bio
iMol 0.4
iMol is a free molecular visualization application for Mac OS X operating system. The program is an indispensable tool for chemists and molecular biologists more>> iMol is a free molecular visualization application for Mac OS X operating system. The program is an indispensable tool for chemists and molecular biologists. iMol allows loading molecules using several file formats: PDB, MOL2, HIN, CAR, ALC, BIO. The molecules can be saved as PDB or BIO files. The BIO file stores all view and rendering settings (e.g. colors, lighting, orientation of molecules). iMol can easily handle both small and large molecules, it can load multiple molecules, move and rotate them independently.
The program can meaure distances, angles, and torsional angles between atoms. Molecules can be superimposed and RMSD (Root Mean Square Deviation) between atom coordinates can be calculated. Additionaly, protein chains can be structurally aligned to detect regions of high structural similarity. iMol can load multimodel PDB files and display them as a dynamics trajectory.
iMol uses OpenGL graphics to display molecules. The molecules can be rendered using various styles: wires, points, Van der Waals spheres, balls and sticks, polygons, strands, ribbon, cartoons, spring, tube, ladder. Individual atoms and/or residues can be selected and rendered independly. The rendering styles can be mixed up to visualize complex molecular systems in a more convienient way. There are several predefined color schemes available (e.g. residuum order, secondary structure, hydrophobicity), as well as custom colors. Also, different materials (e.g. plastic, metal, glass) can be used. The rendered images may be exported as a bitmap, as a PostScript file, or as a POV-Ray file.
Several rendering effects are available, including automatic rotation, motion blur, depth cueing (fog), background gradient, perspective, and stereo projection (using both side-by-side and red/blue anaglyph methods). Various rendering parameters can be fine-tuned.
Mac OS X 10.2 or later.
Version 0.4:
- Several Intel-transition-related bugs fixed.
- Anti-aliased bitmaps of arbitrary resolution can be saved.
- Fixed cartoon and solid ribbon rendering mode.
Bochs 2.4.1
A portable x86 PC emulation software package. more>> A portable x86 PC emulation software package.
Bochs is a portable x86 PC emulation software package that emulates enough of the x86 CPU, related AT hardware, and BIOS to run Windows, Linux, *BSD, Minix, and other OSs, all on your workstation.
Bochs is a highly portable open source IA-32 (x86) PC emulator written in C++, that runs on most popular platforms.
Bochs includes emulation of the Intel x86 CPU, a custom BIOS and common I/O devices. Currently, Bochs can be compiled to emulate a 386, 486, Pentium/PentiumII/PentiumIII/Pentium4 or x86-64 CPU including optional SSEx, MMX, and 3DNow! instructions.
Bochs is capable of running most Operating Systems inside the emulation including Linux, Windows 95, DOS, and Windows NT 4. Bochs was written by Kevin Lawton and is currently maintained by this project.
Bochs can be compiled and used in a variety of modes, some which are still in development. The typical use of Bochs is to provide complete x86 PC emulation, including the x86 processor, hardware devices, and memory.
This allows you to run OSes and software within the emulator on your workstation, much like you have a machine inside of a machine. For instance, lets say your workstation is a Unix/X11 workstation, but you want to run Win95 applications.
Bochs will allow you to run Win 95 and associated software on your Unix/X11 workstation, displaying a window on your workstation, simulating a monitor on a PC.
Enhancements
- Fixed bunch of CPUID issues
- Bochs is now able to install and boot 64-bit Windows images!
- Several bugfixes in CPU emulation (mostly for x87 instructions)
- Fixed two critical deadlock bugs in the Win32 gui.
- Fixes related to the show ips feature
- Removed conflicting win32-specific alarm() functions (win32 and sdl gui)
- Feature now works in wx on win32
- Added support for gdb stub on big endian machine.
- Rewritten obsolete hash_map code in dbg symbols module.
- BIOS: implemented missing INT 15h/89h.
Bochs 2.3pre2
Bochs is a portable x86 PC emulation software package more>>
It is a highly portable open source IA-32 (x86) PC emulator written in C++, that runs on most popular platforms. It includes emulation of the Intel x86 CPU, common I/O devices, and a custom BIOS. Currently, Bochs can be compiled to emulate a 386, 486, Pentium, Pentium Pro or AMD64 CPU, including optional MMX, SSE, SSE2 and 3DNow instructions. Bochs is capable of running most Operating Systems inside the emulation including Linux, Windows 95, DOS, and Windows NT 4. Bochs was written by Kevin Lawton and is currently maintained by this project.
Bochs can be compiled and used in a variety of modes, some which are still in development. The typical use of Bochs is to provide complete x86 PC emulation, including the x86 processor, hardware devices, and memory. This allows you to run OSes and software within the emulator on your workstation, much like you have a machine inside of a machine. For instance, lets say your workstation is a Unix/X11 workstation, but you want to run Win95 applications. Bochs will allow you to run Win 95 and associated software on your Unix/X11 workstation, displaying a window on your workstation, simulating a monitor on a PC.
Enhancements:
- fix corrupt saved configuration files (Christophe Bothamy)
- fix missing break statements in apic (Shai Fultheim)
- fix compiling sb16 under FreeBSD (Volker Ruppert)
- updates to the documentation (Volker)
- fix text mode colors 8 to 15 (Volker)
- fix FPU integer load bug (Volker)
- stop pasting on hardware reset (Volker).
Geneious 3.0.6
Geneious - Molecular biology & genomics research tool more>>
As we complete testing of this Beta version we will be making Geneious 1.0 available to all scientists to make data management, organisation and filtering easy, rapid and automatic.
Geneious is a tool that provides sophisticated genome & proteome research tools, protein or molecular visualization, publication literature search and storage tools and more, with revolutionary usability.
So you get more done. And faster results faster to publication or faster to discovery.
Geneious is a usability revolution in the organization and visualization of bio-data (genome, proteome & publications). It includes an advanced and integrated suite of tools for
Sequence alignment and phylogenetics
Sequence analysis
Automatic search and storage of publications, BLAST. Protein structure viewing, NCBI, EMBL
Superstition 1.0
Superstition is a set of 7 icons about human Superstitions more>>
The initial inspiration for this icon set is the song "The Artist" by Big Rude Jake (Bio: http://www.maplemusic.com/artists/brj/bio.asp). If you have heard the song I think youll draw a connection, though I have tried to avoid offending anyone and have excluded any drawings depicting religious objects.
When I was 4 or 5 years old my family spent the night at my grandmother and grandfathers house, which was a cottage in a pine tree forest near Hanover, Ontario. Sometime that night I woke up and my gaze fell on the night sky outside the bedroom window. I remember clearly seeing a shooting star briefly arc above the pine trees and then I fell back to sleep.
The "shooting star" icon is composed from that personal memory.
CLC Main Workbench 5.5
CLC Main Workbench is described as a convenient as well as powerful tool that lets you aggregate all DNA sequence analyses of CLC Gene Workbench and all protein sequence analyses of CLC Protein Workbench. more>> <<less
CLC bio A/S - CLC Main WorkbenchLicense:update/patch
CLC bio A/S - 5.0.2 offers you a professional and highly-efficient math and science program. This 4-week fully functional demoDOSBox 0.73
Free and open source DOS-emulator for your Mac. more>> Free and open source DOS-emulator for your Mac.
DOSBox is a DOS-emulator that uses the SDL-library which makes DOSBox very easy to port to different platforms. DOSBox has already been ported to many different platforms, such as Windows, BeOS, Linux, Mac OS X.
Its statically compiled against SDL and built upon the Cocoa, Carbon, OpenGL, QuickTime, and AudioUnit frameworks.
DOSBox also emulates CPU:286/386 realmode/protected mode, Directory FileSystem/XMS/EMS, Tandy/Hercules/CGA/EGA/VGA/VESA graphics, a SoundBlaster/Gravis Ultra Sound card for excellent sound compatibility with older games.
This is a rather trivial port of DOSBox to MacOS X. What if you just want to play some old games? This port of DOSBox may be your answer.
Its statically compiled against SDL, is built upon the Cocoa, Carbon, OpenGL, QuickTime, and AudioUnit frameworks, and thus, is only MacOS 10.3.x (or Panther) compatible. It has partial protected mode emulation, a subset of VESA 1.2 functionality (800x600x8) via S3 Trio emulation, and internal modem support via the SDL_net framework.
You can "re-live" the good old days with the help of DOSBox, it can run plenty of the old classics that dont run on your new computer.
System requirements:
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Enhancements
- Add two new opl2+opl3 emulators. (better speed, different implementation approach)
- Improved DRO recording/better file structure.
- Add EGA emulation.
- Add special vga machine mode. Supports more of the exotic tricks like changing the palette during screen updates, 9x16 fonts etc.
- Added special machine modes for the following svga cards:S3ParadiseTseng
- Fix problems with the vga split line feature.
- Improve vesa emulation.
- Add optional selection of old vesa mode for games that dont work with certain vesa features.
- Improve video BIOS emulation to behave more like a real bios.
- Fixes for emulated 4bpp graphics modes.
- Fixes to paging system.
- Various fixes and improvements for the recompiling core.
- Add arm backend for the recompiling core.
- Add some mscdex quirks when dealing with files that are exactly 8.3 long.
- Small fixes to batch file handling.
- Small fixes to the XMS memory handling.
- Various fixes for aligned memory on hosts that want it.
- Various improvements to the mouse.
- Fixes and small speed ups to the debugger.
- Fix and improve lots of compilation problems. (curses detection, GCC 3.4 and GCC 4.X fixes)
- Added some basic auto keyboard layout handling. (windows only currently)
- Add basic support for evdev keyboard driver.
- Various fixes to the timer. (improve mode 2 timer changes, implement mode 1, improve gate2 handling)
- Add audio extraction and mci audio support. Should enable CDROM audio for Vista and adds volume control.
- Improve the directory cache speed a lot, especially with mounting slow media like network paths.
- Various fixes to the create temporary file call.
- Dont keep batchfiles open during execution. Allows rewriting of the active batchfile. (menu programs use this trick sometimes)
- Fix problems with filenames with 2 extensions.
- Add some more lowlevel dos tables.
- Fixes to hercules emulation.
- Fix flag handling for special case of ROR.
- Make the batchfile handling in regard to IF more flexible.
- Fixes to scrolling/panning feature.
- Add prefetch queue emulation.
- Make the emulated cpu type selectable. This is mainly the identification commands and the way paging works.
- Some special EMS functionality added. (OS handles, zero-page handling)
- Improve support for EMS when booting a different OS.
- Improve cdrom speed detection by games.
- Improve stability of cycle guessing code, when there is background activity.
- Fix various mscdex and cdrom detection schemes.
- Added Coremidi support on Mac OS X.
- Improve support for DOS devices when used to detect the existance of directories in various ways.
- Add IRQ 2 emulation on VRET. (ega only)
- Added video parameter table and video state functionality.
- Increase default freespace to 250 MB.
- Some fixes to the fat filesystem handling for disk images.
- Some soundblaster fixes and command additions.
- Fix mixer 16bit direct transfers on bigendian hosts.
Articles By Autoresponder 3.1
Articles By Autoresponder is an e-book supporting you free content for your Web site, e-zine, newsletter. more>>
Articles By Autoresponder 3.1 is an e-book supporting you free content for your Web site, e-zine, newsletter. It is for your reading enjoyment. There is a complete list of articles in 45 categories including Business, Internet Marketing, Web Site Design, Parenting, Relationships, Weight Loss, Self-Improvement, and more. Choose from more than 900 free articles. Every one is available by autoresponder for immediate delivery.
This eBook has search capabilities. It is available in both EXE and PDF formats. Plus, it includes a contents list with each category and a bio on each author. You can also have your own custom copy made with your articles listed on the front page.
1-Click Answers for Mac 1.0.19
1-Click Answers for Mac is regarded as a high-speed and powerful answer engine - the ultimate online reference library, with quick accurate dictionary, thesaurus, encyclopedia, bios, tech terms, news, sports, and weather. more>>
1-Click Answers for Mac 1.0.19 is regarded as a high-speed and powerful answer engine - the ultimate online reference library, with quick accurate dictionary, thesaurus, encyclopedia, bios, tech terms, news, sports, and weather. With 1-Click Answers, just click on any word (Command+Option+G) in any application (e-mail, browser, Office, and so on), and get a quick definition or explanation. The Answers Widget is available as a separate download.
Enhancements: Version 1.0.19 includes unspecified updates.
Flarestorm 2.0
Flarestorm - Playstation emulator more>>
Has advanced unbelievably quickly, the quickest seen in any Playstation emulator development.
Emulation is possible emulation the Playstation BIOS (basic input/output system) file which communicates between the operating system and the underlying hardware, and gives basic sets of instructions for the PSX console and must be used by emulators to play PSX games on a Computer unless you reverse engineer the Playstation.
And, needs PlayStation BIOS ROM to run. Requirements: Mac OS X 10.1 or later. Enhancements: Version 1.2a2 adds the following: Fixed CPU bugs. Fixed some GTE bugs. Fixed the handler for Flat shadingDCMetroWidget 0.9
DCMetroWidget - Late Trains - Know Before You Go! more>> Biolabs Absynth Sounds is a collection of nearly 400 presets for Absynth which includes a 300 MB specially-created sample library. The sounds have been expertly programmed by Biomechanoid, a respected sound designer and one of the principal authors of both the Absynth and Cameleon 5000 factory sounds. Were giving away 30 free demo presets for you to get a taste!
The library includes three volumes of 128 sounds: bio:synthesis, bio:rhythmics and bio:sfx+atmospheres. Every preset has at least four specially-selected rapid access controllers, giving you fast access to the most important parameters. The sounds have also been tagged with attributes to make it easy to search for the sounds you need.
Features:
- A huge library of nearly 400 presets
- 300 MB specially-recorded sample library
- Rapid access parameters for each patch - perfect for live tweaking.
- Attribute tagged to make searching for the presets you require fast and easy<<less
CLC Protein Workbench 5.2
CLC Protein Workbench is designed for providing a wide range of advanced protein analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. more>> <<less
CLC bio A/S - CLC Protein Workbench. CLC Protein Workbench 5.1 is a useful tool which provides a wide range of advanced protein analyses, and is based on the same user-friendlyCLC bio A/S - CLC Protein Workbench. CLC Protein Workbench 5.0.2 brings an advanced program which is capable of providing a wide range of advanced protein analysesCLC RNA Workbench 4.2
CLC RNA Workbench brings you an easy way to a range of complex algorithms and options. RNA secondary structures can be predicted using state-of-the-art free energy minimization algorithms. more>>
CLC RNA Workbench 4.2 brings you an easy way to a range of complex algorithms and options. RNA secondary structures can be predicted using state-of-the-art free energy minimization algorithms.
Major Benefits:
- You will have easy access to a large number of integrated research tools:
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- Secondary structure prediction
- Graphical view and editing of secondary structure
- Tabular view of structures and energy contributions
- Symbolic representation in sequence view
- You can make your computer a High Performance Computing center
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- Unleash the hidden powers in your CPU with the Bioinformatics Cell
- Plug in the Bioinformatics Cube and increase your search speed up to 200 times
- Your research work will be easy to carry out
- The program is graphically based, intuitive, and user-friendly
- Share data with your colleagues using CLC Database Solution
- You will have a bioinformatics solution that continuously evolves
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- The frequent program updates keep you up to date with the latest scientific developments. Your ideas for future improvements will have top priority.
- You can customize your workbench
- You have the possibility to customize your workbench through our Software Developer Kit.
Major Features:
- Bioinformatics features in CLC RNA Workbench
- Secondary structure prediction
- Graphical view and editing of secondary structure
- Tabular view of structures and energy contributions
- Symbolic representation in sequence view
- Pattern search
- Search for sequence matches
- Motif search for basic patterns
- Motif search using regular expressions
- Motif search with ProSite patterns
- Pattern discovery (unknown patterns)
- Project and data management
- Full integration of data input, data management, calculation results, and data export
- Detailed history log
- All types of files can be saved in local projects, and launched from the program
- Import and export of data in a large number of file formats
- Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects
- Other bioinformatics features
- DNA, RNA and protein sequence editor displaying both linear and circular molecules
- Multiple alignment of DNA, RNA, and proteins
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- Two proprietary algorithms
- ClustalW
- Muscle
- T-Coffee
- MAFFT
- Kalign
- Joining multiple alignments into one
- DNA, RNA, and protein alignment editor
- Interactive logo graphs along both DNA, RNA and Protein alignments
- Batch processing of analyses on multiple sequences in one work-step
- Advanced re-alignment and fix-point alignment option
- Manual annotation of sequences
- Dot plot based analyses
- Local complexity region analyses and complexity plots
- Gap fraction graphs
- G/C content analysis and graphs
- Advanced pairwise comparison
- Extract annotations
- Database searches
- Web based sequence search using BLAST
- BLAST on local databases
- Build local BLAST databases
- GenBank Entrez searches
- PubMed lookup
- Web based lookup in UniProt, NCBI, and Google
Enhancements:
- New features:
-
- Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
- Advanced view of elements in a folder including batch editing.
- Extract sequences improvements
- You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)
- "Find" in text view now accepts Enter as command to find the next hit
- Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
- Export of annotations in GFF format (note that annotations with joined regions are not supported)
- Bug fixes:
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- Fixed tblastn numbering issue
- Problem rendering scatter plots without lines
- DNA strider files could loose name upon import
- Rare misplacement of annotations when editing very large sequences
- Various bug-fixes
CLC bio A/S - CLC RNA Workbench. CLC RNA Workbench 4.1 is a powerful utility which gives the user easy access to a range of complex algorithms and options. RNA secondary structuresCLC bio A/S - CLC RNA Workbench. CLC RNA Workbench 4.0.2 is a complete tool which is able to give the user fast and easy access to a range of complex algorithms and options. RNA
CLC DNA Workbench 5.5
CLC DNA Workbench 5.5 is a helpful program that creates a software environment enabling users to make a large number of advanced DNA sequence analyses, combined with smooth data management, and excellent graphical viewing and output options. more>>
CLC DNA Workbench 5.5 is helpful program that creates a software environment enabling users to make a large number of advanced DNA sequence analyses, combined with smooth data management, and excellent graphical viewing and output options. This 4-week fully functional demo of CLC Gene Workbench provides a wide range of advanced DNA sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench.
Major Features:
- DNA sequence analysis
- Editor for graphically and algorithmically advanced primer design
- Assembly of DNA sequence data
- Multiplexing - Process Tagged Sequences has an option to filter away groups with few sequences.
- Molecular cloning
- Automatic SNP annotation of sequences
- Local complexity region analyses
- Reverse translation from protein to gene, based on translation tables from a number of species
- Advanced restriction enzyme analysis and management
- Dot plot based analyses
- DNA statistics report including a number of characteristics of a given molecule
- NCBI sequence data search
- Access to web info from PubMed
- Pattern search
- Search for sequence matches
- Motif search for basic patterns
- Motif search using regular expressions
- Motif search with ProSite patterns
- Pattern discovery (unknown patterns)
- Database searches
- Web-based sequence search using BLAST
- BLAST on local databases
- Build local BLAST databases
- GenBank Entrez searches
- UniProt searches (SwissProt/TrEMBL)
- PubMed lookup
- Web-based lookup in UniProt, NCBI, and Google
- SNP annotation using BLAST
- Project and data management
- Full integration of data input, data management, calculation results, and data export
- Detailed history log
- All types of files can be saved in local projects, and launched from the program
- Import and export of data in a large number of file formats
- Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects
- Other bioinformatics features
- DNA, RNA and protein sequence editor displaying both linear and circular molecules
- Multiple alignment of DNA, RNA, and proteins
-
- Two proprietary algorithms
- ClustalW
- Muscle
- T-Coffee
- MAFFT
- Kalign
- Joining multiple alignments into one
- DNA, RNA, and protein alignment editor
- Interactive logo graphs along both DNA, RNA and Protein alignments
- Batch processing of analyses on multiple sequences in one work-step
- Advanced re-alignment and fix-point alignment option
- Manual annotation of sequences
- Dot plot based analyses
- Local complexity region analyses and complexity plots
- Gap fraction graphs
- G/C content analysis and graphs
- Advanced pairwise comparison
- Extract annotations
Enhancements:
- Gateway cloning. Simple and easy-to-use support for creating Gateway entry and expression clones.
- Search for matches among all your saved primers. The Find Binding Sites tool has been greatly improved to now allow you to search among all your primers. In addition, you also get a tabular output of the binding sites and possible fragments.
- In silico PCR: create PCR product based on primer pair and template sequence (including primer extensions). As part of the improve...
Requirements:
- Mac OS X 10.4 or later (including Intel-based Macs)
- Windows 2000, XP, Vista, or Windows 7
- Linux: Redhat or SuSE
- 256 MB RAM required
- 2 GB RAM recommended
- 1024 x 768 display recommended
CLC bio A/S - CLC DNA Workbench. CLC DNA Workbench 5.2 is considered as a flexible program that provides a wide range of advanced DNA sequence analyses, and is based on the sameLicense:update/patch
CLC bio A/S - CLC DNA WorkbenchCLC bio A/S - 5.0.2 is designed to be a 4-week completely powerful demo of CLC Gene Workbench which provides a wide range of advanced DNARocketRAID 1810A 1.04
RocketRAID 1810A - Raid controller driver more>>
The RocketRAID 1810As low profile design makes it an ideal storage solution for 1U Rack mount servers.
The RocketRAID 1810A Serial ATA provides multi level RAID support including RAID 0, 1, 5, 10, and JBOD, as well as powerful software management functions.In addition to the BIOS configuration utility, the RocketRAID 1810A includes graphical OS-based RAID configuration software. CLI (Command Line Interface) software is available for Linux Operating Systems.
As a high-performance, affordable RAID solution, the RocketRAID 1810A makes sense for nearly any Server, critical business data storage, gaming, Audio/Video editing, security system, and high-end personal storage.
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