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POV-Ray 3.6
POV-Ray is a high-quality tool for creating 3D graphics. more>>
The Persistence of Vision Ray-Tracer creates three-dimensional, photo-realistic images using a rendering technique called ray-tracing. It reads in a text file containing information describing the objects and lighting in a scene and generates an image of that scene from the view point of a camera also described in the text file.
The Persistence of Vision Ray-Tracer(tm) was developed from DKBTrace 2.12 (written by David K. Buck and Aaron A. Collins) by a bunch of people (called the POV-Team?) in their spare time. The headquarters of the POV-Team is on the internet (see "Where to Find POV-Ray Files" for more details).
The POV-Ray package includes detailed instructions on using the ray-tracer and creating scenes. Many stunning scenes are included with POV-Ray so you can start creating images immediately when you get the package. These scenes can be modified so you do not have to start from scratch.
In addition to the pre-defined scenes, a large library of pre-defined shapes and materials is provided. You can include these shapes and materials in your own scenes by just including the library file name at the top of your scene file, and by using the shape or material name in your scene.
Ray-tracing is not a fast process by any means, but it produces very high quality images with realistic reflections, shading, perspective and other effects.
Ray-tracing is a rendering technique that calculates an image of a scene by simulating the way rays of light travel in the real world. However it does its job backwards. In the real world, rays of light are emitted from a light source and illuminate objects. The light reflects off of the objects or passes through transparent objects. This reflected light hits our eyes or perhaps a camera lens. Because the vast majority of rays never hit an observer, it would take forever to trace a scene.
Ray-tracing programs like POV-Ray start with their simulated camera and trace rays backwards out into the scene. The user specifies the location of the camera, light sources, and objects as well as the surface texture properties of objects, their interiors (if transparent) and any atmospheric media such as fog, haze, or fire.
For every pixel in the final image one or more viewing rays are shot from the camera, into the scene to see if it intersects with any of the objects in the scene. These "viewing rays" originate from the viewer, represented by the camera, and pass through the viewing window (representing the final image).
Every time an object is hit, the color of the surface at that point is calculated. For this purpose rays are sent backwards to each light source to determine the amount of light coming from the source. These "shadow rays" are tested to tell whether the surface point lies in shadow or not. If the surface is reflective or transparent new rays are set up and traced in order to determine the contribution of the reflected and refracted light to the final surface color.
Special features like inter-diffuse reflection (radiosity), atmospheric effects and area lights make it necessary to shoot a lot of additional rays into the scene for every pixel.
Main features:
- Easy to use scene description language.
- Large library of stunning example scene files.
- Standard include files that pre-define many shapes, colors and textures.
- Very high quality output image files (up to 48-bit color).
- 16 and 24 bit color display on many computer platforms using appropriate hardware.
- Create landscapes using smoothed height fields.
- Many camera types, including perspective, orthographic, fisheye, etc.
- Spotlights, cylindrical lights and area lights for sophisticated lighting.
- Photons for realistic, reflected and refracted, caustics. Photons also interact with media.
- Phong and specular highlighting for more realistic-looking surfaces.
- Inter-diffuse reflection (radiosity) for more realistic lighting.
- Atmospheric effects like atmosphere, ground-fog and rainbow.
- Particle media to model effects like clouds, dust, fire and steam.
- Several image file output formats including Targa, BMP (Windows only), PNG and PPM.
- Basic shape primitives such as ... spheres, boxes, quadrics, cylinders, cones, triangle and planes.
- Advanced shape primitives such as ... Tori (donuts), bezier patches, height fields (mountains), blobs, quartics, smooth triangles, text, superquadrics, surfaces of revolution, prisms, polygons, lathes, fractals, isosurfaces and the parametric object.
- Shapes can easily be combined to create new complex shapes using Constructive Solid Geometry (CSG). POV-Ray supports unions, merges, intersections and differences.
- Objects are assigned materials called textures (a texture describes the coloring and surface properties of a shape) and interior properties such as index of refraction and particle media (formerly known as "halos").
- Built-in color and normal patterns: Agate, Bozo, Bumps, Checker, Crackle, Dents, Granite, Gradient, Hexagon, Leopard, Mandel, Marble, Onion, Quilted, Ripples, Spotted, Spiral, Radial, Waves, Wood, Wrinkles and image file mapping. Or build your own pattern using functions.
- Users can create their own textures or use pre-defined textures such as ... Brass, Chrome, Copper, Gold, Silver, Stone, Wood.
- Combine textures using layering of semi-transparent textures or tiles of textures or material map files.
- Display preview of image while rendering (not available on all platforms).
- Halt and save a render part way through, and continue rendering the halted partial render later.
<<lessThe Persistence of Vision Ray-Tracer(tm) was developed from DKBTrace 2.12 (written by David K. Buck and Aaron A. Collins) by a bunch of people (called the POV-Team?) in their spare time. The headquarters of the POV-Team is on the internet (see "Where to Find POV-Ray Files" for more details).
The POV-Ray package includes detailed instructions on using the ray-tracer and creating scenes. Many stunning scenes are included with POV-Ray so you can start creating images immediately when you get the package. These scenes can be modified so you do not have to start from scratch.
In addition to the pre-defined scenes, a large library of pre-defined shapes and materials is provided. You can include these shapes and materials in your own scenes by just including the library file name at the top of your scene file, and by using the shape or material name in your scene.
Ray-tracing is not a fast process by any means, but it produces very high quality images with realistic reflections, shading, perspective and other effects.
Ray-tracing is a rendering technique that calculates an image of a scene by simulating the way rays of light travel in the real world. However it does its job backwards. In the real world, rays of light are emitted from a light source and illuminate objects. The light reflects off of the objects or passes through transparent objects. This reflected light hits our eyes or perhaps a camera lens. Because the vast majority of rays never hit an observer, it would take forever to trace a scene.
Ray-tracing programs like POV-Ray start with their simulated camera and trace rays backwards out into the scene. The user specifies the location of the camera, light sources, and objects as well as the surface texture properties of objects, their interiors (if transparent) and any atmospheric media such as fog, haze, or fire.
For every pixel in the final image one or more viewing rays are shot from the camera, into the scene to see if it intersects with any of the objects in the scene. These "viewing rays" originate from the viewer, represented by the camera, and pass through the viewing window (representing the final image).
Every time an object is hit, the color of the surface at that point is calculated. For this purpose rays are sent backwards to each light source to determine the amount of light coming from the source. These "shadow rays" are tested to tell whether the surface point lies in shadow or not. If the surface is reflective or transparent new rays are set up and traced in order to determine the contribution of the reflected and refracted light to the final surface color.
Special features like inter-diffuse reflection (radiosity), atmospheric effects and area lights make it necessary to shoot a lot of additional rays into the scene for every pixel.
Main features:
- Easy to use scene description language.
- Large library of stunning example scene files.
- Standard include files that pre-define many shapes, colors and textures.
- Very high quality output image files (up to 48-bit color).
- 16 and 24 bit color display on many computer platforms using appropriate hardware.
- Create landscapes using smoothed height fields.
- Many camera types, including perspective, orthographic, fisheye, etc.
- Spotlights, cylindrical lights and area lights for sophisticated lighting.
- Photons for realistic, reflected and refracted, caustics. Photons also interact with media.
- Phong and specular highlighting for more realistic-looking surfaces.
- Inter-diffuse reflection (radiosity) for more realistic lighting.
- Atmospheric effects like atmosphere, ground-fog and rainbow.
- Particle media to model effects like clouds, dust, fire and steam.
- Several image file output formats including Targa, BMP (Windows only), PNG and PPM.
- Basic shape primitives such as ... spheres, boxes, quadrics, cylinders, cones, triangle and planes.
- Advanced shape primitives such as ... Tori (donuts), bezier patches, height fields (mountains), blobs, quartics, smooth triangles, text, superquadrics, surfaces of revolution, prisms, polygons, lathes, fractals, isosurfaces and the parametric object.
- Shapes can easily be combined to create new complex shapes using Constructive Solid Geometry (CSG). POV-Ray supports unions, merges, intersections and differences.
- Objects are assigned materials called textures (a texture describes the coloring and surface properties of a shape) and interior properties such as index of refraction and particle media (formerly known as "halos").
- Built-in color and normal patterns: Agate, Bozo, Bumps, Checker, Crackle, Dents, Granite, Gradient, Hexagon, Leopard, Mandel, Marble, Onion, Quilted, Ripples, Spotted, Spiral, Radial, Waves, Wood, Wrinkles and image file mapping. Or build your own pattern using functions.
- Users can create their own textures or use pre-defined textures such as ... Brass, Chrome, Copper, Gold, Silver, Stone, Wood.
- Combine textures using layering of semi-transparent textures or tiles of textures or material map files.
- Display preview of image while rendering (not available on all platforms).
- Halt and save a render part way through, and continue rendering the halted partial render later.
Download (8.8MB)
Added: 2005-05-04 License: GPL (GNU General Public License) Price:
4144 downloads
WW2D 0.99.5
WW2D is cross-platform port of NASA WorldWind application. more>>
WW2D is cross-platform, free and open-source version of NASA World Wind software, see http://worldwind.arc.nasa.gov for details. WW2D allows you to explore Earth using satellite imagery, topographic maps and image from other data sources also providing large placenames and boundaries database and allowing you to install additional data packs for even more information about our planet.
In basic configuration WW2D uses images from Blue Marble (1 km/pixel), LandSat7 (15 m/pixel), USGS Topo Maps, USGS Digital Ortho imagery, USGS Urban Area imagery.
WW2D is designed to dynamically download needed data from internet, however you can download data you want for faster access and offline usage.
Main features:
- Cross-platform code
- BlueMarble, LandSat 7, USGS imagery
- World, US, Canadian, Norwegian, Swedish boundaries
- Large Placenames database
- Search and Quicksearch
- Semi-transparent layers
- Support for worldwind:// links
- Partial support for WorldWind data (conversion needed)
<<lessIn basic configuration WW2D uses images from Blue Marble (1 km/pixel), LandSat7 (15 m/pixel), USGS Topo Maps, USGS Digital Ortho imagery, USGS Urban Area imagery.
WW2D is designed to dynamically download needed data from internet, however you can download data you want for faster access and offline usage.
Main features:
- Cross-platform code
- BlueMarble, LandSat 7, USGS imagery
- World, US, Canadian, Norwegian, Swedish boundaries
- Large Placenames database
- Search and Quicksearch
- Semi-transparent layers
- Support for worldwind:// links
- Partial support for WorldWind data (conversion needed)
Download (4.5MB)
Added: 2005-08-27 License: GPL (GNU General Public License) Price:
1737 downloads
LMarbles 1.0.7
LMarbles is an Atomix clone with a slight change in concept. more>>
LMarbles is an Atomix clone with a slight change in concept. Instead of assembling molecules you create figures out of marbles. Nevertheless, the basic game play is the same: If a marble starts to move it will not stop until it hits a wall or another marble.
To make it more interesting there are obstacles like one-way streets, crumbling walls and portals.
As Marbles is meant as a puzzle game you play against a move limit and not a time limit. This way you have as much time as you need to think.
<<lessTo make it more interesting there are obstacles like one-way streets, crumbling walls and portals.
As Marbles is meant as a puzzle game you play against a move limit and not a time limit. This way you have as much time as you need to think.
Download (0.80MB)
Added: 2005-04-02 License: GPL (GNU General Public License) Price:
1673 downloads
BioBrew Linux 3.0.2.04
BioBrew Linux is an open source Linux distribution based on the NPACI Rocks cluster software and enhanced for bioinformaticists. more>>
BioBrew Linux is an open source Linux distribution that is enhanced for life scientists. It is customized for cluster and bioinformatics computing. It automates cluster installation, includes all the HPC software a cluster enthusiast needs, and contains popular bioinformatics applications.
BioBrew Linux is an open source Linux distribution based on the NPACI Rocks cluster software and enhanced for bioinformaticists and life scientists. While it looks, feels, and operates like ordinary Red Hat Linux, BioBrew Linux includes popular cluster software e.g. MPICH, LAM-MPI, PVM, Modules, PVFS, Myrinet GM, Sun Grid Engine, gcc, Ganglia, and Globus, *and* popular bioinformatics software e.g. the NCBI toolkit, BLAST, mpiBLAST, HMMER, ClustalW, GROMACS, PHYLIP, WISE, FASTA, and EMBOSS.
It runs on everything from notebook computers to large clusters. BioBrew Linux for the Itanium architecture is only available for purchase at this time through Callident. Please contact Brewmeister Glen Otero for information regarding BioBrew Linux on Itanium.
<<lessBioBrew Linux is an open source Linux distribution based on the NPACI Rocks cluster software and enhanced for bioinformaticists and life scientists. While it looks, feels, and operates like ordinary Red Hat Linux, BioBrew Linux includes popular cluster software e.g. MPICH, LAM-MPI, PVM, Modules, PVFS, Myrinet GM, Sun Grid Engine, gcc, Ganglia, and Globus, *and* popular bioinformatics software e.g. the NCBI toolkit, BLAST, mpiBLAST, HMMER, ClustalW, GROMACS, PHYLIP, WISE, FASTA, and EMBOSS.
It runs on everything from notebook computers to large clusters. BioBrew Linux for the Itanium architecture is only available for purchase at this time through Callident. Please contact Brewmeister Glen Otero for information regarding BioBrew Linux on Itanium.
Download (1980MB)
Added: 2005-05-18 License: GPL (GNU General Public License) Price:
1622 downloads
Ultratron 1.5
Ultratron is an arcade game where you have to destroy the four evil robots of the Apocalypse! more>>
Ultratron is an arcade game where you have to destroy the four evil robots of the Apocalypse!
The last human has been slain by evil killer robots. You are the one remaining humanoid battle droid. Your mission is to avenge the human race, and destroy the four bots of the Apocalypse - Ieiunitas, Bellum, Lues and Letum!
Power up your droid with ever more powerful weaponry as you blast your way through the levels, avoiding Chasers, Turrets, Spawners, Minelayers, bombs, and bullets!
Main features:
- 70+ different robots to destroy
- 40+ levels of frantic shooter action
- 4 giant boss robots
- 10 powerups
- Bonus stages
- Online hiscore table
<<lessThe last human has been slain by evil killer robots. You are the one remaining humanoid battle droid. Your mission is to avenge the human race, and destroy the four bots of the Apocalypse - Ieiunitas, Bellum, Lues and Letum!
Power up your droid with ever more powerful weaponry as you blast your way through the levels, avoiding Chasers, Turrets, Spawners, Minelayers, bombs, and bullets!
Main features:
- 70+ different robots to destroy
- 40+ levels of frantic shooter action
- 4 giant boss robots
- 10 powerups
- Bonus stages
- Online hiscore table
Download (MB)
Added: 2006-03-16 License: Freeware Price:
1604 downloads
Bioinformatics Benchmark System 3
Bioinformatics Benchmark System is a bioinformatics benchmark system for platform performance measurement. more>>
The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems.
What we are trying to do is to create a framework for testing, and a core set of tests that all may download and use to probe specific elements of systems performance.
Moreover, the source to these tests are available under GPL, and are hosted on Bioinformatics.org and Scalable Informatics LLC The idea is to enable end users, consumers, systems developers, and others to easily build and use meaningful tests for measurement and tuning reasons.
Joe Landman from Scalable Informatics LLC conceived the idea and wrote the original codes. We are looking for additional benchmark code suggestions, tests, data sets, etc.
Current baseline tests are several NCBI BLAST runs, several HMMer runs, and a variety of others. We plan to include ClustalW, X!Tandem, various chemistry, dynamics, and related tests, as well as several others.
Tests such as LINPACK or HPL simply do not provide meaningful performance indicators or predictive models for high performance informatics. Unfortunately, nor do a number of more recent and focused tests.
This is a problem as LINPACK and HPL specifically test the performance on various matrix operations, where you have effectively regular memory access patterns, and specific mathematical operations.
These codes are most useful for comparison to codes with heavy floating point operations, and interleaved memory traffic. These codes were not designed for comprehensive systems benchmarking, where disk I/O, memory latency, and other factors all contribute to the performance issues.
The best tests are the ones that are most similar to the codes you will run on the machine. The tests themselves should be reasonable approximations to a real execution of your code, using real data. You may need to pare it back in order to get realistic run times.
You should have a reasonable subset of data sizes. A single test does not tell you how your system scales, and one of the reasons for the existance of this test is specifically to allow you to test the performance while you increase various aspects of the workload.
You rarely get a quiescent system in a cluster, so we would recommend that you try to run in as realistic an operating environment as possible. A baseline in a quiescent system is fine, but it may set your expectations unreasonably.
top
<<lessWhat we are trying to do is to create a framework for testing, and a core set of tests that all may download and use to probe specific elements of systems performance.
Moreover, the source to these tests are available under GPL, and are hosted on Bioinformatics.org and Scalable Informatics LLC The idea is to enable end users, consumers, systems developers, and others to easily build and use meaningful tests for measurement and tuning reasons.
Joe Landman from Scalable Informatics LLC conceived the idea and wrote the original codes. We are looking for additional benchmark code suggestions, tests, data sets, etc.
Current baseline tests are several NCBI BLAST runs, several HMMer runs, and a variety of others. We plan to include ClustalW, X!Tandem, various chemistry, dynamics, and related tests, as well as several others.
Tests such as LINPACK or HPL simply do not provide meaningful performance indicators or predictive models for high performance informatics. Unfortunately, nor do a number of more recent and focused tests.
This is a problem as LINPACK and HPL specifically test the performance on various matrix operations, where you have effectively regular memory access patterns, and specific mathematical operations.
These codes are most useful for comparison to codes with heavy floating point operations, and interleaved memory traffic. These codes were not designed for comprehensive systems benchmarking, where disk I/O, memory latency, and other factors all contribute to the performance issues.
The best tests are the ones that are most similar to the codes you will run on the machine. The tests themselves should be reasonable approximations to a real execution of your code, using real data. You may need to pare it back in order to get realistic run times.
You should have a reasonable subset of data sizes. A single test does not tell you how your system scales, and one of the reasons for the existance of this test is specifically to allow you to test the performance while you increase various aspects of the workload.
You rarely get a quiescent system in a cluster, so we would recommend that you try to run in as realistic an operating environment as possible. A baseline in a quiescent system is fine, but it may set your expectations unreasonably.
top
Download (5.0MB)
Added: 2005-08-12 License: GPL (GNU General Public License) Price:
1533 downloads
Pathological 1.1.3
Pathological is an enriched clone of the game Logical by Rainbow Arts. more>>
Pathological is an enriched clone of the game "Logical" by Rainbow Arts. To solve a level, fill each wheel with four marbles of matching color.
Various board elements such as teleporters, switches, filters, etc., make the game interesting and challenging. New levels can be created using your favorite text editor.
Main features:
- Sharp 800x600 graphics
- 50 diverse and challenging levels (more to come...)
- A cool 6-minute ambient soundtrack by an award-winning musician
<<lessVarious board elements such as teleporters, switches, filters, etc., make the game interesting and challenging. New levels can be created using your favorite text editor.
Main features:
- Sharp 800x600 graphics
- 50 diverse and challenging levels (more to come...)
- A cool 6-minute ambient soundtrack by an award-winning musician
Download (6.3MB)
Added: 2005-08-16 License: GPL (GNU General Public License) Price:
1531 downloads
Jump n Bumb 1.55
Jump & bump is a multiplayer game only with up to four players simultaneously. more>>
Youre a cute little bunny and you have to avoid the other bunnies from stomping on you and at the same time try to stomp as many opponents as possible.
Jump & bump is multiplayer only with up to four players simultaneously. Gather the local crew and have a blast.
<<lessJump & bump is multiplayer only with up to four players simultaneously. Gather the local crew and have a blast.
Download (0.45MB)
Added: 2005-09-06 License: GPL (GNU General Public License) Price:
1522 downloads
Vigyaan 1.0
Vigyaan is a Linux live CD for computational biology and chemistry. more>>
Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry.
It has been designed to meet the needs of both beginners and experts. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modeling software. VigyaanCD v0.1 is based on KNOPPIX v3.3.
At present the following ready to use software comes on VigyaanCD: Artemis, Bioperl, BLAST (NCBI-tools), ClustalX, Cn3D, EMBOSS tools, Garlic, GROMACS, Ghemical, GNU R, Gnuplot, GIMP, ImageMagick, Jmol, MPQC, NJPlot, Open Babel, Octave, PSI3, PyMOL, Rasmol, Raster3D, SMILE, TINKER, XDrawChem, Xmgr and Xfig. GNU C/C++/Fortran compilers and additional Linux tools (such as ps2pdf) are also available.
VigyaanCD also provides tools required to compile and install other applications (from source). Therefore, making testing of Linux applications possible on computers with other OS.
Enhancements:
- This release is based on KNOPPIX 3.7.
- Most software packages have been updated and new applications added.
<<lessIt has been designed to meet the needs of both beginners and experts. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modeling software. VigyaanCD v0.1 is based on KNOPPIX v3.3.
At present the following ready to use software comes on VigyaanCD: Artemis, Bioperl, BLAST (NCBI-tools), ClustalX, Cn3D, EMBOSS tools, Garlic, GROMACS, Ghemical, GNU R, Gnuplot, GIMP, ImageMagick, Jmol, MPQC, NJPlot, Open Babel, Octave, PSI3, PyMOL, Rasmol, Raster3D, SMILE, TINKER, XDrawChem, Xmgr and Xfig. GNU C/C++/Fortran compilers and additional Linux tools (such as ps2pdf) are also available.
VigyaanCD also provides tools required to compile and install other applications (from source). Therefore, making testing of Linux applications possible on computers with other OS.
Enhancements:
- This release is based on KNOPPIX 3.7.
- Most software packages have been updated and new applications added.
Download (638MB)
Added: 2005-09-07 License: Freely Distributable Price:
1509 downloads
OZONE 0.15
OZONE is a free, modular 3-D marble game, released under the terms of the GNU General Public Licence. more>>
OZONE is a free, modular 3-D "marble game", released under the terms of the GNU General Public Licence, either version 2, or (at your option) any later version.
Binaries are available for both Windows and Linux; ihope is working on an OS X version but is having little success at the moment.
OZONE uses OpenGL,SDL,ODE, and others, see Libs.
<<lessBinaries are available for both Windows and Linux; ihope is working on an OS X version but is having little success at the moment.
OZONE uses OpenGL,SDL,ODE, and others, see Libs.
Download (6.3MB)
Added: 2005-10-04 License: GPL (GNU General Public License) Price:
1481 downloads
PHPrbl 0.4
PHPrbl is a quick and easy tool that keeps clients using open proxies away from your site in order to reduce referrer spam. more>>
PHPrbl is a quick and easy tool that keeps clients using open proxies away from your site in order to reduce referrer spam.
Ever had those annoying referrer spammers ruin your websites statistics? If you run a big website, or a weblog, you must be getting fed up with this blasted referrer spam.
Youre not alone, I have this problem as well and got fed up with the whole thing. After weeks of playing with the idea of blocking referrer spammers using rewrite rules, I got fed up wit the high amount of energy it would demand of me just to block IP addresses that seemed to be open proxies anyway.
Enhancements:
- Streamlined the code based on input given by Steven Lynn. Fewer queries are now used to do the same thing. Thanks!
- New feature: keywords checking; referrers are now matched to keywords given by the site admin. If a match occurs, the client will be blocked. (For myself this feature has already proven to be very, very effective)
- First start of an admin area for PHPrbl, for now, only the ability to add and removed keywords is present. Whitelisting and local IP blocklist management will be added soon.
<<lessEver had those annoying referrer spammers ruin your websites statistics? If you run a big website, or a weblog, you must be getting fed up with this blasted referrer spam.
Youre not alone, I have this problem as well and got fed up with the whole thing. After weeks of playing with the idea of blocking referrer spammers using rewrite rules, I got fed up wit the high amount of energy it would demand of me just to block IP addresses that seemed to be open proxies anyway.
Enhancements:
- Streamlined the code based on input given by Steven Lynn. Fewer queries are now used to do the same thing. Thanks!
- New feature: keywords checking; referrers are now matched to keywords given by the site admin. If a match occurs, the client will be blocked. (For myself this feature has already proven to be very, very effective)
- First start of an admin area for PHPrbl, for now, only the ability to add and removed keywords is present. Whitelisting and local IP blocklist management will be added soon.
Download (0.016MB)
Added: 2005-10-26 License: GPL (GNU General Public License) Price:
1458 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
Papagayo 1.1
Papagayo is a lip-sync program to synchronize animation with audio. more>>
Papagayo is a lip-sync program to synchronize animation with audio.
Papagayo is a lip-syncing program designed to help you line up phonemes (mouth shapes) with the actual recorded sound of actors speaking.
Papagayo makes it easy to lip sync animated characters by making the process very simple - just type in the words being spoken (or copy/paste them from the animations script), then drag the words on top of the sounds waveform until they line up with the proper sounds.
Papagayo is designed to be used with Moho, a 2D cartoon animation program, but since its open source, it can be modified for use with other animation applications.
<<lessPapagayo is a lip-syncing program designed to help you line up phonemes (mouth shapes) with the actual recorded sound of actors speaking.
Papagayo makes it easy to lip sync animated characters by making the process very simple - just type in the words being spoken (or copy/paste them from the animations script), then drag the words on top of the sounds waveform until they line up with the proper sounds.
Papagayo is designed to be used with Moho, a 2D cartoon animation program, but since its open source, it can be modified for use with other animation applications.
Download (2.5MB)
Added: 2005-12-06 License: GPL (GNU General Public License) Price:
1429 downloads
qgreylistrbl 0.5
qgreylistrbl is an add-on for qmail. more>>
qgreylistrbl is an add-on for qmail.
Now there are a lot of methods against spam, I have combined two of them: greylisting only for dialin nodes and nodes listed on a RBL. NDNs with more than one recipient will be rejected with permanent error messages and without a greylist entry. A test for EHLO/HELO spoofing was added: if a string is obviously spoofed, the connection will be rejected with a permanent error message, without a greylist entry, and advice to RFC2821. You can define a maximum number of recipients per email.
Greylisting returns a temporary SMTP error at the first delivery attempt. Most spam is sent from bulk mailers that dont retry, so these attempts are blocked. Real mail servers will retry later after a temporary error, allowing the message to go through.
Of course cannot all mail be delayed half an hour or longer to our customers. Thats why I have decided to modify the program qgreylist from Jon Atkins. I have added a RBL request to accept emails from not RBL listed nodes and to delay only dialin lines and RBL listed nodes. The script tests the PTR record of each connecting host for a regular expression to detect dialin nodes.
qgreylist from Jon Atkins puts all files in one base dir. qgreylistrbl creates here a directory structure because of performance reasons. The cleanup is now done by a separate cronjob script and not by qgreylistrbl itself, because when there were some ten thousand files inside the mail server nearly stands still.
Most bulk mailers and zombies,too, do not have queue management. They blast that much emails out into the net, they would be swamped with it. An Example: We use a UW-160 Raid 10 for the queue, but the usual zombie out there has only one IDE disc. Beside even a layman would ask why his hard drive was running all the time.
Effect
80% less spam. Yes, truly. No false positives, NO email gets lost.
Usage
qgreylistrbl is a replacement for rblsmtpd by D.J. Bernstein. Simply put qgreylistrbl instead of rblsmtpd in the command line for starting qmail-smtpd.
Performance
qgreylistrbl is a Perl script. Expect some CPU usage. If you run a QMAILQUEUE-patched version of qmail-smtpd and spamassassin, the load will decrease extensive, because most connection attempts do not cause a mail delivery. With perl > 5.6.1 you can precompile the source code with perlcc.
Installation:
Just copy the perl script wherever you want and edit the start script for qmail-smtpd. qgreylistrbl is a simple replacement for rblsmtpd from D.J. Bernstein and can be used the same way.
Create the greylist IP folder:
# mkdir /var/qmail/qgreylistrbl
# chown qmaild /var/qmail/qgreylistrbl
Adjust User
If you need to install the perl module Mail:RBL, just do the following:
From the root prompt on your server, invoke the CPAN shell:
# perl -MCPAN -e shell
Once the Perl interpreter has loaded (and been configured), you can install modules by issuing the command install MODULENAME.
The first thing you should do is upgrade your CPAN:
cpan> install Bundle::CPAN
Once its done (it will take a while, just enter all questions), type:
cpan> reload cpan
Now, enter the following command to retrieve all of the required modules:
cpan> install Mail::RBL
Then you can be shure everything is installed to correct locations.
Configuration:
At the beginnung of the script you have to adjust a few variables. See script for more details. Important are hostname, working directory, some paths and RBL services. You have to add a crontab entry as follows:
*/20 * * * * vpopmail /var/qmail/bin/qgreylist_cleanup.pl
Adjust user, path and time before.
Dont forget so set up logging facility in /etc/syslog.conf
<<lessNow there are a lot of methods against spam, I have combined two of them: greylisting only for dialin nodes and nodes listed on a RBL. NDNs with more than one recipient will be rejected with permanent error messages and without a greylist entry. A test for EHLO/HELO spoofing was added: if a string is obviously spoofed, the connection will be rejected with a permanent error message, without a greylist entry, and advice to RFC2821. You can define a maximum number of recipients per email.
Greylisting returns a temporary SMTP error at the first delivery attempt. Most spam is sent from bulk mailers that dont retry, so these attempts are blocked. Real mail servers will retry later after a temporary error, allowing the message to go through.
Of course cannot all mail be delayed half an hour or longer to our customers. Thats why I have decided to modify the program qgreylist from Jon Atkins. I have added a RBL request to accept emails from not RBL listed nodes and to delay only dialin lines and RBL listed nodes. The script tests the PTR record of each connecting host for a regular expression to detect dialin nodes.
qgreylist from Jon Atkins puts all files in one base dir. qgreylistrbl creates here a directory structure because of performance reasons. The cleanup is now done by a separate cronjob script and not by qgreylistrbl itself, because when there were some ten thousand files inside the mail server nearly stands still.
Most bulk mailers and zombies,too, do not have queue management. They blast that much emails out into the net, they would be swamped with it. An Example: We use a UW-160 Raid 10 for the queue, but the usual zombie out there has only one IDE disc. Beside even a layman would ask why his hard drive was running all the time.
Effect
80% less spam. Yes, truly. No false positives, NO email gets lost.
Usage
qgreylistrbl is a replacement for rblsmtpd by D.J. Bernstein. Simply put qgreylistrbl instead of rblsmtpd in the command line for starting qmail-smtpd.
Performance
qgreylistrbl is a Perl script. Expect some CPU usage. If you run a QMAILQUEUE-patched version of qmail-smtpd and spamassassin, the load will decrease extensive, because most connection attempts do not cause a mail delivery. With perl > 5.6.1 you can precompile the source code with perlcc.
Installation:
Just copy the perl script wherever you want and edit the start script for qmail-smtpd. qgreylistrbl is a simple replacement for rblsmtpd from D.J. Bernstein and can be used the same way.
Create the greylist IP folder:
# mkdir /var/qmail/qgreylistrbl
# chown qmaild /var/qmail/qgreylistrbl
Adjust User
If you need to install the perl module Mail:RBL, just do the following:
From the root prompt on your server, invoke the CPAN shell:
# perl -MCPAN -e shell
Once the Perl interpreter has loaded (and been configured), you can install modules by issuing the command install MODULENAME.
The first thing you should do is upgrade your CPAN:
cpan> install Bundle::CPAN
Once its done (it will take a while, just enter all questions), type:
cpan> reload cpan
Now, enter the following command to retrieve all of the required modules:
cpan> install Mail::RBL
Then you can be shure everything is installed to correct locations.
Configuration:
At the beginnung of the script you have to adjust a few variables. See script for more details. Important are hostname, working directory, some paths and RBL services. You have to add a crontab entry as follows:
*/20 * * * * vpopmail /var/qmail/bin/qgreylist_cleanup.pl
Adjust user, path and time before.
Dont forget so set up logging facility in /etc/syslog.conf
Download (0.73MB)
Added: 2005-12-20 License: GPL (GNU General Public License) Price:
1408 downloads
KCheckers 0.8.1
KCheckers is the Qt version of the classic boardgame more>>
Qt version of the classic boardgame "checkers". KCheckers game is also known as "draughts".
KCheckers is distributed under the GNU GPL.
Main features:
- Pure Qt.
- Built-in checkers engine.
- English and Russian rules of play.
- Beginner, Novice, Average, Good, Expert and Master levels of skill.
- Green, Marble and Wooden themes of the board.
- Portable Draughts Notation database format support.
- PDN preview widget.
- Saving, loading and restarting of game.
- Auto change of the mens color.
- Undo of last move.
- Auto saving of settings.
- Optional numeration of the board.
- Game information box.
- The on-line description of the plays rules.
- Threads support.
- Internationalization support (now German and Russian).
- Network capabilities.
Rules of play:
- In the beginning of game you have 12 checkers (men).
- The men move forward only. The men can capture:
- by jumping forward only (english rules);
- by jumping forward or backward (russian rules).
- A man which reaches the far side of the board becomes a king.
- The kings move forward or backward:
- to one square only (english rules);
- to any number of squares (russian rules).
- The kings capture by jumping forward or backward.
- Whenever a player is able to make a capture he must do so.
Enhancements:
- A bug that occurred in SuSE 9.3 when compiling with GCC 3.3 was fixed.
- Unused code was removed.
<<lessKCheckers is distributed under the GNU GPL.
Main features:
- Pure Qt.
- Built-in checkers engine.
- English and Russian rules of play.
- Beginner, Novice, Average, Good, Expert and Master levels of skill.
- Green, Marble and Wooden themes of the board.
- Portable Draughts Notation database format support.
- PDN preview widget.
- Saving, loading and restarting of game.
- Auto change of the mens color.
- Undo of last move.
- Auto saving of settings.
- Optional numeration of the board.
- Game information box.
- The on-line description of the plays rules.
- Threads support.
- Internationalization support (now German and Russian).
- Network capabilities.
Rules of play:
- In the beginning of game you have 12 checkers (men).
- The men move forward only. The men can capture:
- by jumping forward only (english rules);
- by jumping forward or backward (russian rules).
- A man which reaches the far side of the board becomes a king.
- The kings move forward or backward:
- to one square only (english rules);
- to any number of squares (russian rules).
- The kings capture by jumping forward or backward.
- Whenever a player is able to make a capture he must do so.
Enhancements:
- A bug that occurred in SuSE 9.3 when compiling with GCC 3.3 was fixed.
- Unused code was removed.
Download (0.080MB)
Added: 2005-12-30 License: GPL (GNU General Public License) Price:
1395 downloads
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