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The main purpose of AmplifX is to seek in a collection of primers, such as any molecular biologist will get in his refrigerators, those which can be used to amplify a fragment into a target sequence. For example, and particularly, to design strategies to screen recombinant clones by PCR. Some information is associated with each primer, some automatically computed by AmplifX (like TM, Quality, length) and others given by the user (name, comments,...) This allows general aspects of primer management (sequences and real tubes). AmplifX can also design new primers.
A plasmid Editor - It is designed to be an all-in-one molecular biology workbench. It can read strider, EMBL, genbank, Fasta sequence file formats. In addition it can read and display ABI trace files. It can query and download from the NCBI EMBL database and can blast sequences directly at the NCBI BLAST server. Sequence features can be added individually or automatically from pre-defined feature definition libraries. It can draw graphic (liear or circular) and text-based restriction maps that include annotated features of the sequence. It contains a restriction enzyme choser that can perform boolean queries for enzymes that match cut frequency and enzyme property parameters. It can show virtual agarose gels. It can align two sequences or a sequence and an ABI trace file. It can search selected sequence for potential PCR primers matching given parameters. All analysis functions are hyperlinked back to the original sequence.
The Atomic Mac 6.9.1
The Atomic Mac is the award winning periodic table of the elements for the Macintosh. In addition to the usual information found in such programs, The Atomic Mac also contains a wealth of nuclear information on each isotope, including half life, decay mode, and daughter products. No other periodic table of the elements has more data than The Atomic Mac.
Download File Size: 3.0 MB
Atom in a Box 1.1
Atom in a Box is an application that aids in visualizing the Hydrogenic atomic orbitals, a prime and otherwise unwieldy example of quantum mechanics. Unlike other tools in this category, this program raytraces through a three-dimensional cloud density that represents the wavefunction's probability density and presents its results in real-time. The user interface is very interactive and provides a wide degree of flexibility.
Download File Size: 404 Kb - version 1.0.8
Ball & Stick 3.8b3
Ball & Stick generates images and animations of three dimensional molecular models at atomic resolution. It requires input files from either structure libraries (e.g. protein data bank) or generated by experimental methods (e.g. X-ray crystallography, NMR,...) of by computatioanl chemistry (e.g. molecular mechanics, quantum-mechanics,...)
Beware of Molecules 3.3.4
Beware of Molecules 3 is a small application designed as a small helper for calculating the weight on different molecules. It comes loaded with over a hundred compounds, and more can be added.
BioAssistant was written to assist PCR Chemists design DNA Probes. With BioAssistant you can do all the things you could do with Probe Assistant, such as determine probe Melting Points (Tm), Molecular Weights, Hybridization information and other useful tidbits, but with a much cleaner and easy to use interface. It also extends on Probe Assistant feature set by introducing several useful tools, such as a Master Mix Calculator.
BLAST is a popular open source biotechnology application used by life science researchers to find matches in DNA and protein sequences - a highly processor - intensive task. Developed by ACG in collaboration with Genentech, Inc. and the Stanford University Genetics Department, Apple/Genentech BLAST provides improved accuracy and speed over the standard NCBI BLAST, depending on search parameters such as the nucleotide match-length.
Bone Age 2.1
Assess bone age and stature according to the reference standards of Greulich and Pyle (2nd ed). A graph of bone age is plotted against chronological age which is then available for importing into the medical record.
Due to copyright restrictions the software does not include the source reference standards and images, which may be obtained here [Stanford University].
The Cell Culture Laboratory Information Management System (CCLims) is an all emcompasing solution that manages all facets of your Cell Culture Laboratory. The CCLims was designed by Cell Culture Specialists for Cell Culture Specialists. No other LIMS comes close to supporting Cell Culture the way the CCLims does.
Just a few of the things you can do with the CCLims...
* Seamlessly manage all of your dewars and freezers.
* See a list of growing cells with one click.
* Get reminders for upcoming tasks like medium changes or dosings.
* Quickly print labels for all of your flasks.
* Easily keep separate records for each user in your laboratory.
* Track all inventory used for any experiment automatically.
* Set up complicated formulas in advance of an experiment using a integreated calculation engine.
* Automatically link customers, users and vendors.
* Organize your whole day in just a few minutes.
* Print and configure reports for any and all data within the CCLims.
* Maintain continuity of procedures and data as specialists come and go.
Whether your challenge is to introduce new computer technology to your curriculum, or bring the lab experience to on-line students or a need for an alternative to dangerous, expensive or environmentally hazardous labs, then Model ChemLab is the classroom proven solution for you.
Model ChemLab is a unique product incorporating both an interactive simulation and a lab notebook workspace with separate areas for theory, procedures and student observations. Commonly used lab equipment and procedures are used to simulate the steps involved in performing an experiment. Users step-through the actual lab procedure while interacting with animated equipment in a way that is similar to the real lab experience.
CrystalDiffract works with CrystalMaker, reading from saved crystal files to simulate and display powder diffraction patterns on screen. You can drag-and-drop a crystal file into CrystalDiffract, or use CrystalMaker's Transform > Diffraction Pattern > Powder command to obtain a diffraction pattern for any displayed crystal structure.
Diffraction patterns can be displayed as traditional greyscale "films", or as diffractometer traces (graphs of intensity versus two-theta, d-spacing, 1/d, time-of-flight or energy). Tools allow you to measure peak positions, intensities, and their Miller indices. You can precisely scroll the diffraction pattern, or select a plot range and zoom. Other tool buttons provide scaling functions, as well as x and y-axis offsets.
CrystalMaker is a program for generating, displaying, and manipulating all kinds of crystal and molecular structures, in stunning photo-realistic colour. CrystalMaker is a very powerful crystallographic tool - but is designed to be used by everyone, not just professional crystallographers. CrystalDiffract is a program to generate, display and manipulate x-ray and neutron powder diffraction patterns - straight from your CrystalMaker binary files.
EarthDesk is the only cross-platform dynamic desktop map, supporting real time clouds and accurate moonlight.
- 4320x2160 resolution
- Multi-display support
- Multiple projections
- City lights glow at night
- Accurate moonlight
- Beautiful, crisp images
EarthBrowser is a revolutionary new platform for viewing and creating geographically based information. Based on Adobe AIR, EarthBrowser has an integrated web browser and can be seamlessly installed and updated right from this web page.
Animated weather model forecasts from the NOAA are continuously updated for the entire world.
Datasets include Precipitation, Snowfall, Temperature, Pressure, Humidity, Wind Speed/Direction and more.
Embedded Web Browser
Seamless web integration enables location based information to be easily found and bookmarked.
Create, store and share your own web links, placemarks and photos
Explore, investigate and research information about the entire world in the information rich EarthBrowser interface. Perfect for home study and classroom settings.
Download File Size: 9.7 MB - Earth Browser 2.11.0 - Non-Adobe Air Version
Designed as a sister application to MoonDock - it provides a lightweight view of the Earth day-light/seasonal cycles and takes up few system resources so it can be left running on your desktop.
EMBOSS, The European Molecular Biology Open Source Software Suite, is a package of high-quality FREE Open Source software for sequence analysis.
EMBOSS includes hundreds of applications. They share a similar interface, but each comes with its own documentation.
EnzymeX is a program for molecular biologists, developed to help you determine which restriction enzymes you should use to cut your DNA of interest. In addition, it gives you all the specific properties of these enzymes so that you can make sure that every single digestion is a success.
The aim is to introduce a computer simulation that simulates the origin of species in a population of virtual animals caused by evolution.
4Peaks is a program that helps molecular biologists to visualize and edit their DNA sequence files. At last there is a decent solution for analyzing trace files on the MacOSX platform, taking another step away from slow and non-native programs from the MacOS9 period. Also, 4Peaks supports most commonly used sequence file formats right out of the box, you no longer have to convert them first using AppleScripts or other painstaking methods. Analyzing your sequence was never so much fun!
GearTrain calculates the angular velocity of the final driven gear in a gear chain. The user enters the revolutions per minute and driection of the first driver gear along with information about the number of teeth of each gear in the series. The program will output the RPM and direction of the final driven gear in the gear train. It was designed as a tool for educators and students wishing to learn or check calculations for a gear chain in a Technology Education or Robotics program.
GenChemLab is an OpenGL-based application intended to simulate several common general chemistry exercises. It is meant to be used to help students prepare for actual lab experience. It could also be used in cases where laboratory facilites are not accessible, for instance in K-12 schools or home schooling.
At present, supported experiments include titration, calorimetry, freezing point depression, vapor pressure, and spectrophotometry.
Gene Construcktion Kit 2.5
The Gene Construction Kit allows graphic manipulation of DNA sequences and sophisticated plasmid drawing capabilities. The Gene Construction Kit represents a breakthrough in interface design that allows graphic manipulation of DNA sequences in addition to providing sophisticated drawing capabilities. It is ideal for designing and managing complex construction projects or assembling DNA sequences for use in DNA analysis programs such as the DNA Inspector. It readily generates high quality black and white or color illustrations for slides, posters, or papers.
Direct Download - Manual
Gene Inspector 1.6.7
The Gene Inspector can perform many sophisticated sequence analyses, but this new software is much more than just another sequence analysis product. Imagine having the ability to define an entire suite of analyses to be performed each time you have a new sequence, and to design custom style sheets which specify exactly how your output will look for each analysis. Because you can predefine and store analysis parameters for any analysis to fit your needs, anyone in the lab will be able to obtain meaningful and consistent results, whether they are a novice just entering the lab, or an experienced researcher familiar with the analysis routines. The combination of notebook with navigation and drawing tools and sophisticated analyses provides the ability to annotate experimental results and analyses in a single location, rather than keeping your sequence analyses separate from you lab notes.
Golly is an open source, cross-platform Game of Life simulator currently under development by Andrew Trevorrow and Tomas Rokicki. Our goal is to write a world-class Life simulator, solicit ideas and help from the planet's best Life hackers, and share some of our excitement.
Golly's key features:
Unbounded universe (limited only by memory).
Fast, memory-efficient conventional algorithm.
Super fast hashing algorithm for highly regular patterns.
Responsive even while generating or garbage collecting.
Reads RLE, Life 1.05/1.06, and macrocell formats.
Can paste in patterns from the clipboard.
Auto fit option keeps patterns sized to the window.
Full screen option (no menu/status/tool/scroll bars).
Built-in HTML help system (thanks to wxWidgets).
Google Earth 5.0.11729.10146
Want to know more about a specific location? Dive right in -- Google Earth combines satellite imagery, maps and the power of Google Search to put the world's geographic information at your fingertips.
Fly from space to your neighborhood. Type in an address and zoom right in.
Search for schools, parks, restaurants, and hotels. Get driving directions.
Tilt and rotate the view to see 3D terrain and buildings.
Save and share your searches and favorites. Even add your own annotations.
Google Earth puts a planet's worth of imagery and other geographic information right on your desktop. View exotic locales like Maui and Paris as well as points of interest such as local restaurants, hospitals, schools, and more.
ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh.
It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.
Download File Size: 1.3 MB - ImageJ 1.42e Jar Update - December 17, 2008
The easiest way to upgrade to the latest version of ImageJ is to use the Plugins>Utilities>Update ImageJ command, available in version 1.39 or later. Use the ImageJ Updater plugin to upgrade earlier versions.
You can also upgrade by downloading the latest JAR file (ij.jar) from rsb.info.nih.gov/ij/upgrade/ij.jar and copying it into the ImageJ folder.
iMass (short for isotopeMass) includes a molecular mass calculator, a periodic table of the elements, an isotope distribution graph and a calculator that computes elemental compositions matching a given mass. iMass understands complex chemical formulas as well as user defined abbreviations for commonly used formulas.
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, XYZ, MOL2, HIN, CAR, ALC, BIO. The molecules can be saved as PDB, XYZ 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.
Are you longing for an NMR software as stylish as the iMac, as intuitive as the iPod, as surprising as iLife and as cheap as iWork? Fast, interactive and perfectly integrated with Tiger? Look no further. Enter iNMR. It is continuosly tailored to the needs of the customers and, at the same time, strictly adhers to the conventions of the Acqua interface. Ours is the only NMR software written for Mac OS X. While others say: "running under" we say: "written for". What a difference two words make!
Ising is a Monte Carlo simulation of the two-dimensional Ising model, demonstrating phase transitions of a magnetic system. You can adjust the temperature, magnetic field, and lattice size (up to 400x400) while the simulation is running. Besides graphical output, the program keeps track of the current value, average, and standard deviation of the energy and magnetization, which you can copy and paste into a spreadsheet for further analysis.
Download File Size: 728 Kb
This application provides an interface for running simulations of the Ising model of magnetically interacting spins on a 2-dimensional lattice. It is intended as a demonstration of the possibilities for interactive exploration of scientific models - the computing power available in modern machines is sufficient to perform sophisticated calculations on the fly as the parameters are changed.
Source code is also available via the IsingCocoa home page.
This is a small application which displays "Life" a simulation of cells which live & die by three simple rules. Life was created by John Conway and popularized in Scientific American's Mathematical Recreations column. A classic in the computer world.
LifeLab is a Mac application for exploring John Conway's Game of Life and other cellular automata. CAs were first studied in the mid-1950s by Stanislaw Ulam and John von Neumann. The subject became much more widely known in 1970 when Life was described by Martin Gardner in his Scientific American column.
Life is played on an arbitrary-sized grid of square cells. Each cell has two states: "dead" or "alive". The state of every cell changes from one "generation" to the next according to the states of its 8 nearest neighbors: a dead cell becomes alive (a "birth") if it has exactly 3 live neighbors; a live cell dies out if it has less than 2 or more than 3 live neighbors. The "game" of Life simply involves starting off with a pattern of live cells and watching it evolve.
Live Deskpicture 3.1
An alternative to a static desktop picture - Install a self-updating time-zone map of the earth with day, night, twilight and city lights. The map updates automatically as the world turns. High resolution maps and graphics are individually crafted for 16 different monitor sizes from 800 x 600 all the way up to 2560 x 1600 pixels (The new Apple 30" display). While you work or while you leave your computer just sitting there, the newest desk picture keeps slipping behind your icons as often as you choose. The process repeats every time the earth rotates one pixel on your screen. Program operation is time-sliced in order to avoid interruptions of your work. The dock icon menu lets you highlight time zones to find the time at any worldwide location. If you are using two monitors, Live Deskpicture X works with either one or both.
Download File Size: 1.9 MB - version 1.2.2
Mac Brownian Motion 1.3b3
Mac Brownian Motion is a program that simulates (tah dah...) Brownian Motion. Brownian Motion is exhibited in a variety of situations, including motion of particles. Much of stochastic analysis (introduced in a graduate statistics program) is based on the properties of Brownian Motion. Physicists, engineers, economists, and statisticians all rely on its nice properties. It is primarily an educational tool. In fact, its purpose is (originally) rather narrow: to visualize Brownian Motion in one dimension over time.
MacClade is used as a tool for phylogenetic analysis. But by its nature it also embodies a world view, a portrayal of a phylogenetic approach to studying diversity and evolution. It is relatively easy to see the diversity of living organisms, but it has proved more difficult to see that diversity in terms of its history; the slow development of a thoroughly phylogenetic perspective in biology attests to this challenge. Together the MacClade manual and program present methods for analyzing and exploring phylogenetic hypotheses, including hypotheses about character evolution. MacClade is one attempt to give our mind's eye phylogenetic lenses, to help us think about and see lineages and evolution.
Download File Size: 1.5 MB - 4.0.8 updater
Researchers who want a simple, but comprehensive, desktop sequence analysis application continually turn to MacVector, the leading sequence analysis package for the Macintosh. MacVector provides sequence editing, primer design, Internet database searches, protein analysis, sequence confirmation, contig assembly capabilities, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a wide variety of other functions. With MacVector, you can view the results of any analysis in graphical or text format.
Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed. Analyses include:
Reconstruction of ancestral states (parsimony, likelihood)
Tests of process of character evolution, including correlation
Simulation of character evolution (categorical, DNA, continuous)
Parametric bootstrapping (integration with programs such as PAUP* and NONA)
Morphometrics (PCA, CVA, geometric morphometrics)
Coalescence (simulations, other calculations)
Tree comparisons and simulations (tree similarity, Markov speciation models)
Direct Download File Size: 7.9 MB
Molecules is a two-dimensional molecular dynamics simulation of a collection of structureless, interacting particles (such as noble gas atoms). Click the image at right to see a demonstration applet. Uses of this program range from visualizing frictionless motion to quantitative study of phase transformations. The full-featured user interface lets you create up to 1000 particles of two different types, adjust their sizes, masses, and interaction strengths, add a gravitational field, monitor the temperature and pressure, and save configurations for later use.
Download File Size: 792 Kb
Mr. Tides 3.0r16
Mr. Tides 3.0 is a Universal application for Mac OS X 10.4 that displays tides and currents for locations around the world. Written completely in Objective-C, Mr. Tides 3 is compatible with both Intel and PPC Macintosh computers.
Download File Size: 8.3 MB - version 126.96.36.199
Download File Size: 12.6 MB
MutantMaker helps researchers performing site directed mutagenesis screen their potential mutants with restriction enzyme digests rather than costly sequencing. The oligonucleotide sequences suggested by MutantMaker will create or destroy restriction sites while both creating the desired mutant and retaining flanking amino acids.
Using a simple and elegant user interface, researchers enter their original DNA sequence into a text field, drag a codon selector over the codon to mutate, and choose how to mutate their selected amino acid.
MutantMaker has 492 unique restriction enzymes built right in, not including isoschizomers! Users can select any set of enzymes based on commercial availability or size.
MutantMaker results are even multi-colored showing exactly which nucleotides were mutated.
In typical fashion, results can be saved and reloaded for later use. And for reliability, data files are human-readable XML.
ODLog is an easy-to-use application for the accurate timing and recording of observational data. ODLog is typically used by scientists in:
naturalistic field observation studies
animal behavioral experiments
human psychological experiments
Oligo is a multi-functional program that searches for and selects oligonucleotides from a sequence file for polymerase chain reaction (PCR), DNA sequencing, site-directed mutagenesis, and various hybridization applications. It calculates hybridization temperature and secondary structure of oligonucleotides based on the nearest neighbor thermodynamic values.It is also a good tool for construction of synthetic genes, finding an appropriate sequencing primer among those already synthesized, finding and multiplexing consensus prmers and probes, and even finding potential restriction sites in a protein.
The Oligo software has been broadly accepted as the industry software standard for selecting and analyzing oligonucleotides for various molecular biology applications. The first commercial version of the software has been introduced in 1989.
A program to let you check which of your oligos you can use in a PCR for any given template (on my 1 GHz Powerbook it checks my 409 oligos against a 2 kB template in about 1.5 seconds).
Upon selecting two oligos for a PCR it will show the sequence (and inverted sequence) and size of the PCR product as well as the alignment of the oligos with the template.
It is not a program to help you design oligos - there are already programs out there which do this (e.g. the $1,200 Oligo, or online with Primer3).
Neither is it 's main purpose to run a PCR simulation
OSXBackstrip performs 1D Backstripping of sedimentary Strata. Backstripping is not a difficult task but it is tedious. OSXBackstrip makes backstripping enjoyable.
OSXFlex2D is a program that implements the "elastic" , "flexural" model. Flexural modeling is not a difficult task but it is tedious. OSXFlex2D makes flexural modeling easy.
OSXGeoCalc is a Structural Geology Calculator. It operates on lines and planes, strains, and stresses. Individual computations can be made using the calculator's interface. Multiple computations can be performed using text files. Lines and planes can be visualized in a Stereonet.
OSXGeoCalc was made for geologists, but it can be used by anyone who is interested in planes and lines, strains, and stresses (physicists, engineers, geotechnicians, etc.).
OSXplanet is a live desktop program based on xplanet.
Periodic Table 4.2
Packed with data and easy to use features, Periodic Table 4 is superb for chemists and chemistry students, as well as anyone who is fascinated with science or the world around them! It's not just for chemists! Periodic Table includes a variety of historical information on element discoveries, element name etymologies and more!
Whether you're looking for aluminum or actinium (or aluminium), melting points or magnetic susceptiblities, or zinc or zirconium, Synergy Creations' Periodic Table has it.
Download File Size: 2.2 MB
The Periodic Table 1.4
It's a simple periodic table where you can click on the elements to display basic information: Symbol, Name, Atomic Number, Mass, and Phase under standard conditions. Double-clicking on an element will open a link to that element's wikipedia page for additional information. I've added the ability to select different elemental properties, and the table will remap the colors around these property values. This allows people to observe some basic periodic trends. The user preferences are also stored now, so the widget will always restart with the user's preferred style.
Physics 101 SE 7.2
The perfect solution for physics students and teachers everywhere, Physics 101 SE is the premier physics calculation tool, allowing you to focus on physics and not mathematical busywork. With its ability to instantly solve for almost any variable in over 125+ (list of formulas) of the most commonly used physics formulas, you'll be able to quickly and accurately complete physics assignments like never before. Just select the formula you need, enter values like distance and time, then click "calculate." With Physics 101 SE, it's that simple, every time.
Not only is PTE a printable Periodic Table of Elements and contains detailed information on each of the elements, but allows users to get specific information in a snap, or view everything in a sortable list! Users can easily bring up two or more windows to compare elements, or copy the data into another application.
With its easy to use interface and affordability to students, we hope our software will aid in your chemistry projects, homework, and everything else you need to become an expert!
Radiology Anatomy Atlas. This is a free program that allows viewing of labeled images of human anatomy. The labels are linked to a database that offers in-depth descriptions of the parts of anatomy. An image or series of images is stored in a folder and then accessed by the program. The user can download as many of these folders of images as desired and then access them using their own personal computer.
Tide Widget 2.21
The Tide widget displays the current tide or current for locations worldwide, using the XTIDE tide engine to predict the tides.
Wooster Physics Software
The College of Wooster Computational Physics Project showcases some of the best computer software created by Wooster physics majors. These applications are written in C++ and exploit many of the features of the modern Macintosh Graphical User Interface.
Download File Size: 50 Kb - Foucault - Animates a Foucault pendulum at user defined latitudes.
Download File Size: 127 Kb - Duffing - Interactively explore the phase space flow of the famous Duffing nonlinear oscillator
Download File Size: 86 Kb - Sandpile - 3D OpenGL sandpile automaton.
Download File Size: 78 Kb - Thomson's Sphere - Repulsive particles move on a 2-sphere to minimum-energy configurations.
Download File Size: 85 Kb - Drumhead - Waves on a square drumhead rendered in 3D. Adjust damping and initial state.
Download File Size: 98 Kb - Protein Folding - Chain of hydrophilic and hydrophobic monomers fold at finite temperature to form an energy minimizing polypeptide.
Denotes Mac OS X Intel Native
Denotes Mac OS X Intel & PPC Native
Denotes Mac OS X PPC Native
Denotes Mac OS 8/9 PPC Native
Denotes Mac OS 680x0 Native
Denotes Non-OS Specific Code