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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
High Performance Linpack 1.0a

High Performance Linpack 1.0a


High Performance Linpack is a highly parallel, high performance benchmarking tool. more>>
HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.

The algorithm used by HPL can be summarized by the following keywords: Two-dimensional block-cyclic data distribution - Right-looking variant of the LU factorization with row partial pivoting featuring multiple look-ahead depths - Recursive panel factorization with pivot search and column broadcast combined - Various virtual panel broadcast topologies - bandwidth reducing swap-broadcast algorithm - backward substitution with look-ahead of depth 1.

The HPL package provides a testing and timing program to quantify the accuracy of the obtained solution as well as the time it took to compute it. The best performance achievable by this software on your system depends on a large variety of factors.

Nonetheless, with some restrictive assumptions on the interconnection network, the algorithm described here and its attached implementation are scalable in the sense that their parallel efficiency is maintained constant with respect to the per processor memory usage.

The HPL software package requires the availibility on your system of an implementation of the Message Passing Interface MPI (1.1 compliant). An implementation of either the Basic Linear Algebra Subprograms BLAS or the Vector Signal Image Processing Library VSIPL is also needed. Machine-specific as well as generic implementations of MPI, the BLAS and VSIPL are available for a large variety of systems.
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Added: 2005-04-11 License: BSD License Price:
1682 downloads
Performance Co-Pilot 2.5.0

Performance Co-Pilot 2.5.0


Performance Co-Pilot is a performance monitoring toolkit and API. more>>
Performance Co-Pilot (PCP) is a framework and services to support system-level performance monitoring and performance management.
The services offered by PCP are especially attractive for those tackling harder system-level performance problems. For example this may involve a transient performance degradation, or correlating end-user quality of service with platform activity, or diagnosing some complex interaction between resource demands on a single system, or management of performance on large systems with lots of "moving parts".
The distributed PCP architecture makes it especially useful for those seeking centralized monitoring of distributed processing (e.g. in a cluster or webserver farm environment), especially where a large number hosts are involved.
Main features:
- A single API for accessing the performance data that hides details of where the data comes from and how it was captured and imported into the PCP framework.
- A client-server architecture allows multiple clients to monitor the same host, and a single client to monitor multiple hosts (e.g. in a Beowulf cluster). This enables centralized monitoring of distributed processing.
- Integrated archive logging and replay so a client application can use the same API to process real-time data from a host or historical data from an archive.
- The framework supports APIs and configuration file formats that enable the scope of performance monitoring to be extended at all levels.
- An "plugin" framework (libraries, APIs, agents and daemon) to collect performance data from multiple sources on a single host, e.g. from the hardware, the kernel, the service layers, the application libraries, and the applications themselves.
- Libraries and sample implementations encourage the development of new "plugins" (or agents) to capture and export the performance data that matters in your application environment, along side the other generic performance data.
- An endian-safe transport layer for moving performance metrics between the collector and the monitoring applications over TCP/IP. This means an IRIX desktop with PCP can monitor one or more Linux systems with the Open Source release of PCP installed.
- A Linux agent that exports a broad range of performance data from most kernels circa 2.0.36 (RedHat 5.2) or later. This includes coverage of activity in the areas of: CPU, disk, memory, swapping, network, NFS, RPC, filesystems and all the per-process statistics.
- Other agents export performance data from:
- Web server activity logs
- arbitrary application-level tracing (via a PCP trace library)
- Cisco routers
- sendmail
- the mail queue
- the PCP infrastructure itself
- Assorted simple monitoring tools that use the PCP APIs to retrieve and display either arbitrary performance metrics, or specific groups of metrics (as in pmstat a cluster-aware vmstat lookalike).
- The PCP inference engine supports automated monitoring through a rule-based language and interpreter that performs user-defined actions when rule predicates are found to be true.
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Added: 2006-10-25 License: LGPL (GNU Lesser General Public License) Price:
1094 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
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
Performance Co-Pilot viewer 0.0.2

Performance Co-Pilot viewer 0.0.2


pcpViewer is a 3D viewer of data gathered through the excellent Performance Co-Pilot library. more>>
pcpViewer is a 3D viewer of data gathered through the excellent "Performance Co-Pilot" library.

You can see usage of CPU time, net devices, memory, hard drives, and virtually any data exported by the pcp library and daemon.

I first started this "pet project" as a 3D xosview replacement (thanks for inspiration), so one of the goal is to get the same level of responsiveness as xosview.

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Added: 2005-05-26 License: GPL (GNU General Public License) Price:
1611 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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Added: 2006-07-14 License: GPL (GNU General Public License) Price:
1204 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
Objectrefenceanalyser 1.01

Objectrefenceanalyser 1.01


Objectrefenceanalyser (ora) helps developers find bugs or design errors by showing Java object references in an easy way. more>>
Objectrefenceanalyser (ora) helps developers find bugs or design errors by showing Java object references in an easy way.

It can be plugged into other programs for taking and saving "snapshots" of the object model at runtime for analysis.

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Added: 2007-08-07 License: LGPL (GNU Lesser General Public License) Price:
811 downloads
Performance Application Programming Interface 3.9.0

Performance Application Programming Interface 3.9.0


Performance Application Programming Interface is an API for a CPU performance counter. more>>
PAPI aims to provide the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors.
PAPI enables software engineers to see, in near real time, the relation between software performance and processor events.
The Performance API (PAPI) project specifies a standard application programming interface (API) for accessing hardware performance counters available on most modern microprocessors.
These counters exist as a small set of registers that count Events, occurrences of specific signals related to the processors function. Monitoring these events facilitates correlation between the structure of source/object code and the efficiency of the mapping of that code to the underlying architecture.
This correlation has a variety of uses in performance analysis including hand tuning, compiler optimization, debugging, benchmarking, monitoring and performance modeling. In addition, it is hoped that this information will prove useful in the development of new compilation technology as well as in steering architectural development towards alleviating commonly occurring bottlenecks in high performance computing.
PAPI provides two interfaces to the underlying counter hardware; a simple, high level interface for the acquisition of simple measurements and a fully programmable, low level interface directed towards users with more sophisticated needs.
The low level PAPI interface deals with hardware events in groups called EventSets. EventSets reflect how the counters are most frequently used, such as taking simultaneous measurements of different hardware events and relating them to one another.
For example, relating cycles to memory references or flops to level 1 cache misses can indicate poor locality and memory management. In addition, EventSets allow a highly efficient implementation which translates to more detailed and accurate measurements.
EventSets are fully programmable and have features such as guaranteed thread safety, writing of counter values, multiplexing and notification on threshold crossing, as well as processor specific features. The high level interface simply provides the ability to start, stop and read specific events, one at a time.
PAPI provides portability across different platforms. It uses the same routines with similar argument lists to control and access the counters for every architecture. As part of PAPI, we have predefined a set of events that we feel represents the lowest common denominator of every good counter implementation.
Our intent is that the same source code will count similar and possibly comparable events when run on different platforms. If the programmer chooses to use this set of standardized events, then the source code need not be changed and only a fresh compilation and link is necessary. However, should the developer wish to access machine specific events, the low level API provides access to all available events and counting modes.
If an event or feature does not exist on the current platform, PAPI returns an appropriate error code. This significantly reduces the porting effort of code using PAPI because the semantics of each call to PAPI remains the same, just the argument lists need updating. In addition to the standard set, each PAPI implementation supports all native events through the ability to directly accept platform specific counter numbers. Definitions for most, if not all of these, are included as conditional macros in the header file. In this way, PAPI avoids having inefficient code to translate all events for all platforms into a uniform representation and back again.
This translation is only done for the relatively few events defined in the standardized set. Some processors like those in the POWER series have counter groups. They enable access to specific groups of counters, instead of individual events. This presents a serious portability problem, thus PAPI abstracts hardware counters from their groups with a packed naming scheme. Each counter control value or event is made up of the counter group number and the number of the specific counter in that group.
PAPI can be divided into two layers of software. The upper layer consists of the API and machine independent support functions. The lower layer defines and exports a machine independent interface to machine dependent functions and data structures. These functions access the substrate, which may consist of the operating system, a kernel extension or assembly functions to directly access the processors registers.
PAPI tries to use the most efficient and flexible of the three, depending on what is available. Naturally, the functionality of the upper layers heavily depends on that provided by the substrate. In cases where the substrates do not provide highly desirable features, PAPI attempts to emulate them as described below.
PAPI makes sure the underlying operating system or library guards against overflow of counter values.
Each counter can potentially be incremented multiple times in a single clock cycle. This combined with increasing clock speeds and the small precision of some of the physical counters means that overflow is likely to occur.
One of the more advanced features of PAPI is to provide a portable implementation of asynchronous notification when counters exceed a user specified value.
This functionality provides the basis for PAPIs SVR4 compatible profiling calls, that generate an accurate histogram of performance interrupts based on hardware metrics, not on time. Such functionality provides the basis for all line level performance analysis software, from the antiquated days of AT&Ts prof to SGIs SpeedShop. Thus for any architecture with even the most rudimentary access to hardware performance counters, PAPI provides the foundation for a truly portable, source level, performance analysis tool based on real processor statistics.
Enhancements:
- The API was extended to decouple abstraction layers from hardware support and to provide initial support for different types of performance counters.
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Added: 2007-04-23 License: BSD License Price:
925 downloads
JPerfmeter 1.4

JPerfmeter 1.4


JPerfmeter is a Java Performance statistics monitor. more>>
JPerfmeter is a Java Performance statistics monitor.

JPerfmeter is a simple performance statistics monitor in the style of perfmeter, full Java.

Note that JPerfmeter needs the rpc.rstatd daemon to be running on the system its monitoring (available on Solaris systems and other various UNIX/Linux systems).

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Added: 2007-03-28 License: BSD License Price:
945 downloads
gperfmeter 2.1.0

gperfmeter 2.1.0


gperfmeter displays performance statistics for a given hostname. more>>
gperfmeter displays performance statistics for a given hostname.

If no host is specified, statistics on the current host are metered. You can display performance values in a solid or line strip chart.

The performance data automatically scales to accommodate increasing or decreasing values for the host machine. The gperfmeter preferences sheet provides a simple interface for accessing all of the application resources.
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Added: 2005-10-03 License: GPL (GNU General Public License) Price:
1481 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
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
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