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Bio::NEXUS::WeightSet 0.67

Bio::NEXUS::WeightSet 0.67


Bio::NEXUS::WeightSet is a Perl module that represents column weights in alignment ( for each character). more>>
Bio::NEXUS::WeightSet is a Perl module that represents column weights in alignment ( for each character).

SYNOPSIS

new Bio::NEXUS::WeightSet($name, @weights, $iswt);

A module representing column weights in alignment (for each character)

METHODS

new

Title : new
Usage : $node = new Bio::NEXUS::WeightSet($name, @weights);
Function: Creates a new Bio::NEXUS::WeightSet object
Returns : Bio::NEXUS::WeightSet object
Args : none

set_weights

Title : set_weights
Usage : $weight->set_weights(@weights);
Function: stores it in the list weights
Returns : none
Args : list of weights

get_weights

Title : get_weights
Usage : @wts=@{$weightset->get_weights()};
Function: Returns the weights array
Returns : reference to array containing weights
Args : none

select_weights

Title : select_weights
Usage : $set->select_weights($columns);
Function: select a subset of characters
Returns : new self with subset of weights
Args : column numbers

is_wt

Title : is_wt
Usage : croak unless $weight->is_wt();
Function: Returns if object has weights (1 yes, 0 no)
Returns : weight existence (integer)
Args : none

set_name

Title : set_name
Usage : $weight->set_name($name);
Function: Sets the name of the weightset
Returns : none
Args : name (string)

get_name

Title : get_name
Usage : $name=$weight->get_name();
Function: Returns the name of the weightset
Returns : name (string)
Args : none

equals

Name : equals
Usage : $set->equals($another);
Function: compare if two WeightSet objects are equal
Returns : boolean
Args : an WeightSet object

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Download (0.15MB)
Added: 2006-12-19 License: Perl Artistic License Price:
1039 downloads
Graph::Weighted 0.1301

Graph::Weighted 0.1301


Graph::Weighted is an abstract, weighted graph implementation. more>>
Graph::Weighted is an abstract, weighted graph implementation.

SYNOPSIS

use Graph::Weighted;

$g = Graph::Weighted->new(
data => [
[ 0, 1, 2, 0, 0 ], # A vertex with two edges.
[ 1, 0, 3, 0, 0 ], # "
[ 2, 3, 0, 0, 0 ], # "
[ 0, 0, 1, 0, 0 ], # A vertex with one edge.
[ 0, 0, 0, 0, 0 ] # A vertex with no edges.
]
);

$g = Graph::Weighted->new(
data => {
weight => {
a => { b => 1, c => 2 }, # A vertex with two edges.
b => { a => 1, c => 3 }, # "
c => { a => 2, b => 3 }, # "
d => { c => 1 }, # A vertex with one edge.
e => {} # A vertex with no edges.
}
foo => [
[ 1, 2, 3 ],
[ 4, 5, 6 ],
[ 7, 8, 9 ]
],
}
);

$g = Graph::Weighted->new(
data => $Math_Matrix_object,
retrieve_as => ARRAY,
);

$data = $g->weight_data;

$w = $g->graph_weight;

$w = $g->vertex_weight($v1);
$w = $g->vertex_weight($v1, $w + 1);

$w = $g->edge_weight($v1, $v2);
$w = $g->edge_weight($v1, $v2, $w + 1);

$vertices = $g->heaviest_vertices;
$vertices = $g->lightest_vertices;

$w = $g->max_weight; # Weight of the largest vertices.
$w = $g->min_weight; # Weight of the smallest vertices.

# Call the weight methods of the inherited Graph module.
$x = $g->MST_Kruskal;
$x = $g->APSP_Floyd_Warshall;
$x = $g->MST_Prim($p);

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Download (0.011MB)
Added: 2007-08-07 License: Perl Artistic License Price:
812 downloads
Weight Loss Recipe Book 3.1

Weight Loss Recipe Book 3.1


Weight Loss Recipe Book is a free, online, community-built recipe book. more>>
Weight Loss Recipe Book is a free, online, community-built recipe book. Weight Loss Recipe Book contains everything you need to allow your web site visitors to submit recipes and everything your administrator needs to administer the recipes.
When a visitor submits a recipe, the recipe is added to a database and awaits approval from the administrator before being added to the public site.
Main features:
- Community built, meaning you just have to approve entries and watch your web site expand!
- Captcha validation to prevent automated entries into the recipe book.
- Complete administrator system - add administrators, recipe categories, manage recipes and more!
- Best of all, Weight Loss Recipe Book is totally free!
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Download (0.061MB)
Added: 2006-05-08 License: Freeware Price:
1267 downloads
SmokePing 2.1.0

SmokePing 2.1.0


SmokePing is a network latency monitor similar to MRTG. more>>
SmokePing is a delux latency measurement tool. SmokePing project can measure, store and display latency, latency distribution and packet loss. SmokePing uses RRDtool to maintain a longterm datastore and to draw pretty graphs, giving up to the minute information on the state of each network connection.
SmokePing uses latency measurement plugins for seamless extendability.
SmokePing comes with a smart alarm system. Apart from simple threshold alarms, you have the option of defining latency or loss patterns and use them to trigger alarms.
This allows you to define a pattern which would generate a single alarm when the loss goes from below 1% to over 20% and stays over 20% for more than 10 minutes. The advantage of this approach is the virtual elimination of duplicate alarms which you would get with a simple threshold based system.
Alarms can be sent to a mail address or a pager and if you want you can also start an external script to handle the alarms.
Complex Alarms can be written as plug-ins.
SmokePing can also deal with machines who frequently change their IP address by allowing the remote host to call SmokePings attention to its new IP address. In such a setup SmokePing monitors also for how long the remote system could keep its IP address.
To ensure that it is not suddenly monitoring the wrong host, SmokePing further tries to fingerprint each of its Dynamic IP targets via SNMP.
SmokePing is written in Perl. It consists of a daemon process responsible for data collection and a CGI script presenting the data on the web.
The CGI script uses SpeedyCGI to achieve mod_perl like performance without the need to deploy mod_perl on your web server. SmokePing sports a plug-in architecture to easily add new latency measurement capabilities to SmokePing. SmokePing works happily on all Unix platforms.
Enhancements:
- The scoreboard has a list of hottest targets.
- Echoping V6 compatibility.
- Mail templates.
- A failover server for alert email messages.
- Many new plugins.
- Several bugfixes.
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Download (0.37MB)
Added: 2007-04-29 License: GPL (GNU General Public License) Price:
922 downloads
CLC Free Workbench 4.0

CLC Free Workbench 4.0


Bioinformatics program for DNA, RNA, and protein sequence analysis more>>
CLC Free Workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management, combined with excellent graphical viewing and output options.
Main features:
- GenBank searching and viewing (linear and circular views)
- Multiple alignment of DNA, RNA and proteins (2 alignment algorithms)
- Open reading frame determination
- Translation from DNA to proteins (all genetic translation tables)
- Reports with residue composition, molecular weight and iso electric point (for proteins)
- Neighbor-joining and UPGMA phylogenies
- Restriction site analysis and viewing
- Other reporting facilities
- Import/export to a number of data formats
- Launch of external files
- Detailed History Log
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Download (45.1MB)
Added: 2007-06-28 License: Freeware Price:
849 downloads
UMLet 7.1

UMLet 7.1


UMLet is a lightweight tool for rapidly drawing UML diagrams. more>>
UMLet project is an open-source Java tool for rapidly drawing UML diagrams with a pop-up-free, light-weight user interface.
UMLet lets you draw diagram sketches fast; export diagrams to eps, pdf, jpg, svg, and sys.
Add elements to a diagram with a double click. Edit elements using the lower-right text panel. Select multiple elements using Ctrl or lasso. Press C to copy diagram to the system clipboard
Main features:
- fast
- text-based sequence diagram
- call from command line.
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Download (4.9MB)
Added: 2006-11-22 License: GPL (GNU General Public License) Price:
657 downloads
Chaos Visualization 0.9

Chaos Visualization 0.9


Chaos Visualization is a program for quickly calculating the amount of predictability in a very simple system. more>>
Chaos Visualization is a program for quickly calculating the amount of predictability in a very simple system: a spring with one side connected to the origin and the other to a weight under gravity.

This amount is chaos is visualized in TIFF images, which can be put in a sequence to show the evolution of chaotic behaviour in this system.

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Added: 2006-10-30 License: GPL (GNU General Public License) Price:
1095 downloads
lwIP 0.5.3

lwIP 0.5.3


LwIP is a light-weight implementation of the TCP/IP protocol suite. more>>
lwIP is a light-weight implementation of the TCP/IP protocol suite that was originally written by Adam Dunkels of the Swedish Institute of Computer Science but now is being actively developed by a team of developers distributed world-wide headed by Leon Woestenberg.
Since its release, lwIP very interesting and and today is being used in many commercial products. lwIP has been ported to several platforms and operating systems and can be run either with or without an underlying OS.
The focus of the lwIP TCP/IP implementation is to reduce the RAM usage while still having a full scale TCP. This makes lwIP suitable for use in embedded systems with tens of kilobytes of free RAM and room for around 40 kilobytes of code ROM.
Main features:
- IP (Internet Protocol) including packet forwarding over multiple network interfaces
- ICMP (Internet Control Message Protocol) for network maintenance and debugging
- UDP (User Datagram Protocol) for datagram data
- TCP (Transmission Control Protocol) with congestion control, RTT estimation and fast recovery/fast retransmit
- Specialized no-copy API for enhanced performance
- Optional Berkeley socket API
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Added: 2006-07-03 License: Freeware Price:
1210 downloads
lfwmail 2.4

lfwmail 2.4


lfwmail is a light weight web mail program written in perl. more>>
lfwmail is a light weight web mail program written in perl.
It will run with acceptable speed even on a Pentium 100Mhz Linux mailserver.
It has just basic features and no calendar or folders but it is fully
mime compatible and can handle attachments.
If you dont like browser cookies, this program is very suitable for you, because you dont have to enable cookies.
It is also very secure when you use https (encryption). HTML
mails are converted to ASCII text for security reasons but
you can still see the HTML mail if you want.
The code is clean and structured. Installation is straight forward
and you dont need a lot of non standard modules.
You can run it in mod_perl if you want. Remember to restart the
server when you do changes in the lfwmC.pm or any other file.
Response time will be very fast with mod_perl however for most people
normal cgi-bin will be good enough. lfwmail is already quite fast.
lfwmail is a light weight mail program. It does not keep track on what
you have read and what is new. You have to remember the dates of the
mails. There is however a small help to keep track on what you have seen
and what is new. It works for Mozilla (not netscape 4), Opera and MS IE
only as it depends on javascript style objects: the background color of e-mails
you have clicked on is changed. This is to keep track on what you have
read and what is new. This information does also survive between sessions since
version 1.5.
Enhancements:
- make it possible to call lfwmail with uid=xxx in the url. e.g https://my.host/cgi-perl/lfwmail?uid=joe_wm
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Download (0.019MB)
Added: 2006-06-10 License: GPL (GNU General Public License) Price:
1231 downloads
Orpheus 1.6

Orpheus 1.6


Orpheus is a light-weight text mode menu- and window-driven audio player application for CDs. more>>
Orpheus is a light-weight text mode menu- and window-driven audio player application for CDs, MP3, Vorbis OGG and internet stream broadcasts.
Main features:
Text mode user interface
- Based on the ncurses library
- Provides windows, menus and dialogs
- Configurable color schemes
- Configuration is done with dialogs
Player
- Supports MP3 (through mpg123), OGG (with ogg123), CD tracks and internet broadcasts
- Saves and loads playlists
- Provides quick access to recent lists played
- Can combine CD, MP3 and OGG tracks in the same playlist
- Edit MP3 and OGG ID tags feature
- "Repeat track", "Repeat play list" and "Random" play modes
- Play list sorting and search options
- Auto-generated currently_playing file which makes it possible to easily find out from other applications what is playing now
- Internal mixer controller
- Command line interface for controlling an already running instance of the program
Network
- CDDB information retrieval for CDs
- HTTP proxy support
- Auto-load of the Internet radio presets directory from the network
Enhancements:
- This release converts from utf-8 for OGG tracks and supports Internet radio.
- Broadcasts can now be added to the playlist along with the other items.
- For the initial stations directory, the presets directory from the screamer-radio project is used.
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Download (0.20MB)
Added: 2006-05-15 License: GPL (GNU General Public License) Price:
1260 downloads
Kate OS 3.2

Kate OS 3.2


Kate OS is an independently developed light-weight Linux distribution. Some of its concepts were derived from Slackware Linux. more>>
Kate OS is an independently developed light-weight Linux distribution. Some of its concepts were derived from Slackware Linux.
Enhancements:
- Kate OS 3.2 is the third edition of the III series. It brings, as usual, many fixes, updates, and novelties the community has been waiting for. It includes a new graphical package management tool, KatePKG, which allows for easy and intuitive installation, removal, and updating of packages. KatePKG can handle any number of repositories, including user-created ones on the local drive. KatePKG was written in PHP using the PHP-GTK2 library. Kate OS 3.2 uses glibc library 2.5 which ensures binary compatibility with future editions. It also includes the Xfce environment version 4.4RC2, GNOME 2.16.2, KDE 3.5.5, OpenOffice.org 2.0.4, Firefox 2.0, and many other current applications.
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Download (697MB)
Added: 2006-12-22 License: GPL (GNU General Public License) Price:
1063 downloads
Kemistry 0.7

Kemistry 0.7


Kemistry is a collection of chemistry applications for the K Desktop Environment. more>>
Kemistry is a collection of chemical applications for the K Desktop Environment (release 3.x).

Originally the applications were distributed in a single source package, but currently every application is distributed in a standalone package. The available applications are

* KMolCalc - molecular weight and elemental composition calculator
* KemBabel - a file conversion program based on Open Babel
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Download (1.15MB)
Added: 2005-04-01 License: GPL (GNU General Public License) Price:
1666 downloads
KoffeePhoto 1.1 Beta

KoffeePhoto 1.1 Beta


KoffeePhoto is a free software that allows you to manage your personal photo library. more>>
KoffeePhoto is a free software that allows you to manage your personal photo library. You can manage your photo albums with KoffeePhoto, and share them with your friends or family very easily. Your albums will be saved on the KoffeePhoto network, which will let you access them anytime and anywhere.

KoffeePhoto allows you to pick your photos on your hard disk or on your camera, and to organize them in albums. Thanks to several ways of sorting your photos, by date, topic, place, person, or any combination of these categories, you will always have an easy way to find all your photos again.

KoffeePhoto saves your whole photo library on its peer-to-peer KoffeePhoto network. This is carried out in a completely seamless way. Your photos are encrypted to ensure confidentiality, and are saved without any loss in quality (no format reduction, no data compression), and no storage expiration date. You can access your photo library from several computers if you wish. In case of any data loss, you can recover your whole photo library very easily!

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Download (0.003MB)
Added: 2006-10-20 License: Freeware Price:
1174 downloads
subPersistence 0.10.0

subPersistence 0.10.0


subPersistence is an abstract, light-weight, yet flexible framework for working with O/R persistence mappers. more>>
subPersistence is an abstract, light-weight yet flexible framework for working with O/R persistence mappers. It provides for independence of a specific O/R mapper such as Hibernate or Castor.
While you can use Hibernate or Castor (or other O/R mappers) directly, coupling your application too tightly to those can be a bad thing. subPersistence makes it easy to switch underlying O/R mappers, thereby decoupling the application layer from those.
It abstracts away differences between the mappers, while still making it possible to use their specific features if needed.
Enhancements:
- This version updates to Java 5 features such as Generics and is the first version to require Hibernate 3.
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Download (0.040MB)
Added: 2005-07-01 License: GPL (GNU General Public License) Price:
1575 downloads
StepStats 1.0

StepStats 1.0


StepStats is a smart and simple application that allows you to keep track of your sport successes. more>>
StepStats is a smart and simple application that allows you to keep track of your sport successes. The application is perfectly suitable for all sports, where you want to create stats on distance, time or speed.
Main features:
- simple, understandable interface
- keeps track of date, distance, steps and time
- gives you stats with overall values and a nice graph with your speed
- automatic backup of your data once a week to prevent data loss or corruption
- available for MacOS X, Windows and Linux
- and best of all - It is Freeware
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Download (2.5MB)
Added: 2007-08-06 License: Freeware Price:
809 downloads
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