Free static analysis 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.

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.

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.

Cache::Static is a Perl module used for caching without freshness concerns.

SYNOPSIS

HTML::Mason instructions

In handler.pl: use Cache::Static;

In any component you where you have a well defined set of dependencies which change the output:

< %init >
my $_cs_deps = [
#file dependencies - only regenerate if a file has changed
file|/path/to/some_configuration_file,

#DBI dependencies - still under development - WONT WORK
#DBI dependencies: note the third argument is a DSN
_DBI|table|mysql:scache_test_db|test_table,
_DBI|db|mysql:scache_test_db,

#not yet implemented:
#column level depends, e.g. "DBI|column|$dsn|$tablename|$columname"
#row depends, e.g. "DBI|row|$dsn|$tablename|$uid_column_name|$uid_value"

#XML::Comma dependencies - only regenerate if a Doc or Store has changed
"_XML::Comma|Doc|$doc_key",
"_XML::Comma|Store|$def|$store",

#time dependencies (WARNING: these are discouraged, see doc/NOTE-time-deps)
time|15s, #every 15 seconds
time|M:15s, #every 15 seconds after the minute
time|H:2m, #every 2 minutes past the hour
time|W:2d3h5m0s, #every Tuesday at 3:05 AM

#modifiers (indicate behavior when the file cannot be found)
file-0|/tmp/foo, #if ! -e /tmp/foo, regenerate
file-1|/tmp/foo, #if ! -e /tmp/foo, serve
file|/tmp/foo, #use config value "dep_file_not_found_returns"

#note modifiers also work on extensions, e.g.
_DBI-1|db|mysql:scache_test_db,
_XML::Comma-0|Store|mm_item|post,

#etc... but modifiers CANNOT be used with times (since they have no
#file backing on disk)
];

#whatever you have in $_cs_deps above...
return if Cache::Static::HTML_Mason_Util::cache_it($r, $m, 1, $_cs_deps);

#...
#rest of init block
#...
< /%init >

dim_STAT 8.3 is yet another excellent utility you should not miss. It is actually a performance analysis and monitoring tool for Solaris and Linux (as well all other UNIX) systems.

Major Features:

1. Web based interface
2. Data storage in a SQL database
3. Several data views
4. Interactive (Java) or static (PNG) graphs
5. Real-time monitoring
6. Multi-host monitoring
7. Post analyzing
8. Statistics integration
9. Professional reporting with automated features, and more.

Enhancements: Jul.2009

• Fixes :
• • security issue on STAT-service!!
  • execution dim_STAT CLI from the web services
  • fixed LANG=C and LC_ALL=C via the main STAT-service script
• Improvements :
• • Optional Admin password may be given on a database creation and then it'll be required for any admin action!
  • Database error messages are now handled separately from LOG messages
  • Java WebDRAW Applet updated
  • add color LEDs near hostnames to signal running or stopped hosts
  • add #Records column to have an idea about a number of database rows per collect
  • Admin LOG management is working more friendly now with a long lists of messages
    
  • STAT-service daemon may listen exclusively on a given IP address now [IP:port]
  • Whole database backup is added to the Admin menu
• Database schema :
• • iostat disk names are moved to varchar(64)
  • all float values are moved to float(25,5) to have an easily human reading
  • Add-On name limit is 14 characters now
• Report Tool :
• • wiki-like syntax is added to simplify writing!
  • look & feel updated
  • some minor fixes here & there
• EasySTAT additional options :
• • COMPRESS=gzip (to automatically compress each output file)
  • TIMER=yes (automatically adding timestamps and sync tags within output files)
• New Add-Ons :
• • HAR v2 (CPU chip counters, ex. mips, cache miss, etc.)
  • Solaris CPU-Set STAT (mpstat -a)
  • Linux MPSTAT v2
  • MySQL STAT
  • InnoDB STAT
  • InnoDB I/O STAT (adoption of Neel's DTrace script )
  • PgSQL STAT (PostgreSQL stats)
  • ZoneLOAD: zoneid => zonename

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.

Oxalis is web site editor.
Oxalis project is created for editing static web sites.
Main features:
- Markdown syntax for writing pages
- templates
- site management
- upload to server via FTP
- it is free software