest articles in date order. It supports per-feed customizable update times, and uses ETags, Last-Modified, and gzip compression to minimize network bandwidth usage.
rawdogs output format is similar to that of PyDS and Hep.
Enhancements:
- This release handles "A-IM: feed" encoding in a more sensible way.
- Several other small bugs have been fixed.

bandwidthd tracks usage of TCP/IP network subnets and builds HTML files with graphs to display network utilization. Charts are built by individual IP to show their utilization over 2, 8, 45, and 400 day periods. It color codes HTTP, HTTPS, TCP, UDP, ICMP, VPN, and P2P traffic.
BandwidthD runs on most platforms including windows. For unix nex libraries are only required: libpcap, libgl and libpng.
Most of the info youre looking for is on the SourceForge project page. At SourceForge we keep all new releases, the bug tracker and the support forums.
Bandwidthd now produces output in 2 ways. The first is as a standalone application that produces static html and png output every 200 seconds. The second is as a sensor that transmits its data to a backend database which is then reported on by dynamic php pages. The visual output of both is simular, but the database driven system allows for searching, filtering, multiple sensors and custom reports.
Enhancements:
- Big Feature - Added optional postgresql database logging mode and php for dynamic graph creation from databases. Great for big sites, multiple sensors with very low overhead collect traffic statistics and log them to database. Graphs are created when a user visits the page instead of burning CPU cycles night and day. Logging/Multiple sensor support is completed.
- Big Feature - Implemented auto conf
- Ported to and compiles on:
- ix86 Fedora Core 2
- ix86 Solaris 9
- ix86 OpenBSD 3.4
- ix86 Debian 2.2
- ix86 FreeBSD 4.8
- AMD64 Fedora Core 3
- PPC MaxOsX 10.2
- ix86 Microsoft Windows
- Changed default interval to 200 seconds to save ram and cpu power
- Huge performance gain in graphing engine due to bug fix (Peak Send and Total Sent strings font operations were being done to each graphic almost 1000 times instead of just 1)
- Removed need of Sys V IPC shared memeory
- log rotation on all logs implemented - secondary logs rotate every RANGE?/RANGE1 HUPs
- Added syslog support, removed all printfs except a few early errors, closed stdin, stdout, and stderr before beginning capture loop
- Bandwidthd collects the pids of its children and distributes HUP and TERM signals when issued to the first process
- Changed yy parser name to bdconfig_ to avoid a bug in BSD
- Added some semi-colons to conf.y to fix BSD flex/bison compatability bug
- Fixed bug that caused memory corruption when ram datastore had data on more than IP_NUM ips.
- Fixed some longs that missed being converted to unsigned long long.
- Fixed bug in CDF recovery that would cause bandwidthd to ignore some CDF logs during recovery
- Bandwidthd now checks for ./etc/bandwidthd.conf, and if it doesnt exist it checks for
- /usr/local/bandwidthd/etc/bandwidthd.conf, if that exists it will htdir("/usr/local/bandwidthd")
- Fixed problem that caused bandwidthd to sit and never create graphs if graph is set to false do not store data in ram, do not fork unless output_cdf is true log names changed to be consistent so all logs could be rotated with same function

Single Marker Association is a simple tool that calculates the single marker association between individual SNP markers and a case/control dichotomy.
Usage:
The tool reads two files as input, the first is a set of case and the second a case of control haplotypes. The format of the files is one line per haplotype, where the SNP data is represented as 0 or 1, separated by white-space.
- The tool outputs a list of statistics for each marker
- The marker number (from left to right in the input data)
- The frequency of the 0 allele for the cases file
- The chi-square contingency table statistics for the marker
- The CDF of the chi-square statistics
- The p-value of the statistics (1-CDF)
Installation:
The SMA tool is written in C++. It should compile on any Unix like system. To install, download the source code and unpack it (tar xzf sma-v.tar.gz, where v is the version number of sma), then run make in the subdirectory sma-v created during unpacking.
Enhancements:
- Support for (unphased) genotype data.

XML::TMX::Writer is a Perl extension for writing TMX files.

SYNOPSIS

use XML::TMX::Writer;

my $tmx = new XML::TMX::Writer();

$tmx->start_tmx(ID => paulojjs);

$tmx->add_tu(SRCLANG => en, en => some text, pt => algum texto);
$tmx->add_tu(SRCLANG => en,
en => some text,
pt => algum texto,
-note => [32, 34 ],
-prop => { q => 23,
aut => "jj"}
);

$tmx->end_tmx();

This module provides a simple way for writing TMX files.

METHODS

The following methods are available:

new

$tmx = new XML::TMX::Writer();

Creates a new XML::TMX::Writer object

start_tmx

$tmx->start_tmx(OUTPUT => some_file.tmx);

Begins a TMX file. Several options are available:

OUTPUT

Output of the TMX, if none is defined stdout is used by default.

TOOL

Tool used to create the TMX. Defaults to XML::TMX::Writer

TOOLVERSION

Some version identification of the tool used to create the TMX. Defaults to the current module version

SEGTYPE

Segment type used in the < tu > elements. Possible values are block, paragraph, sentence and phrase. Defaults to sentence.

SRCTMF

Specifies the format of the translation memory file from which the TMX document or segment thereof have been generated.

ADMINLANG

Specifies the default language for the administrative and informative elements < note > and < prop >.

SRCLANG

Specifies the language of the source text. If a element does not have a srclang attribute specified, it uses the one defined in the element. Defaults to *all*.

DATATYPE

Specifies the type of data contained in the element. Depending on that type, you may apply different processes to the data.

The recommended values for the datatype attribute are as follow (this list is not exhaustive):

unknown
undefined
alptext
WinJoust data
cdf
Channel Definition Format
cmx
Corel CMX Format
cpp
C and C++ style text
hptag
HP-Tag
html
HTML, DHTML, etc
interleaf
Interleaf documents
ipf
IPF/BookMaster
java
Java, source and property files
javascript
JavaScript, ECMAScript scripts
lisp
Lisp
mif
Framemaker MIF, MML, etc
opentag
OpenTag data
pascal
Pascal, Delphi style text
plaintext
Plain text (default)
pm
PageMaker
rtf
Rich Text Format =item sgml
SGML
stf-f
S-Tagger for FrameMaker
stf-i
S-Tagger for Interleaf
transit
Transit data
vbscript
Visual Basic scripts
winres
Windows resources from RC, DLL, EXE
xml
XML
xptag
Quark XPressTag

SRCENCODING

All TMX documents are in Unicode. However, it is sometimes useful to know what code set was used to encode text that was converted to Unicode for purposes of interchange. This option specifies the original or preferred code set of the data of the element in case it is to be re-encoded in a non-Unicode code set. Defaults to none.

ID

Specifies the identifier of the user who created the element. Defaults to none.