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lx_lib structural memory library 20060226-1
lx_lib handles memory allocations as structures, keeping important information such as the remaining allocated space. more>>
lx_lib handles memory allocations as structures, keeping important information such as the remaining allocated space and the length of the used string internal to each variable (or descriptor).
Much of it was initially inspired by Dan Bernsteins stralloc library, but the two are not compatible, nor has there ever been any intention to make them compatible.
Main features:
- strings need not be scanned to determine their length
- the amount of allocated string remaining is easily determined
- promotes more secure programming practices
- if used correctly, lx_lib can offer a significant speed increase over traditional methods
- easy-to-use methods for manipulating strings
- generic descriptor support for buffered i/o
- generic descriptors enable fast scanning of input for specific characters (e.g. a newline)
Enhancements:
- Bits of the lx_map() interface have been updated for use with the 20060228-1 release of libnaw.
<<lessMuch of it was initially inspired by Dan Bernsteins stralloc library, but the two are not compatible, nor has there ever been any intention to make them compatible.
Main features:
- strings need not be scanned to determine their length
- the amount of allocated string remaining is easily determined
- promotes more secure programming practices
- if used correctly, lx_lib can offer a significant speed increase over traditional methods
- easy-to-use methods for manipulating strings
- generic descriptor support for buffered i/o
- generic descriptors enable fast scanning of input for specific characters (e.g. a newline)
Enhancements:
- Bits of the lx_map() interface have been updated for use with the 20060228-1 release of libnaw.
Download (0.024MB)
Added: 2006-04-13 License: GPL (GNU General Public License) Price:
1292 downloads
Test::Struct 0.01
Test::Struct is a Perl extension for testing for structural equivelence. more>>
Test::Struct is a Perl extension for testing for structural equivelence.
SYNOPSIS
use Test::Struct;
deep_eq($hairy_struct,$expected,Hairy structural test);
is($x,$y); # and everything else Test::More has to offer!
Test::Struct is used for doing deep structural comparisons of two objects. The module contains only one subrotuine which is intended to be used as a mix-in with other more generic Test::Builder derived modules like Test::More or Test::Simple. The code normally uses Scalar::Util for inspecting the data, but it will also use additional fine tuned comparison tools from Data::Dump::Streamer if they are available.
deep_eq($got,$expected,$name)
Does a deep level comparison of two objects. It traverses the two structures in parallel checking as many attributes as it can for differences. If the objects differ it will output a diagnostic message containing a list of the differences it encountered before it finished the comparison. Some types of mismatch prevent further comparison so the list may not be exhaustive.
The intention of this routine is that it will pass the test only if $got is functionally identical to $expected. However, at current time there are some data types it does not handle properly, such as CODE refs.
<<lessSYNOPSIS
use Test::Struct;
deep_eq($hairy_struct,$expected,Hairy structural test);
is($x,$y); # and everything else Test::More has to offer!
Test::Struct is used for doing deep structural comparisons of two objects. The module contains only one subrotuine which is intended to be used as a mix-in with other more generic Test::Builder derived modules like Test::More or Test::Simple. The code normally uses Scalar::Util for inspecting the data, but it will also use additional fine tuned comparison tools from Data::Dump::Streamer if they are available.
deep_eq($got,$expected,$name)
Does a deep level comparison of two objects. It traverses the two structures in parallel checking as many attributes as it can for differences. If the objects differ it will output a diagnostic message containing a list of the differences it encountered before it finished the comparison. Some types of mismatch prevent further comparison so the list may not be exhaustive.
The intention of this routine is that it will pass the test only if $got is functionally identical to $expected. However, at current time there are some data types it does not handle properly, such as CODE refs.
Download (0.005MB)
Added: 2006-12-01 License: Perl Artistic License Price:
1057 downloads
Shotoku 1.0 Alpha3
Shotoku is designed to provide easy access to content repositories. more>>
Shotoku is designed to provide easy access to content repositories in which you can store data, revision content, bind metadata, and provide branching and merging strategies.
This means Shotoku can interface with repositories such as the Java Content Repository (JSR 170: JCR), Subversion, and file-system based repository implementations that aim to support basic revisioning mechanisms.
Main features:
- Three content managers: the first and default SVN-based, JCR-based and a local file system repository.
- Because a local working copy is present, data reading is very fast (SVN repository implementation).
- Data writing is reliable, because data is sent straight to the repository, without touching the working copy (SVN repository implementation).
- Shotoku can work in "embedded" mode in stand-alone applications, as well as a component in an application server.
- Shotoku allows you to "inject" content into any POJO using annotations (currently supported only in app server mode). POJOs which are Shotoku aware are automatically updated when a user updates a node in a Subversion repository Shotoku is configured to reference. Content can be anything and there are no structural requirements placed on the repository - even existing Subversion repositories can be referenced by Shotoku without modification.
- A simple search mechanism.
- Integeration with Apache Velocity - you can easily store templates in Shotoku to create higher level application features such as content and blog engines.
- Feeds component - automatic generation of rss, atom and rdf feeds/ podcasts, configured through a xml file, together with arbitrary feeds aggregation. You can see feeds already at work on JBoss Labs - just click the "Feeds" link in navigation or simply here.
- Blog component.
- A simple cache with "renewable" values - a value can be updated on regular intervals of time or when some of watched resources in a content manager change (see wiki for details).
<<lessThis means Shotoku can interface with repositories such as the Java Content Repository (JSR 170: JCR), Subversion, and file-system based repository implementations that aim to support basic revisioning mechanisms.
Main features:
- Three content managers: the first and default SVN-based, JCR-based and a local file system repository.
- Because a local working copy is present, data reading is very fast (SVN repository implementation).
- Data writing is reliable, because data is sent straight to the repository, without touching the working copy (SVN repository implementation).
- Shotoku can work in "embedded" mode in stand-alone applications, as well as a component in an application server.
- Shotoku allows you to "inject" content into any POJO using annotations (currently supported only in app server mode). POJOs which are Shotoku aware are automatically updated when a user updates a node in a Subversion repository Shotoku is configured to reference. Content can be anything and there are no structural requirements placed on the repository - even existing Subversion repositories can be referenced by Shotoku without modification.
- A simple search mechanism.
- Integeration with Apache Velocity - you can easily store templates in Shotoku to create higher level application features such as content and blog engines.
- Feeds component - automatic generation of rss, atom and rdf feeds/ podcasts, configured through a xml file, together with arbitrary feeds aggregation. You can see feeds already at work on JBoss Labs - just click the "Feeds" link in navigation or simply here.
- Blog component.
- A simple cache with "renewable" values - a value can be updated on regular intervals of time or when some of watched resources in a content manager change (see wiki for details).
Download (5.7MB)
Added: 2006-05-31 License: GPL (GNU General Public License) Price:
1241 downloads
StrBio 1.0
StrBio is a set of Java classes useful for development of software for computational structural biology research. more>>
StrBio is a set of Java classes and libraries useful for development of software for computational structural biology research.
They are licenced under the LGPL.
he strbio.org classes are the basis for several published research projects, including the Pred2ary secondary structure prediction program and the ASTRAL database of protein domain sequences.
The most interesting structural biology applications included are:
Pred2ary protein secondary structure prediction
JThread protein fold prediction
ConvertProtein for interconversion of protein file formats (FASTA, PDB, MSF, ALN, CASP, DSSP, HSSP, YAPF)
Filters to exchange data with commonly used molecular biology applications (e.g., BLAST, MinArea, MODELLER)
MakeRAF tool to create the Rapid Access Format sequence maps for the ASTRAL database.
Other more general-purpose functionality that is included:
Neural network library, including Scaled Conjugate Gradient or Steepest Descent optimization
Hooke and Jeeves derivative-free global optimization algorithm
Misc mathematical objects and algorithms (vectors, matrices, etc)
Efficient string formatting using Printf-based syntax (printf, atoi, atof, etc.)
<<lessThey are licenced under the LGPL.
he strbio.org classes are the basis for several published research projects, including the Pred2ary secondary structure prediction program and the ASTRAL database of protein domain sequences.
The most interesting structural biology applications included are:
Pred2ary protein secondary structure prediction
JThread protein fold prediction
ConvertProtein for interconversion of protein file formats (FASTA, PDB, MSF, ALN, CASP, DSSP, HSSP, YAPF)
Filters to exchange data with commonly used molecular biology applications (e.g., BLAST, MinArea, MODELLER)
MakeRAF tool to create the Rapid Access Format sequence maps for the ASTRAL database.
Other more general-purpose functionality that is included:
Neural network library, including Scaled Conjugate Gradient or Steepest Descent optimization
Hooke and Jeeves derivative-free global optimization algorithm
Misc mathematical objects and algorithms (vectors, matrices, etc)
Efficient string formatting using Printf-based syntax (printf, atoi, atof, etc.)
Download (12.7MB)
Added: 2005-11-14 License: LGPL (GNU Lesser General Public License) Price:
1440 downloads
VESTA 1.0b
VESTA software is a 3D visualization program for structural models and 3D pixel data such as electron/nuclear densities. more>> <<less
Download (1.7MB)
Added: 2007-07-16 License: Free To Use But Restricted Price:
834 downloads
Gretl 1.6.5
Gretl is a cross-platform software package for econometric analysis, written in the C programming language. more>>
Gretl is a cross-platform software package for econometric analysis, written in the C programming language. It is is free, open-source software.
You may redistribute it and/or modify it under the terms of the GNU General Public License (GPL) as published by the Free Software Foundation.
Main features:
- Easy intuitive interface (now in French, Italian, Spanish, Polish and German as well as English)
- A wide variety of least-squares based estimators, including two-stage least squares and nonlinear least squares
- Single commands to launch things like augmented Dickey-Fuller test, Chow test for structural stability, Vector Autoregressions, ARMA estimation
- Output models as LaTeX files, in tabular or equation format
- Integrated scripting language: enter commands either via the gui or via script
- Command loop structure for Monte Carlo simulations and iterative estimation procedures
- GUI controller for fine-tuning Gnuplot graphs
- Link to GNU R for further data analysis
<<lessYou may redistribute it and/or modify it under the terms of the GNU General Public License (GPL) as published by the Free Software Foundation.
Main features:
- Easy intuitive interface (now in French, Italian, Spanish, Polish and German as well as English)
- A wide variety of least-squares based estimators, including two-stage least squares and nonlinear least squares
- Single commands to launch things like augmented Dickey-Fuller test, Chow test for structural stability, Vector Autoregressions, ARMA estimation
- Output models as LaTeX files, in tabular or equation format
- Integrated scripting language: enter commands either via the gui or via script
- Command loop structure for Monte Carlo simulations and iterative estimation procedures
- GUI controller for fine-tuning Gnuplot graphs
- Link to GNU R for further data analysis
Download (3.0MB)
Added: 2007-05-17 License: GPL (GNU General Public License) Price:
897 downloads
PDL::Internals 2.4.3
PDL::Internals is a Perl module that contains a description of some aspects of the current internals. more>>
PDL::Internals is a Perl module that contains a description of some aspects of the current internals.
Intro
This document explains various aspects of the current implementation of PDL. If you just want to use PDL for something, you definitely do not need to read this. Even if you want to interface your C routines to PDL or create new PDL::PP functions, you do not need to read this man page (though it may be informative). This document is primarily intended for people interested in debugging or changing the internals of PDL. To read this, a good understanding of the C language and programming and data structures in general is required, as well as some Perl understanding. If you read through this document and understand all of it and are able to point what any part of this document refers to in the PDL core sources and additionally struggle to understand PDL::PP, you will be awarded the title "PDL Guru" (of course, the current version of this document is so incomplete that this is next to impossible from just these notes).
Warning: If it seems that this document has gotten out of date, please inform the PDL porters email list (pdl-porters@jach.hawaii.edu). This may well happen.
Piddles
The pdl data object is generally an opaque scalar reference into a pdl structure in memory. Alternatively, it may be a hash reference with the PDL field containing the scalar reference (this makes overloading piddles easy, see PDL::Objects). You can easily find out at the Perl level which type of piddle you are dealing with. The example code below demonstrates how to do it:
# check if this a piddle
die "not a piddle" unless UNIVERSAL::isa($pdl, PDL);
# is it a scalar ref or a hash ref?
if (UNIVERSAL::isa($pdl, "HASH")) {
die "not a valid PDL" unless exists $pdl->{PDL} &&
UNIVERSAL::isa($pdl->{PDL},PDL);
print "This is a hash reference,",
" the PDL field contains the scalar refn";
} else {
print "This is a scalar ref that points to address $$pdl in memoryn";
}
The scalar reference points to the numeric address of a C structure of type pdl which is defined in pdl.h. The mapping between the object at the Perl level and the C structure containing the actual data and structural that makes up a piddle is done by the PDL typemap. The functions used in the PDL typemap are defined pretty much at the top of the file pdlcore.h. So what does the structure look like:
struct pdl {
unsigned long magicno; /* Always stores PDL_MAGICNO as a sanity check */
/* This is first so most pointer accesses to wrong type are caught */
int state; /* Whats in this pdl */
pdl_trans *trans; /* Opaque pointer to internals of transformation from
parent */
pdl_vaffine *vafftrans;
void* sv; /* (optional) pointer back to original sv.
ALWAYS check for non-null before use.
We cannot inc refcnt on this one or wed
never get destroyed */
void *datasv; /* Pointer to SV containing data. Refcnt inced */
void *data; /* Null: no data alloced for this one */
int nvals; /* How many values allocated */
int datatype;
PDL_Long *dims; /* Array of data dimensions */
PDL_Long *dimincs; /* Array of data default increments */
short ndims; /* Number of data dimensions */
unsigned char *threadids; /* Starting index of the thread index set n */
unsigned char nthreadids;
pdl *progenitor; /* Im in a mutated family. make_physical_now must
copy me to the new generation. */
pdl *future_me; /* Im the "then" pdl and this is my "now" (or more modern
version, anyway */
pdl_children children;
short living_for; /* perl side not referenced; delete me when */
PDL_Long def_dims[PDL_NDIMS]; /* Preallocated space for efficiency */
PDL_Long def_dimincs[PDL_NDIMS]; /* Preallocated space for efficiency */
unsigned char def_threadids[PDL_NTHREADIDS];
struct pdl_magic *magic;
void *hdrsv; /* "header", settable from outside */
};
This is quite a structure for just storing some data in - what is going on?
<<lessIntro
This document explains various aspects of the current implementation of PDL. If you just want to use PDL for something, you definitely do not need to read this. Even if you want to interface your C routines to PDL or create new PDL::PP functions, you do not need to read this man page (though it may be informative). This document is primarily intended for people interested in debugging or changing the internals of PDL. To read this, a good understanding of the C language and programming and data structures in general is required, as well as some Perl understanding. If you read through this document and understand all of it and are able to point what any part of this document refers to in the PDL core sources and additionally struggle to understand PDL::PP, you will be awarded the title "PDL Guru" (of course, the current version of this document is so incomplete that this is next to impossible from just these notes).
Warning: If it seems that this document has gotten out of date, please inform the PDL porters email list (pdl-porters@jach.hawaii.edu). This may well happen.
Piddles
The pdl data object is generally an opaque scalar reference into a pdl structure in memory. Alternatively, it may be a hash reference with the PDL field containing the scalar reference (this makes overloading piddles easy, see PDL::Objects). You can easily find out at the Perl level which type of piddle you are dealing with. The example code below demonstrates how to do it:
# check if this a piddle
die "not a piddle" unless UNIVERSAL::isa($pdl, PDL);
# is it a scalar ref or a hash ref?
if (UNIVERSAL::isa($pdl, "HASH")) {
die "not a valid PDL" unless exists $pdl->{PDL} &&
UNIVERSAL::isa($pdl->{PDL},PDL);
print "This is a hash reference,",
" the PDL field contains the scalar refn";
} else {
print "This is a scalar ref that points to address $$pdl in memoryn";
}
The scalar reference points to the numeric address of a C structure of type pdl which is defined in pdl.h. The mapping between the object at the Perl level and the C structure containing the actual data and structural that makes up a piddle is done by the PDL typemap. The functions used in the PDL typemap are defined pretty much at the top of the file pdlcore.h. So what does the structure look like:
struct pdl {
unsigned long magicno; /* Always stores PDL_MAGICNO as a sanity check */
/* This is first so most pointer accesses to wrong type are caught */
int state; /* Whats in this pdl */
pdl_trans *trans; /* Opaque pointer to internals of transformation from
parent */
pdl_vaffine *vafftrans;
void* sv; /* (optional) pointer back to original sv.
ALWAYS check for non-null before use.
We cannot inc refcnt on this one or wed
never get destroyed */
void *datasv; /* Pointer to SV containing data. Refcnt inced */
void *data; /* Null: no data alloced for this one */
int nvals; /* How many values allocated */
int datatype;
PDL_Long *dims; /* Array of data dimensions */
PDL_Long *dimincs; /* Array of data default increments */
short ndims; /* Number of data dimensions */
unsigned char *threadids; /* Starting index of the thread index set n */
unsigned char nthreadids;
pdl *progenitor; /* Im in a mutated family. make_physical_now must
copy me to the new generation. */
pdl *future_me; /* Im the "then" pdl and this is my "now" (or more modern
version, anyway */
pdl_children children;
short living_for; /* perl side not referenced; delete me when */
PDL_Long def_dims[PDL_NDIMS]; /* Preallocated space for efficiency */
PDL_Long def_dimincs[PDL_NDIMS]; /* Preallocated space for efficiency */
unsigned char def_threadids[PDL_NTHREADIDS];
struct pdl_magic *magic;
void *hdrsv; /* "header", settable from outside */
};
This is quite a structure for just storing some data in - what is going on?
Download (2.1MB)
Added: 2007-07-07 License: Perl Artistic License Price:
839 downloads
Scala 2.5.1 / 2.6.0 RC1
Scala is a modern multi-paradigm programming language. more>>
Scala is a modern multi-paradigm programming language designed to express common programming patterns in a concise, elegant, and type-safe way.
Scala smoothly integrates features of object-oriented and functional languages including mixins, algebraic datatypes with pattern matching, genericity, and more.
It is well integrated with Java and .NET: the Scala compiler produces standard Java class files or .NET assemblies, and Java/.NET libraries and frameworks can be used without glue code or additional declarations.
Scala is a pure object-oriented language in the sense that every value is an object. Types and behavior of objects are described by classes and traits. Class abstractions are extended by subclassing and a flexible mixin-based composition mechanism as a clean replacement for multiple inheritance.
Whats New in 2.6.0 RC1 Development Release:
- This version introduces some language changes (existential types, lazy values, structural types, etc.) and fixes many bugs.
<<lessScala smoothly integrates features of object-oriented and functional languages including mixins, algebraic datatypes with pattern matching, genericity, and more.
It is well integrated with Java and .NET: the Scala compiler produces standard Java class files or .NET assemblies, and Java/.NET libraries and frameworks can be used without glue code or additional declarations.
Scala is a pure object-oriented language in the sense that every value is an object. Types and behavior of objects are described by classes and traits. Class abstractions are extended by subclassing and a flexible mixin-based composition mechanism as a clean replacement for multiple inheritance.
Whats New in 2.6.0 RC1 Development Release:
- This version introduces some language changes (existential types, lazy values, structural types, etc.) and fixes many bugs.
Download (13.2MB)
Added: 2007-07-28 License: BSD License Price:
825 downloads
MKDoc::XML::Stripper 0.75
MKDoc::XML::Stripper is a Perl module to remove unwanted XML / XHTML tags and attributes. more>>
MKDoc::XML::Stripper is a Perl module to remove unwanted XML / XHTML tags and attributes.
SYNOPSIS
use MKDoc::XML::Stripper;
my $stripper = new MKDoc::XML::Stripper;
$stripper->allow (qw /p class id/);
my $ugly = < p class="para" style="color:red" >Hello, < strong >World< /strong >!< /p >;
my $neat = $stripper->process_data ($ugly);
print $neat;
Should print:
< p class="para" >Hello, World!< /p >
MKDoc::XML::Stripper is a class which lets you specify a set of tags and attributes which you want to allow, and then cheekily strip any XML of unwanted tags and attributes.
In MKDoc, this is used so that editors use structural XHTML rather than presentational tags, i.e. strip anything which looks like a tag, a style attribute or other tags which would break separation of structure from content.
<<lessSYNOPSIS
use MKDoc::XML::Stripper;
my $stripper = new MKDoc::XML::Stripper;
$stripper->allow (qw /p class id/);
my $ugly = < p class="para" style="color:red" >Hello, < strong >World< /strong >!< /p >;
my $neat = $stripper->process_data ($ugly);
print $neat;
Should print:
< p class="para" >Hello, World!< /p >
MKDoc::XML::Stripper is a class which lets you specify a set of tags and attributes which you want to allow, and then cheekily strip any XML of unwanted tags and attributes.
In MKDoc, this is used so that editors use structural XHTML rather than presentational tags, i.e. strip anything which looks like a tag, a style attribute or other tags which would break separation of structure from content.
Download (0.040MB)
Added: 2006-09-19 License: Perl Artistic License Price:
1131 downloads
Python Macromolecular Library 1.0.0
Python Macromolecular Library is a software toolkit and library of routines for the analysis of macromolecular structural models more>>
Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.
Python Macromolecular Library is accessed via a layered, object-oriented application programming interface, and provides a range of useful software components for parsing mmCIF, and PDB files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer.
The mmLib data model is designed to provide easy access to the various levels of detail needed to implement high-level application programs for macromolecular crystallography, NMR, modeling, and visualization.
This includes specialized classes for proteins, DNA, amino acids, and nucleic acids. Also included is a extensive monomer library, element library, and specialized classes for performing unit cell calculations combined with a full space group library.
<<lessPython Macromolecular Library is accessed via a layered, object-oriented application programming interface, and provides a range of useful software components for parsing mmCIF, and PDB files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer.
The mmLib data model is designed to provide easy access to the various levels of detail needed to implement high-level application programs for macromolecular crystallography, NMR, modeling, and visualization.
This includes specialized classes for proteins, DNA, amino acids, and nucleic acids. Also included is a extensive monomer library, element library, and specialized classes for performing unit cell calculations combined with a full space group library.
Download (7.9MB)
Added: 2007-05-22 License: Artistic License Price:
888 downloads
TMHarvest 0.1 Pre1
TMHarvest provides a tool which harvests topicmaps from structured datasources. more>>
TMHarvest provides a tool which harvests topicmaps from structured datasources.
The TMHarvest library is based on TM4J and provides a convenient way to automatically generate topic maps from different data sources. A rules files with embedded templates (written in XML) defines from which data sources topic map constructs should be taken into account, as well how new or existent topics should be associated.
Main features:
- TMHarvest creates topic maps from existing data sources. Currently it supports the following source-types: SQL-Databases, CSV-Files, XPath-Queries. In addition it is possible to integrate custom model-providers, written in Java. See for details.
- The harvesting is driven by a model-file. The model may be processed as often as you like. Since the data sources are queried at processing time, it is possible to build topic paps periodically in order to reflect changing content.
- The model-file has a modular setup. The resulting topic map is populated step by step from distinct templateActions. The static parts of the topic map (the structural parts, for example the topics that define the ontology of the topic map) may be merged from static files and therefore seperated from the actual harvest.
Pros and Cons
The process which creates the topic map is serialized in the model-file. Once the process is defined, it runs as often as you like. This enables the creation of topic maps, that are refreshed periodically in an automated way.
Working with the templates leads to a certain interactive experience. Shaping the model, letting TMHarvest run, revisiting the results, reshape the model... let you converge the final form
The fact that the model-file must be written by hand, excludes many users, which lack the necessary technical affinity. The development of graphical interfaces or wizards would be really helpful.
<<lessThe TMHarvest library is based on TM4J and provides a convenient way to automatically generate topic maps from different data sources. A rules files with embedded templates (written in XML) defines from which data sources topic map constructs should be taken into account, as well how new or existent topics should be associated.
Main features:
- TMHarvest creates topic maps from existing data sources. Currently it supports the following source-types: SQL-Databases, CSV-Files, XPath-Queries. In addition it is possible to integrate custom model-providers, written in Java. See for details.
- The harvesting is driven by a model-file. The model may be processed as often as you like. Since the data sources are queried at processing time, it is possible to build topic paps periodically in order to reflect changing content.
- The model-file has a modular setup. The resulting topic map is populated step by step from distinct templateActions. The static parts of the topic map (the structural parts, for example the topics that define the ontology of the topic map) may be merged from static files and therefore seperated from the actual harvest.
Pros and Cons
The process which creates the topic map is serialized in the model-file. Once the process is defined, it runs as often as you like. This enables the creation of topic maps, that are refreshed periodically in an automated way.
Working with the templates leads to a certain interactive experience. Shaping the model, letting TMHarvest run, revisiting the results, reshape the model... let you converge the final form
The fact that the model-file must be written by hand, excludes many users, which lack the necessary technical affinity. The development of graphical interfaces or wizards would be really helpful.
Download (1.7MB)
Added: 2007-02-16 License: The Apache License Price:
980 downloads
Bongo Project 0.2.0
Bongo is an easy-to-use mail and calendar system, offering a simple yet powerful user interface. more>>
Bongo is an easy-to-use mail and calendar system, offering a simple yet powerful user interface. Bongo project goal is to make sharing, organisation, and communication simpler, quicker, and more useful.
What is Bongo?
Were creating fun and simple e-mail & calendaring software. We want our inboxes to be usable again: e-mail should be a useful tool, not a productivity killer. We want to be able to use our calendars to organise our lives, and we want other people to be able to interact with us through it whether they use Bongo or not.
Although Bongo is a young project, the software itself has a long pedigree and we are simply amongst the latest custodians. But while the core code isnt new, the ideas we have and the direction were taking are. Were not trying to create a "groupware" system to compete with well-known proprietary systems, or create an "enterprise platform" which encompasses everything from document management to project planning.
Best of all, Bongo is free (as in "freedom") software developed by an open community: we pride ourselves on being friendly and welcoming, and we see our project as being complementary to similar community projects.
Enhancements:
- This release is another source-only release intended for developers and very early testers, but it includes major new features such as native anti-spam and anti-virus integration and a brand-new Web administration system.
- Many structural changes have also been implemented, and less obvious improvements such as SMTP encryption are included, as are many bugfixes.
<<lessWhat is Bongo?
Were creating fun and simple e-mail & calendaring software. We want our inboxes to be usable again: e-mail should be a useful tool, not a productivity killer. We want to be able to use our calendars to organise our lives, and we want other people to be able to interact with us through it whether they use Bongo or not.
Although Bongo is a young project, the software itself has a long pedigree and we are simply amongst the latest custodians. But while the core code isnt new, the ideas we have and the direction were taking are. Were not trying to create a "groupware" system to compete with well-known proprietary systems, or create an "enterprise platform" which encompasses everything from document management to project planning.
Best of all, Bongo is free (as in "freedom") software developed by an open community: we pride ourselves on being friendly and welcoming, and we see our project as being complementary to similar community projects.
Enhancements:
- This release is another source-only release intended for developers and very early testers, but it includes major new features such as native anti-spam and anti-virus integration and a brand-new Web administration system.
- Many structural changes have also been implemented, and less obvious improvements such as SMTP encryption are included, as are many bugfixes.
Download (5.2MB)
Added: 2007-05-28 License: GPL (GNU General Public License) Price:
883 downloads
gmuck 1.12
gmuck assists you in producing valid (X)HTML by checking CGI scripts, XSL stylesheets, templates. more>>
gmuck assists you in producing valid (X)HTML by checking CGI scripts, XSL stylesheets, templates, normal HTML files or [you name it] and reporting errors that it finds. The project is not a replacement for real validation tools, but is handy in quick checks and in situations where validation of the actual markup is troublesome.
gmuck assists you in producing valid (X)HTML by checking CGI scripts, XSL stylesheets, templates, normal HTML files or [you name it] and reporting errors that it finds.
It is not a replacement for real validation tools, but is handy in quick checks and in situations where validation of the actual generated markup is troublesome.
gmuck is a line-oriented tool. Because of that, its structural checking capabilities are limited, but it makes an attempt to report syntactical errors as well as provides some lint-like features.
There gmuck distribution consists of the "HTML::GMUCK" module and the "gmuck" command line interface to it.
See the gmuck(1) and HTML::GMUCK(3) manual pages (or before installation, "perldoc bin/gmuck.pod" and "perldoc lib/HTML/GMUCK.pod" in the dir where you unpacked gmuck), and ChangeLog, TODO and BUGS files for more information.
gmuck is short for Generated MarkUp ChecKer, or Generated MUCK if you like. Hmph, thats actually ambiguous, see above for a better explanation. But gmuck sounds cool
<<lessgmuck assists you in producing valid (X)HTML by checking CGI scripts, XSL stylesheets, templates, normal HTML files or [you name it] and reporting errors that it finds.
It is not a replacement for real validation tools, but is handy in quick checks and in situations where validation of the actual generated markup is troublesome.
gmuck is a line-oriented tool. Because of that, its structural checking capabilities are limited, but it makes an attempt to report syntactical errors as well as provides some lint-like features.
There gmuck distribution consists of the "HTML::GMUCK" module and the "gmuck" command line interface to it.
See the gmuck(1) and HTML::GMUCK(3) manual pages (or before installation, "perldoc bin/gmuck.pod" and "perldoc lib/HTML/GMUCK.pod" in the dir where you unpacked gmuck), and ChangeLog, TODO and BUGS files for more information.
gmuck is short for Generated MarkUp ChecKer, or Generated MUCK if you like. Hmph, thats actually ambiguous, see above for a better explanation. But gmuck sounds cool
Download (0.023MB)
Added: 2007-04-02 License: GPL (GNU General Public License) Price:
935 downloads
mcl-algorithm 06-021
mcl-algorithm is a scalable cluster algorithm for graphs based on stochastic flow. more>>
mcl-algorithm is a scalable cluster algorithm for graphs based on stochastic flow.
The flow process employed by the algorithm is mathematically sound and intrinsically tied to cluster structure in graphs, which is revealed as the imprint left by the process.
The threaded implementation has handled graphs of up to one million nodes within hours, and is widely used in the field of protein family analysis. It comes with a wide range of sibling utilities for handling and analyzing graphs, matrices, and clusterings.
The MCL algorithm simulates flow using (alternating) two simple algebraic operations on matrices. Its formulation is simple and elegant. There are no high-level procedural instructions for assembling, joining, or splitting of groups - cluster structure is bootstrapped via a flow process that is inherently affected by any cluster structure present.
The first operation used by MCL is expansion, which coincides with normal matrix multiplication. Expansion models the spreading out of flow, it becoming more homogeneous. The second is inflation, which is mathematically speaking a Hadamard power followed by a diagonal scaling. Inflation models the contraction of flow, it becoming thicker in regions of higher current and thinner in regions of lower current. The MCL process causes flow to spread out within natural clusters and evaporate inbetween different clusters.
- By varying parameters, clusterings on different scales of granularity can be found. The number of clusters can not and need not be specified in advance, but the algorithm can be adapted to different contexts.
- The issue how many clusters? is not dealt with in an arbitrary manner, but rather by strong internal logic. Cluster structure leaves its marks on the flow process simulated by the algorithm, and the flow parameters control the granularity of the cluster imprint.
- The limit of the MCL process (the process simulated by the algorithm) is in general extremely sparse, and the iterands are sparse in a weighted sense. This gives the means to scale the algorithm drastically, leading to a worst-case complexity of order Nk^2, where N is the number of nodes of the input graph, and where k is a threshold for the number of resources allocated per node.
- The rate of convergence of the MCL process, and projection of the iterands afterwards onto the resulting clustering, give hooks for unsupervised parameter adjustment.
- The iterands of the MCL process have structural properties which allow a cluster interpretation, and which generalize the mapping of MCL limits onto clusterings. The mathematics associated with the MCL process shows that there is an intrinsic relationship between the MCL process and cluster structure in graphs. This is very valuable given the many heuristic approaches in cluster analysis.
Enhancements:
- Numerous cleanups in much of the code.
- Improvements in caching intermediate results.
<<lessThe flow process employed by the algorithm is mathematically sound and intrinsically tied to cluster structure in graphs, which is revealed as the imprint left by the process.
The threaded implementation has handled graphs of up to one million nodes within hours, and is widely used in the field of protein family analysis. It comes with a wide range of sibling utilities for handling and analyzing graphs, matrices, and clusterings.
The MCL algorithm simulates flow using (alternating) two simple algebraic operations on matrices. Its formulation is simple and elegant. There are no high-level procedural instructions for assembling, joining, or splitting of groups - cluster structure is bootstrapped via a flow process that is inherently affected by any cluster structure present.
The first operation used by MCL is expansion, which coincides with normal matrix multiplication. Expansion models the spreading out of flow, it becoming more homogeneous. The second is inflation, which is mathematically speaking a Hadamard power followed by a diagonal scaling. Inflation models the contraction of flow, it becoming thicker in regions of higher current and thinner in regions of lower current. The MCL process causes flow to spread out within natural clusters and evaporate inbetween different clusters.
- By varying parameters, clusterings on different scales of granularity can be found. The number of clusters can not and need not be specified in advance, but the algorithm can be adapted to different contexts.
- The issue how many clusters? is not dealt with in an arbitrary manner, but rather by strong internal logic. Cluster structure leaves its marks on the flow process simulated by the algorithm, and the flow parameters control the granularity of the cluster imprint.
- The limit of the MCL process (the process simulated by the algorithm) is in general extremely sparse, and the iterands are sparse in a weighted sense. This gives the means to scale the algorithm drastically, leading to a worst-case complexity of order Nk^2, where N is the number of nodes of the input graph, and where k is a threshold for the number of resources allocated per node.
- The rate of convergence of the MCL process, and projection of the iterands afterwards onto the resulting clustering, give hooks for unsupervised parameter adjustment.
- The iterands of the MCL process have structural properties which allow a cluster interpretation, and which generalize the mapping of MCL limits onto clusterings. The mathematics associated with the MCL process shows that there is an intrinsic relationship between the MCL process and cluster structure in graphs. This is very valuable given the many heuristic approaches in cluster analysis.
Enhancements:
- Numerous cleanups in much of the code.
- Improvements in caching intermediate results.
Download (1.1MB)
Added: 2006-01-24 License: GPL (GNU General Public License) Price:
1370 downloads
SPindent 1.1
SPindent is a JSP/PHP template structural validator and indenter. more>>
SPindent (Server Page Indenter) is a JSP/PHP structural validator and indenter. It performs structural compatibility check of inner HTML generated from "parallel" branches of process flow statements such as if/else.
It allows for those HTML branches to have different entry and exit HTML stack points, as far as the branches are compatible.
This allows for verification and proper indentation of handy workarounds, as well as rusty pyramids. It is based on MixedCC (Mixed Compiler Compiler).
<<lessIt allows for those HTML branches to have different entry and exit HTML stack points, as far as the branches are compatible.
This allows for verification and proper indentation of handy workarounds, as well as rusty pyramids. It is based on MixedCC (Mixed Compiler Compiler).
Download (0.085MB)
Added: 2005-05-05 License: The Apache License 2.0 Price:
1633 downloads
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