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Sequence Analysis 1.6.0

Sequence Analysis 1.6.0


Sequence Analysis project is a collage of coding projects. more>>
Sequence Analysis project is a collage of coding projects which I have written over the past several years for various clients in my work as a bioinformatics consultant.

These clients have graciously allowed me to release these works into the public domain as freeware for Macintosh OS X in order to promote the platform and to encourage migration from Classic.

The upper window panel can hold several sequences, which are both editable and selectable. The tabs in the lower analysis panel try to keep up with the current sequence selection to provide immediate feedback. The selection is used in some modules as only the portion being analyzed for other modules i.e. Digest is used to determine if enzymes cut in the in or outside of the selection.

Most commonly available sequence formats have been reverse engineered. You can also access a sequences from the NCBI via its GID or UID. This currently cannot be done from behind a firewall.

Most of the analyses are simple enough that they are obvious to use, Composition, pI. Others could stand some documenation i.e. Pairwise and Primer Design. The Publish tab uses a string to control the layout. Click on the Legend button for some help.

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Added: 2006-01-18 License: Freeware Price:
1377 downloads
Market Analysis System 1.6.6t3

Market Analysis System 1.6.6t3


Market Analysis System (MAS) is an open-source software application that provides tools for analysis of financial markets. more>>
Market Analysis System (MAS) is an open-source software application that provides tools for analysis of financial markets using technical analysis.
Market Analysis System provides facilities for stock charting and futures charting, including price, volume, and a wide range of technical analysis indicators. Market Analysis System also allows automated processing of market data - applying technical analysis indicators with user-selected criteria to market data to automatically generate trading signals - and can be used as the main component of a sophisticated trading system.
Main features:
- Includes basic technical analysis indicators, such as Simple Moving Average, Exponential Moving Average, Stochastic, MACD, RSI, On Balance Volume, and Momentum.
- Includes more advanced indicators, such as Standard Deviation, Slope of EMA of Volume, Slope of MACD Signal Line, Bollinger Bands, and Parabolic SAR.
- User can create new technical analysis indicators, including complex indicators based on existing indicators.
- User can configure criteria for automated trading-signal generation.
- Creation of weekly, monthly, quarterly, and yearly data from daily data.
- Handles intraday data.
- Handles stock and futures data.
- Accepts input data from files, from a database, or from the web. (Includes a configuration for obtaining end-of-day data from yahoo.com.)
- Can be configured and run as a server that provides services for several clients at a time running on remote machines.
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Added: 2006-05-24 License: LGPL (GNU Lesser General Public License) Price:
1260 downloads
Net::Analysis 0.04

Net::Analysis 0.04


Net::Analysis are modules for analysing network traffic. more>>
Net::Analysis are modules for analysing network traffic.

SYNOPSIS

Using an existing analyser:

$ perl -MNet::Analysis -e main help
$ perl -MNet::Analysis -e main TCP,v=1 dump.tcp - basic TCP info
$ perl -MNet::Analysis -e main HTTP,v=1 dump.tcp - HTTP stuff
$ perl -MNet::Analysis -e main Example2,regex=img dump.tcp - run an example

Writing your own analyser:

package MyExample;
use base qw(Net::Analysis::Listener::Base);
# Listen to events from other modules
sub tcp_monologue {
my ($self, $args) = @_;
my ($mono) = $args->{monologue};
my $t = $mono->t_elapsed()->as_number();
my $l = $mono->length();
# Emit your own event
$self->emit(name => example_event,
args => { kb_sec => ($t) ? $l/($t*1024) : N/A }
);
}
# Process your own event
sub example_event {
my ($self, $args) = @_;
printf "Bandwidth: %10.2f KB/secn", $args->{kb_sec};
}
1;
__top

ABSTRACT

Net::Analysis is a suite of modules that parse tcpdump files, reconstruct TCP sessions from the packets, and provide a very lightweight framework for writing protocol anaylsers.
__top

I wanted a batch version of Ethereal in Perl, so I could:

- sift through parsed protocols with structured filters
- write custom reports that mixed events from multiple protocols

So here it is. Net::Analysis is a stack of protocol handlers that emit, and listen for, events.

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Added: 2006-07-27 License: Perl Artistic License Price:
1185 downloads
TA-Lib : Technical Analysis Library 0.3.0

TA-Lib : Technical Analysis Library 0.3.0


TA-Lib provides common functions for the technical analysis of stock/future/commodity market data. more>>
TA-Lib provides common functions for the technical analysis of stock/future/commodity market data.
TA-Lib can be reused by trading software developers using Excel, .NET, Java, Perl or C/C++.
Main features:
- More than 120 technical analysis indicators such as ADX, MACD, RSI, Stochastic, Bollinger Bands etc...
- bullet Includes candlestick pattern recognition.
- bullet Optional abstract interface allowing your code to support new technical analysis functions without any code change!
Enhancements:
New Features
- New Functions: BETA, MINMAX, MINMAXINDEX, MININDEX, MAXINDEX
- Debian and RPM packaging available.
- Java JAR packaging available.
- New TA_FunctionDescription() returns XML description of API.
- New ta_func_api.xml file generated in root directory of the package.
- Support for unmanaged static libraries with Visual Studio 2005.
Fixes
- #1526632 : Fix bug in LINEARREG_ANGLE
- #1544555 : Now do proper divide by zero detection in TA_ADX
Other Changes
- Better Java/.NET naming convention.
- ta_func_list.txt moved in root directory of the package.
- Removed dependencies on trio and Mersenne Twister functions.
- Volume and Open Interest are now double instead of integers.
- Add license specific to Excel users.
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Added: 2007-01-31 License: BSD License Price:
1002 downloads
Statistical Traffic Analysis Kit 1.0b2

Statistical Traffic Analysis Kit 1.0b2


Statistical Traffic Analysis Kit is a set of command-line traffic analysis tools. more>>
Statistical Traffic Analysis Kit is a set of command-line traffic analysis tools, designed to help a network administrator to see what is happening at a router at the moment.

Unlike tcpdump (1), the stak set uses statistical and stream-oriented methods, and will rarely produce an output stream at a speed beyond human perception. The output is less accurate.

The kit consists of five different utilities, designed to perform the following tasks:
estimating overall traffic rates (stakrate),
determining network nodes generating the highest traffic (stakhosts)
monitoring the amount of traffic exchanged with particular autonomous
systems (stakasta),
extracting strings from packets (stakextract),
determining connections and flows generating the highest traffic
(stakstreams, experimental),

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Added: 2006-06-29 License: GPL (GNU General Public License) Price:
1219 downloads
Basic Analysis and Security Engine 1.2

Basic Analysis and Security Engine 1.2


BASE is the Basic Analysis and Security Engine. more>>
BASE is the Basic Analysis and Security Engine. It is based on the code from the Analysis Console for Intrusion Databases (ACID) project.
This application provides a web front-end to query and analyze the alerts coming from a SNORT IDS system.
BASE is a web interface to perform analysis of intrusions that snort has detected on your network. It uses a user authentication and role-base system, so that you as the security admin can decide what and how much information each user can see. It also has a simple to use, web-based setup program for people not comfortable with editing files directly.
BASE is supported by a group of volunteers. They are available to answer any questions you may have or help you out in setting up your system. They are also skilled in intrusion detection systems and make use of that knowledge in the development of BASE.
Enhancements:
- This release fixes a number of bugs with PHP 5.
- It also adds a number of new features.
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Added: 2005-10-10 License: GPL (GNU General Public License) Price:
1482 downloads
Directory Analysis Tool 0.0.2

Directory Analysis Tool 0.0.2


Directory Analysis Tool is used to analyze LDAP directories and report on their contents. more>>
Directory Analysis Tool is used to analyze LDAP directories and report on their contents.

Useful if you want to find inactive accounts, people who havent changed passwords, or who has administrator privileges.

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Added: 2006-06-26 License: GPL (GNU General Public License) Price:
1219 downloads
Network Security Analysis Tool 1.5

Network Security Analysis Tool 1.5


Network Security Analysis Tool is a fast, stable bulk security scanner designed to audit remote network services. more>>
Network Security Analysis Tool is a fast, stable bulk security scanner designed to audit remote network services and check for versions, security problems, gather information about the servers and the machine, and much more.

A manpage providing extensive information on NSAT has been included in the distribution. It is available after a make install, or just by typing man doc/nsat.8 from this dir. It is suggested that you inform yourself at least about the -v (scan verbosity) option and edit the configuration file. To learn about changes in this version, please consult doc/CHANGES.

New to this version is support for distributed scanning. The manpage describes how to do a distributed scan. Note that distributed scanning in this version is just a preliminary, proof-of-concept, implementation with no guarantees for its security, reliability, or performance.

Check for updated vulnerability lists, config files, etc. from
http://nsat.sourceforge.net

Currently, these are lists of vulnerabilities:

nsat.cgi (CGI scripts)
nsat.conf (configuration)
src/mod/snmp.h (SNMP community names)
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Download (0.40MB)
Added: 2006-07-14 License: GPL (GNU General Public License) Price:
1204 downloads
UMLGraph 4.8

UMLGraph 4.8


UMLGraph facilitates the declarative specification and drawing of UML class and sequence diagrams. more>>
UMLGraph facilitates the declarative specification and drawing of UML class and sequence diagrams.
One can specify a class design using the Java syntax complemented by Javadoc tags.
Running the UmlGraph doclet on the specification generates a Graphviz diagram specification that can be automatically processed to create Postscript, GIF, SVG, JPEG, fig, or Framemaker drawings.
Similarly, sequence diagrams are specified using declarative pic macros and compiled with the GNU plotutils pic2plot program into a PNG, PNM, (pseudo) GIF, SVG, AI, Postscript, CGM, FIG, PCL, HPGL, Regis, or TEK drawing.
Enhancements:
- This version improves its invocation interface so that it can be run directly as a jar file.
- It has support for sending results to the standard output for direct piping into dot.
- The distribution includes an example shell script and batch file for invoking UMLGraph.
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Added: 2007-05-10 License: BSD License Price:
900 downloads
Plucene::Analysis::PorterStemFilter 1.25

Plucene::Analysis::PorterStemFilter 1.25


Plucene::Analysis::PorterStemFilter - Porter stemming on the token stream. more>>
Plucene::Analysis::PorterStemFilter - Porter stemming on the token stream.

SYNOPSIS

# isa Plucene::Analysis:::TokenFilter

my $token = $porter_stem_filter->next;

This class transforms the token stream as per the Porter stemming algorithm.
Note: the input to the stemming filter must already be in lower case, so you will need to use LowerCaseFilter or LowerCaseTokenizer farther down the Tokenizer chain in order for this to work properly!

The Porter Stemmer implements Porter Algorithm for normalization of English words by stripping their extensions and is used to generalize the searches. For example, the Porter algorithm maps both search and searching (as well as searchnessing) to search such that a query for search will also match documents that contains the word searching.

Note that the Porter algorithm is specific to the English language and may give unpredictable results for other languages. Also, make sure to use the same analyzer during the indexing and the searching.

You can find more information on the Porter algorithm at www.tartarus.org/~martin/PorterStemmer.

A nice online demonstration of the Porter algorithm is available at www.scs.carleton.ca/~dquesnel/java/stuff/PorterApplet.html.

METHODS

next

my $token = $porter_stem_filter->next;

Returns the next input token, after being stemmed.

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Added: 2007-06-11 License: Perl Artistic License Price:
865 downloads
Analysis of Reinforced Concrete Elements 0.2

Analysis of Reinforced Concrete Elements 0.2


Analysis of Reinforced Concrete Elements will assist its user to find out capacity of various Reinforced Concrete Elements. more>>
Analysis of Reinforced Concrete Elements will assist its user to find out capacity of various Reinforced Concrete Structural Elements.

The following professionals are the target audience:

Structural Engineers
Civil Engineers
Architect
Builders

Installation:

The software is web-based, so you need web-server (Apache) running with PHP. The installaton is very simple. If your document root is /var/www/html , then on uncompressing downloaded compressed file in this "document root", the URL for ARCE application become: http://YourWebSite/arce/
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Added: 2006-09-27 License: LGPL (GNU Lesser General Public License) Price:
1125 downloads
The Analysis & Reconstruction Sound Engine 0.1

The Analysis & Reconstruction Sound Engine 0.1


Analysis & Reconstruction Sound Engine is a program that analyses a sound file into a spectrogram. more>>
The Analysis & Reconstruction Sound Engine also known as ARSE, is a program that analyses a sound file into a spectrogram and is able to synthetise this spectrogram, or any other user-created image, back into a sound.
The ARSE consists in two main parts, a spectrographer with a base-2 logarithmic frequency scale, and a spectrogram synthetiser.
Unlike most spectrographers which are based on STFTs and perform the analysis by cutting the signal into small time slices to analyse these slices in the frequency domain, the ARSE is based on a filter bank followed by envelope detection, which means that the signal is cut into small frequency-domain slices, and then analysed in the time domain.
The filter bank is, as of now, made up with overlapping bandpass FIR filters defined logarithmically. Once the original signal is filtered with the filter bank, each resulting signal is sent to envelope detection.
Envelope detection in the ARSE isnt based on a Hilbert transform and peak detection, as its usually done. To achieve envelope detection, we first perform a FFT on the signal, zero-pad the beginning of the signal in the frequency domain according to a user-defined setting, then we perform an IFFT, and, now in the time domain, we turn every negative sample into a positive one, and we low-pass filter (and eventually decimate) the signal according to the same user-defined setting as we previously used.
For instance, lets say we have a signal with a sampling frequency of 44,100 Hz, and that we want to obtain an envelope for it which sampling frequency would be 100 Hz. Once we perform the FFT, we add enough zeroes in the frequency domain at the beginning of our signal so that every frequency component shifts by 50 Hz (100 Hz divided by two, it will later appear obvious why), and we perform an IFFT. Our signal now has a sampling frequency of 44,200 Hz (44,100 + 100 Hz), and the original signal which previously spanned from 0 Hz to 22,050 Hz now spans from 50 Hz to 22,100 Hz.
Now we turn every time-domain sample into its absolute value by turning every negative sample into a positive one. To perform this on a signal means that, for example, a sine wave of a certain frequency would become a signal which periodicity would be twice that frequency. Once we low-pass filter that signal to twice that frequency we obtain that signals envelope. In our case, now that we have obtained the absolute values for our signal, since the periodicity of a sine at the lowest frequency - 50 Hz - would now be 100 Hz, we only low-pass filter our signal at 100 Hz to obtain the original signals envelope. We can now decimate the signal to a sample rate of 100 Hz.
The resulting envelope for each frequency band makes the horizontal lines of the image representing the spectrogram. The amplitude of the envelopes translate linearly into intensity in the image.
The spectrogram synthetiser is based on modulation using horizontal lines of the image as envelopes. Each horizontal line is upsampled to the sampling rate of the desired final signals sampling rate, and is then modulated with, depending on the synthetisation mode chosen by the user, sines matching to the central frequency each horizontal line represents, or noise filtered through the filter bank.
Enhancements:
- Replaced fixed phase sine generation with random phase sine generation
- Changed the PRNG
- Removed the unused code
- Removed every call of nearbyint() due to compatibility issues
- Included the necessary files in order to make using ./configure && make && make install
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Added: 2007-05-29 License: GPL (GNU General Public License) Price:
883 downloads
Stanis Python Editor 0.8.3.c

Stanis Python Editor 0.8.3.c


Stanis Python Editor is a Python IDE with wxGlade, Pychecker, UML, and Blender support. more>>
Stanis Python Editor is a python IDE with auto-indentation, auto completion, call tips, syntax coloring, syntax highlighting, uml viewer, class explorer, source index, auto todo list, sticky notes, integrated pycrust shell, python file browser, recent file browser, drag&drop, context help, ...
Special is its blender support with a blender 3d object browser and its ability to run interactively inside blender. Spe ships with wxGlade (gui designer), PyChecker (source code doctor) and Kiki (regular expression console). Spe is extensible with wxGlade.
Main features:
- Intellisense & autocompletion
- Call tips
- Syntax coloring
- Sidebar with class explorer, index & todo
- Drag & drop
- Tab Controls
- Uml Diagrams
System requirements:
- full python 2.3+
- wxpython 2.6+
- optional blender 2.35
Enhancements:
- This is a maintenance release with mostly bugfixes and some feature updates.
- If you are using wxPython 2.7, youll need to upgrade to this release.
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Added: 2006-10-27 License: Public Domain Price:
1102 downloads
uml2svg 0.18

uml2svg 0.18


uml2svg is an XSLT-based tool for converting XMI-compliant UML Diagrams into SVG. more>>
uml2svg is an XSLT-based tool for converting XMI-compliant UML Diagrams into SVG.
We started the developing uml2svg with six main goals in mind:
- Standard conformance
- Good Documentation
- Modularity
- Extensibility
- Comprehensible SVG
- Multiple diagrams per XMI-file
SVG is a standard language for describing two-dimensional vector graphics in XML. As the open SVG standard gains in popularity and gradually replaces proprietary formats for vectorial graphics, the support provided by the Web browsers is getting better.
Plugins to display SVG exist for most browsers and it is most likely that the next generation of Web browser will provide built-in support for SVG. When that happens there will be no better way to distribute vector graphics on the web. Furthermore, not only web browsers can process SVG in a meaningful way; in fact that is just the tip of the iceberg. SVG can be easily read in, processed, and then transformed into many other formats, being well suited for both text and graphic tools as well as for web agents and screen readers.
UML diagrams are composed of lines, polygons, ellipses and text labels, so they are inherently vectorial. However, the SVG is not very well suited for direct use by UML tools. While some of them can in fact export UML diagrams directly to SVG, they do that by discarding all the information about structure, and converting everything into a shape. Moreover, some tools use the screen-capture function provided by their environment (such as java2d) and then they apply a filter to generate SVG out of the "screenshot".
What comes out of that is a pile of meaningless information, which by accident happens to draw a gorgeous diagram. How will a screen reader interpret such a file? How will a web crawler be able to index it? How will a web agent process it in a meaningful way? A program needs the semantic information that the humans can extract just by looking at a picture. For a machine, an obfuscated SVG file is not easier to process than a PNG file or any other image.
Although for humans it is better to be able to scale the image, for a program this is irrelevant. Programs need a way to "understand" the semantics of the UML models to be able to process and interchange them in a meaningfull way. This was the main idea behind the XML Metadata Interchange (XMI), an OMG specification for model interchange. And probably the best use that XMI has found so far is the exchange of UML models between different modeling tools. And while the XMI provides a standard way for tools to represent models as XML documents, it is still limited to the model elements only.
With the introduction of the UML 2.0 Diagram Interchange Specification as part of the upcoming UML 2.0 standard, it will become possible for tools to exchange the models together with the layout of the diagrams. We think that, once this specification appears, XMI will be used averywhere. Not only will the tools be able to exchange diagrams, but could even represent them internaly as DOM trees. Have you ever considered drawing your UML diagrams online, using only a web browser? This could be done even now by using a custom SVG syntax for the DOM tree, but a solution based on XMI could do even better and be a standard at the same time.
Therefore, we believe that with the advent of UML 2.0 and the increase in the use of SVG, the need for transformations between XMI and SVG will be great. Nevertheless when the uml2svg project was started, there was hardly any good open-source solution to convert XMI diagams into SVG.
The UML 2.0 Diagram Interchange Adopted Specification in its current incipient form references a set of XSL transformations. Although the standard draft covers them to a large extent, the link is actually broken (you can try for yourself). It has been broken for more than a year and most likely it will stay like that forever.
The personal webpage of Professor Mario Jeckle provides an online transformation service capable of dynamically generating SVG from XMI-compliant XML files. The XSL files accomplishing the transformations are also available on that website. These transformations are monolithic and not well documented (the only documentation is in the code, and it is generally written in German). With the tragic accident that took the life of Professor Jeckle, the transformations have no longer been maintained.
Finally, the STZ-IDA research center in Karlsruhe had to convert UML diagrams to SVG, as part of one of their projects. The XSLT stylesheet they created for this purpose was named xmi2svg and is available under the terms of the MIT license. At the time we started work on uml2svg the only type of diagrams supported was class diagrams.
Recently the package reached version 0.2 and it supports more diagram types, without major changes in the code (the opposite of what we were expecting). Andreas Junghans, the author of xmi2svg, provided us with a lot of insightful hints which helped us eliminate many glitches in uml2svg. It looks that the development of uml2svg and xmi2svg will continue in parallel, at least for a while. The good thing about this is that the two (quite different) implementations prove each others validity and the features tend to propagate freely from one side to the other. However, this comes with the prize of having to maintain two different code-trees and possibly confusing some users.
We did not like the two existing solutions because they were:
incomplete - just prototypes, not well suited for production environment
monolithic - hard to maintain and extend
not documented - hard to understand
At first sight, we thought we could find a way to improve one of the existing solutions and just add the features we needed. However, we slowly came to the conclusion that it would be better if we started anew. There are things one can fix in a project, but that does not include what we thought is was bad design. The fact that the two implementations presented above are open source helped us get quickly on the way with our own project.
Enhancements:
- Two annoying bugs were fixed.
- The site and documentation were updated.
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Added: 2007-02-18 License: LGPL (GNU Lesser General Public License) Price:
981 downloads
P-UMLaut 1.2

P-UMLaut 1.2


The P-UMLaut tool allows the user to transform UML 2.0 Sequence Diagrams to semantically equivalent Petri Nets. more>>
The P-UMLaut tool allows the user to transform UML 2.0 Sequence Diagrams to semantically equivalent Petri Nets.
These Petri Nets may then be simulated using the supplied PN simulator (of PEP descent) or operated on with any tool that can work with high level Petri Nets.
By plugging different Realms into the simulation by way of an event filter, the modeled world may then be displayed and interacted with in various fashions. A 3D animation module is supplied as well as two examples utilizing the complete toolchain.
Enhancements:
- A new Petrinet Simulator was implemented in Java which features Highlevel-PN to Lowlevel-PN unfolding and Timed-PN simulation.
- Filtering was enhanced. Irrlicht 0.12 is used.
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Added: 2005-09-27 License: GPL (GNU General Public License) Price:
1488 downloads
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