Free descending software for linux

Bio::SAGE::DataProcessing module processes raw serial analysis of gene expression (SAGE) data.

SYNOPSIS

use Bio::SAGE::DataProcessing;
$sage = Bio::SAGE::DataProcessing->new();

# open sequence and quality files
open( READS, "library.fasta" );
open( QUAL, "library.qual.fasta" );

# collect ditags and statistics from reads
$sage->process_library( *READS, *QUAL );

# close files
close( READS );
close( QUAL );

# output tags in descending order of expression
my %tags = %{$sage->get_tagcounts()};
open( TAGS, ">library.tags" );
map { print TAGS join( "t", $_, $tags{$_} ) . "n" } sort { $tags{$b} $tags{$a} } keys %tags;
close( TAGS );

# tag AAACCGGGTT matches two different genes
# so 15th base pair may help resolve this
$sage->print_extra_base_calculation( $sage->get_extract_base_calculation( "AAACCGGGTT" ) );

This module provides several tools for processing and analyzing serial analysis of gene expression (SAGE) libraries.

Serial analysis of gene expression (SAGE) is a molecular technique for generating a near-global snapshot of a cell population’s transcriptome. Briefly, the technique extracts short sequences at defined positions of transcribed mRNA. These short sequences are then paired to form ditags. The ditags are concatamerized to form long sequences that are then cloned. The cloned DNA is then sequenced. Bioinformatic techniques are then employed to determine the original short tag sequences, and to derive their progenitor mRNA. The number of times a particular tag is observed can be used to quantitate the amount of a particular transcript. The original technique was described by Velculescu et al. (1995) and utilized an ~14bp sequence tag. A modified protocol was introduced by Saha et al. (2002) that produced ~21bp tags.

PURPOSE

This module facilitates the processing of SAGE data. Specifically:

1. extracting ditags from raw sequence reads.
2. extracting tags from ditags, with the option to
exclude tags if the Phred scores (described by
Ewing and Green, 1998a and Ewing et al., 1998b)
do not meet a minimum cutoff value.
3. calculating descriptive values
4. statistical analysis to determine, where possible,
additional nucleotides to extend the length of the
SAGE tag (thus facilitating more accurate tag to
gene mapping).

Both regular SAGE (14mer tag) and LongSAGE (21mer tag) are supported by this module. Future protocols should be configurable with this module.

Tete project is an ear trainer.

Tete allows you to select intervals, chords, or scales and play examples of the selected sounds in a random order.

As each is played, it is highlighted in the list. Once you think you can tell what is playing, you can test yourself.

A series of sounds will be played, again at random, and you attempt to identify what has been played.

You can control how each sound is played back by changing the MIDI instrument, the octave range allowable, the root note, and whether the sounds are played ascending or descending.

Gtk2::devel is the internal workings of the gtk2-perl language bindings.

This document is a supplement to Glib::devel, and assumes you have read and understood all about how the base Glib bindings work. Most of this will seem like nonsense, otherwise.
Here we focus on the ways in which Gtk2 extends Glibs concepts for binding the Gtk+ C libraries to perl, a methodology and set of tools you can use to wrap your own GObject-based libraries.

GtkObject

GtkObject adds the idea of a floating reference to GObject. A GObject is created with one reference which must be explicitly removed by its owner. GtkObject has a floating reference which is sunk by the code which wants to own it. This makes it less painful to create lots of objects in a row (you dont have to unref them).

To allow for this difference in procedure for taking ownership of an object, Glib allows you to register a "sink" function for a particular class. When asked to create a wrapper that owns the object, gperl_new_object will compare the list of registered sink functions with the type of the object; if the object is descended from a type, that sink function will be run on the object. The default one is g_object_unref(), of course. (this is inspired by pygtk.)
Thus, in Gtk2::Objects boot code, we register gtk_object_sink as the sink func for types derived from GtkObject. Now all wrappers for these types will be owned the proper way.

Of course, since gtk_object_sink() does nothing if the object isnt floating, it doesnt hurt anything if you always call gperl_new_object with "own" set to TRUE. So, to make life a little easier, Gtk2 defines another function

SV * gtk2perl_new_gtkobject (GtkObject * o);

Which does nothing more than

{
return gperl_new_object (G_OBJECT (o), TRUE);
}

Its also important to know that this is largely done for you by the typemap.

SharpWebMail is an ASP.NET webmail application that is written in C#. It uses a POP3 or IMAP servers as the mailstore and sends mail through a SMTP server. It is very simple to configure (only a few settings in the web.config file). This application has all the features of a normal webclient for mail. You can compose HTML messages, search your inbox, read mime messages, have multiple address books and more.
Main features:
- Very simple to configure (only a few settings in web.config).
- Multiple POP3 and IMAP servers can be configured to read mail from. The selection of the server is based in login (username) information or (optionally) by the user.
- Tries to minimize the queries to the server caching message info (only headers).
- Authentication is handled by your email server (no additional databases needed).
- Sends mail through a SMTP server (chosen from the login information of your users). Including support for SMTP AUTH.
- HTML editor (FCKeditor) for composing mails.
- Download and send multiple attachments per message (requires write permissions in a temporary folder).
- It is possible to attach a file that we have received in other message without downloading it (with the obvious save in bandwidth and time).
- Reads MIME messages (provided by SharpMimeTools, project born because I needed an open source mime decoder).
- (Optional) Multiple Address books based on fully configurable datasources (ldap, oledb, odbc, ...). It can be read-only or read/write (with import/export capabilities).
- Is possible to sort the inbox elements by number, sender, subject, date and size (ascending and descending) .
- Search the inbox by subject and sender.
- Multilingual user interface
- XP look & feel.
- Tested with IE6 and Mozilla FireFox (1.0.7), but it should work with other versions.
- Simple sanitization of html content.

Hash::NoVivify is a Perl extension for non-vivifying exists and defined functions.

SYNOPSIS

use Hash::NoVivify qw(Defined Exists);

...

if (Exists(%hash, qw(key1 key2 ... keyn ))) {
...
}

if (Defined(%hash, qw(key1 key2 ... keyn))) {
...
}

When used on a hash, the exists() and defined() functions will create entries in a hash in order to evaluate the function.

For instance, the code:

%a = (a => 1, b=> 2);
print "Doesnt existn" unless exists($a{c});
print "Also Doesnt existn" unless exists($a{c}->{d});
print "Oh, my, not goodn" if exists($a{c});

will print out:

Doesnt exist
Also Doesnt exist
Oh, my, not good

The Hash::NoVivify module provides two functions, Defined() and Exists(), which avoid this, at the cost of a slightly convoluted syntax. Both functions take a reference to a hash, followed by a list of descending keys defining the hash entry to be investigated.

Fuzzy sets for Ada is a library providing implementations of confidence factors with the operations not, and, or, xor, +, and *, classical fuzzy sets with the set-theoretic operations and the operations of the possibility theory, intuitionistic fuzzy sets with the operations on them, fuzzy logic based on the intuitionistic fuzzy sets and the possibility theory; fuzzy numbers, both integer and floating-point with conventional arithmetical operations, and linguistic variables and sets of linguistic variables with operations on them. Fuzzy sets for Ada has support for string-oriented I/O.
Main features:
- Confidence factors with the operations not, and, or, xor, +, *;
- Classical fuzzy sets with the set-theoretic operations and the operations of the possibility theory;
- Intuitionistic fuzzy sets with the operations on them;
- Fuzzy logic based on the intuitionistic fuzzy sets and the possibility theory;
- Fuzzy numbers both integer and floating-point ones with conventional arithmetical operations;
- Dimensioned fuzzy numbers;
- Linguistic variables and sets of linguistic variables with operations on them;
- String-oriented I/O is supported.
Enhancements:
- The code was tested with GNAT Ada 2005 (GCC 4.0.2 20051125).
- A bug was fixed in Fuzzy.Linguistics.Sets.Defuzzify, which led to incorrect defuzzification with a descending membership function.

MyChineseFlashCardss goal is to ease the visual and auditory memorization of the 1000 most used Chinese characters.
To reach that goal, MyChineseFlashcards allows the user to learn characters with flash cards method; to access the characters of the dictionary in random, ascending, or descending order; to filter the characters, using one of 31 available filters; and to consult statistics on characters
Main features:
- cross-platform application (Windows (XP, 2000, NT), Mac OS X and Linux.
- currently 500 characters (the remaining 500 hundred characters to come soon),
- pronunciation of the characters,
- characters and its related information can be visualized in a flash cards format or in a tabular format,
- classical or simplified character visualisation,
- 3 cards visualisation orders: random, by ascending, descending,
- three learning mode (character hiding, meaning hiding, both),
- More than 31 character filters (radical, non radical, pictogram, etc),
- graphically close characters selection,
- character type statistics,
- radicals tab,
- cards can be displayed automatically in the automatic navigation mode,
- available in English and French.