Free uml analysis model software for linux

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.

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;
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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.
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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.

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)

Misfit Model 3D is an OpenGL-based 3D model editor that works with triangle-based models. Misfit Model 3D supports multi-level undo, skeletal animations, simple texturing, scripting, command-line batch processing, and a plugin system for adding new model and image filters.
Complete online help is included. It is designed to be easy to use and easy to extend with plugins and scripts.
Misfit Model 3D was written and tested on Linux (2.4 and 2.6 kernels) and has been compiled and tested on most major Linux distributions.
It is not endian-safe so it is unlikely to run on non-x86 hardware platforms--this will probably not change soon unless I get requests for a version thats usable on big-endian archs.
Enhancements:
- The menus have been re-organized. There is a new command to make normals face outward. The texture coordinate window now has a rotate tool. Material support for COB has been improved. Many animation bugs have been fixed. A "File | Export" command has been added to indicate which formats have less reliable write support.

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.

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.

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),

Config::Model provides a framework to help in validating the semantic content of configuration data. The project can also be used to provide a semantic check of options of a complex program like mplayer or transcode.
For most complex software, configuration upgrade is a difficult task for most people. By using Config::Model, a software can provide a smooth upgrade path for their users.
How does this work ?
Using this project, a typical configuration validation tool will be made of 3 parts :
The user interface
The validation engine which is in charge of validating all the configuration information provided by the user.
The storage facility that store the configuration information
Dont we already have some configuration validation tools ?
Youre probably thinking of tools like webmin. Yes, these tools exist and work fine, but they have their set of drawbacks.
Usually, the validation of configuration data is done with a script which performs semantic validation and often ends up being quite complex (e.g. 2500 lines for Debians xserver-xorg.config script which handles xorg.conf file).
In most cases, the configuration model is expressed in instructions (whatever programming language is used) and interspersed with a lot of processing to handle the actual configuration data.
Whats the advantage of this project ?
The Config::Model projects provide a way to get a validation engine where the configuration model is completely separated from the actual processing instruction.
The configuration model is expressed in a declarative form (i.e. a Perl data structure) which is always easier to maintain than a lot of code.
The declaration specifies:
the structure of the configuration data (which can be queried by generic user interfaces)
the properties of each element (boundaries, check, integer or string, enum like type ...)
the default values of parameters (if any)
mandatory parameters
the targeted audience (intermediate, advance, master)
on-line help (for ach parameter or value of parameter)
the level of expertise of each parameter (to hide expert parameters from newbie eyes)
So, in the end:
maintenance and evolution of the configuration content is easier
user will see a *common* interface for *all* programs using this project.
user will not see advanced parameters
upgrade of configuration data is easier and sanity check is performed
audit of configuration is possible to check what was modified by the user compated to default values
What about the user interface ?
Config::Model will also come with a Curses::UI interface that queries the users model and generate the relevant user screens.
What about data storage ?
Since the syntax of configuration files vary wildly form one program to another, most people who want to use this framework will have to provide a dedicated parser/writer.
Nevertheless, this project can also provide a writer/parser for most common format: like ini style file, or provide an interface to the Elektra or debconf projects. This point is open for discussion.
It is entirely possible for a single configuration model to use several parsers and writers so one model will ensure the consistency of several configuration files together.
Enhancements:
- The Xorg model was updated to Config::model version 0.609.
- Some bugs were fixed.