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Name OS URL Description
Bioclipse 9.1 various systems http://www.bioclipse.net/ The Bioclipse project is a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Like any RCP application, Bioclipse uses a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. Via its plugins, Bioclipse provides functionality for chemo- and bioinformatics, and extension points that easily can be extended by other, possibly proprietary, plugins to provide additional functionality. The first stable release of Bioclipse includes a Chemistry Development Kit (CDK) plugin to provide a chemoinformatic backend, a Jmol plugin for 3D-visualization of molecules, and a BioJava plugin for sequence analysis. Recently, the R platform, using StatET, and OpenTox were added.
CellProfiler 9.1 various systems http://cellprofiler.org/ CellProfiler is free, open-source software for quantitative analysis of biological images (cell counting). No prior experience in programming or computer vision is required – this page is intended to help you get up and running
Cytoscape 9.1 various systems http://www.cytoscape.org/ Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store.
DataMelt 9.1 various systems http://jwork.org/dmelt/ DataMelt (or, in short, DMelt) a computation and visualization environment, is an interactive framework for scientific computation, data analysis and data visualization designed for scientists, engineers and students. DataMelt is multiplatform since it is written in Java, thus it runs on any operating system where the Java virtual machine can be installed. The program is designed for interactive scientific plots in 2D and 3D and contains numerical scientific libraries implemented in Java for mathematical functions, random numbers, statistical analysis, curve fitting and other data mining algorithms. DataMelt uses high-level programming languages, such as Jython, Apache Groovy, JRuby, but Java coding can also be used to call DataMelt numerical and graphical libraries. DataMelt is an attempt to create a data-analysis environment using open-source packages with a coherent user interface and tools competitive to commercial programs. The idea behind the project is to incorporate open-source mathematical and numerical software packages with GUI-type user interfaces into a coherent program in which the main user interface is based on short-named Java/Python classes. This was required to build an analysis environment using Java scripting concept.
Deducer 9.1 various systems http://www.deducer.org/ Deducer is designed to be a free easy to use alternative to proprietary data analysis software such as SPSS, JMP, and Minitab. It has a menu system to do common data manipulation and analysis tasks, and an Excel-like spreadsheet in which to view and edit data frames. Deducer provide an intuitive graphical user interface (GUI) for R, encouraging non-technical users to learn and perform analyses without programming getting in their way. Increase the efficiency of expert R users when performing common tasks by replacing hundreds of keystrokes with a few mouse clicks. Also, as much as possible the GUI should not get in their way if they just want to do some programming. Deducer is designed to be used with the Java based R console JGR

Features include:
- Intuitive graphical interface
- Data viewer provides an easy to use, spreadsheet-like environment to view and edit data
- Task based dialogs
- Work with multiple data frames at the same time
- Multiple analyses
- Tests and analyses are formatted into easy to read tables
- Analysis plots
- Perform common tasks with a few mouse clicks
- Online help system
Docear 9.1 various systems http://www.docear.org/ Docear is what the developers call an “academic literature suite”. Comparable to Microsoft Office, which bundles several applications for office workers, Docear bundles several applications for academics. As of now, these applications are BibTeX based reference management, mind mapping, and some pdf management capabilities. For the future, Docear is supposed to integrate a word processor, PDF editor and academic search engine. Docear is written in Java, licensed under the GNU General Public License and based on the open source software Freeplane and JabRef.
EMBOSS 4.1 Unix http://www.emboss.org/ https://www.freshports.org/biology/emboss/ The European Molecular Biology Open Software Suite (EMBOSS) is a comprehensive set (about 100) of open source tools for genetic sequence analysis. EMBOSS is produced by the European Molecular Biology Network (EMBnet - http://www.embnet.org/). All EMBOSS tools are all built around the same set of core libraries - AJAX and NUCLEUS - and therefore share a unified user interface, have similar "look and feel", and implement a uniform sequence addressing methodology. EMBASSY packages are third party applications which have been integrated with the EMBOSS suite, but which are not included in the base EMBOSS distribution for licensing or other reasons. The EMBASSY packages live in the biology/embassy port.
Free Mind 9.1 various systems http://freemind.sourceforge.net/wiki/index.php/Main_Page FreeMind is a free mind mapping application written in Java. It provides extensive export capabilities. As with other mind mapping software packages, FreeMind allows the user to edit a hierarchical set of ideas around a central concept. The non-linear approach assists in brainstorming new outlines and projects as ideas are added around the mind map.
FreeMat 4.1 Unix http://freemat.sourceforge.net/ https://www.freshports.org/math/freemat/ FreeMat is a free open-source numerical computing environment and programming language, similar to MATLAB and GNU Octave. In addition to supporting many MATLAB functions and some IDL functionality, it features a codeless interface to external C, C++, and Fortran code, further parallel distributed algorithm development (via MPI), and has plotting and 3D visualization capabilities. Community support takes place in moderated Google Groups.
GNU Octave 4.1 Unix https://gnu.org/software/octave/ https://www.freshports.org/math/octave-forge/ GNU Octave is software featuring a high-level programming language, primarily intended for numerical computations. Octave helps in solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language. Since it is part of the GNU Project, it is free software under the terms of the GNU General Public License.

Octave is one of the major free alternatives to Matlab, others being Scilab and FreeMat. Scilab, however, puts less emphasis on (bidirectional) syntactic compatibility with Matlab than Octave does
gretl 4.1 Unix http://gretl.sourceforge.net/ https://www.freshports.org/math/gretl/ gretl is an open-source statistical package, mainly for econometrics. The name is an acronym for Gnu Regression, Econometrics and Time-series Library. It has a graphical user interface (GUI) and can be used together with TRAMO/SEATS, R, Stata, Python, Octave, Ox and Julia.
- A wide variety of least-squares-based estimators (including two-stage least squares).
- Easy, intuitive interface.
- Single commands to launch things like augmented Dickey-Fuller test, Chow test for structural stability, Vector Autoregression.
- Reads own format ascii data files, Comma Separated Values files, BOX1 files, own format binary databases (allowing mixed data frequencies and series lengths) and RATS 4 databases. Includes a US macro database and a perl script to create a database off economagic.com.
- Output models as LaTeX files, in tabular or equation format.
- Integrated scripting language: enter commands either via the gui or via scripts.
- Command loop structure for Monte Carlo simulations.
- GUI controller for fine-tuning Gnuplot graphs.
- Link to R for further data analysis.
Image Analyzer 2.3 Microsoft Windows http://meesoft.logicnet.dk/ Advanced image editing, enhancement and analysis software. The program contains both most image enhancement features found in conventional image editors plus a number of advanced features not even available in professional photo suites. For microscopic imaging make HDR pictures from 2 or more pictures, 3d-modelling, z-stack, multifocus and many more usefull tools.
ImageJ 9.1 various systems http://imagej.nih.gov/ij/ ImageJ can display, edit, analyze, process, save, and print 8-bit color and grayscale, 16-bit integer, and 32-bit floating point images. It can read many image file formats, including TIFF, PNG, GIF, JPEG, BMP, DICOM, and FITS, as well as raw formats. ImageJ supports image stacks, a series of images that share a single window, and it is multithreaded, so time-consuming operations can be performed in parallel on multi-CPU hardware. ImageJ can calculate area and pixel value statistics of user-defined selections and intensity-thresholded objects. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as logical and arithmetical operations between images, contrast manipulation, convolution, Fourier analysis, sharpening, smoothing, edge detection, and median filtering. It does geometric transformations such as scaling, rotation, and flips. The program supports any number of images simultaneously, limited only by available memory.
jPort 9.1 various systems http://jwork.org/jport/
The jPort project is an application launcher for portable Java applications on every computer everywhere you go. jPort creates a Java enabled menu to launch dozens of free applications. jPort desktop does not require installation. Simply upload jPort on any desktop and hundreds of awesome applications will be under your fingertips. You can copy the jPort package to a USB flash drive and you can use jPort applications on any computer while you are traveling.
Julia 4.1 Unix https://julialang.org/ https://www.freshports.org/lang/julia/ Julia is a high-level dynamic programming language designed to address the needs of high-performance numerical analysis and computational science, without the typical need of separate compilation to be fast, while also being effective for general-purpose programming, web use or as a specification language. Distinctive aspects of Julia's design include a type system with parametric polymorphism and types in a fully dynamic programming language and multiple dispatch as its core programming paradigm. It allows concurrent, parallel and distributed computing, and direct calling of C and Fortran libraries for linear algebra, random number generation, signal processing, and string processing.without glue code. Julia is garbage-collected, uses eager evaluation and includes efficient libraries for floating-point calculations, linear algebra, random number generation, fast Fourier transforms and regular expression matching.
Jupyter Notebook 9.1 various systems http://jupyter.org/ The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more.
> The Notebook has support for over 40 programming languages, including Python, R, Julia, and Scala.
> Notebooks can be shared with others using email, Dropbox, GitHub and the Jupyter Notebook Viewer.
> Your code can produce rich, interactive output: HTML, images, videos, LaTeX, and custom MIME types.
> Leverage big data tools, such as Apache Spark, from Python, R and Scala. Explore that same data with pandas, scikit-learn, ggplot2, TensorFlow.
jWork.ORG 9.1 various systems http://jwork.org/main/ Our mission is to promote scientific computing for science and education. We believe any knowledge software should be free and accessible for education and research. It should be available on all platforms for all people. Computers and scientific programs help to uncover the world around us. We pledge for sharing scientific algorithms and tools. If you are a professional, contribute with your code here. If not, use our software to learn how to use computers for education and knowledge discovery.
Mango 9.1 various systems http://ric.uthscsa.edu/mango/index.html Mango – short for Multi-image Analysis GUI – is a viewer for medical research images. It provides analysis tools and a user interface to navigate image volumes.
Maxima 4.1 Unix http://maxima.sourceforge.net/ https://www.freshports.org/math/maxima/ Maxima is a system for the manipulation of symbolic and numerical expressions, including differentiation, integration, Taylor series, Laplace transforms, ordinary differential equations, systems of linear equations, polynomials, sets, lists, vectors, matrices and tensors. Maxima yields high precision numerical results by using exact fractions, arbitrary-precision integers and variable-precision floating-point numbers. Maxima can plot functions and data in two and three dimensions.
MICAM 2.3 Microsoft Windows http://science4all.nl/?Microscopy_and_Photography

WebCam as Microscope http://akbar.web.ugm.ac.id/?p=17
As I am a heavy microscope user I need a lot of functionality that can be accessed easily:
> Cropping images to a convenient size.
> Exposure correction inside MICAM after grabbing an image
> Rotation of the image
> Positioning of Scales and labels
> The use of short-cut keys, to make operating MICAM as easy as possible.
> Save the image with a selectable name from a database (so I don't have to type a long name like Micrasterias truncata)
> Save the picture as BMP, JPG, TIF or PNG
> File name can be: Date+Time+Magnification or File name+Number+Magnification (you can Copy (or load from file) a picture in a measuring window.
> After calibration you can measure objects on the photo
> Insert a scale (as you know from electron microscope pictures) and save the file again
> Make calibration files for up to 16 different microscope-webcam combinations
Comprehensive manual
MorphoJ 9.1 various systems http://www.flywings.org.uk/MorphoJ_page.htm MorphoJ is an integrated program package for doing geometric morphometrics. The goal of the program is to provide a platform for the most important types of analyses in geometric morphometrics in a user-friendly package. The program is written for both 2D and 3D data, with some inevitable differences in the graphical output possibilities etc.
MorphoJ Geometric Morphometrics Tutorial 9.1 various systems https://sampenrice.com/tutorials/geometric-morphometrics-tutorial/ I am going to use geometric morphometrics to prove that Disney princesses are all the same, and that Disney has a (consistent) face for evil. If you have used geometric morphometrics before, then this post probably isn’t for you. Unless of course, you want to find out the secrets to Disney faces, in that case, carry on. I am going to take you through the general concepts on geometric morphometrics, and show you a practical example. I will introduce you to some open source (hooray for free) software that can be used to do an analysis. There are links for all of these at the bottom of the page. There are a lot of online help sources for all of them, so if you get stuck, an easy google search will help in most cases.
MorphoJ User's Guide 9.1 various systems http://www.flywings.org.uk/MorphoJ_guide/frameset.htm?index.htm MorphoJ User's Guide web pages. This collection of web pages is intended to provide the essential information on the use of the MorphoJ package and on the methods implemented in it. For more thorough information, the reader is referred to the introductory books in the area of geometric morphometrics and to original publications of methods.
Morphometrics 9.9 no operating system http://life.bio.sunysb.edu/morph/index.html All for handling morphometrics, including a software list for morphometrics
Morphometrics - Modeling body and fin shape 9.9 no operating system http://swordtail.tamu.edu/anyfish/Modeling_body_and_fin_shape_%28morphometrics%29 Contents
1 Overview: geometric morphometrics and TPS grids
1.1 Step-by-step Instructions
2 Stickleback model
3 Poeciliid model
MultiSeq, for proteins and nucleic acids 9.1 various systems http://www.scs.illinois.edu/schulten/multiseq/ MultiSeq is a unified bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids. Special emphasis is placed on analyzing the data within the framework of evolutionary biology.
MyOpenLab 9.1 various systems http://myopenlab.org/ https://myopenlab.de MyOpenLab es un software de desarrollo basado en elementos gráficos, cada elemento cumple con una función específica y tiene propiedades configurables por el usuario, dichos componentes se pueden unir entre si para implementar de una manera sencilla la parte gráfica y lógica de una aplicación.
Neo4j 9.1 various systems https://neo4j.com/ Neo4j is a graph database management system developed by Neo Technology, Inc. Described by its developers as an ACID-compliant transactional database with native graph storage and processing, Neo4j is the most popular graph database according to db-engines.com. Neo4j is implemented in Java and accessible from software written in other languages using the Cypher Query Language through a transactional HTTP endpoint, or through the binary 'bolt' protocol.
Octave 9.1 various systems https://www.gnu.org/software/octave/ GNU Octave is software featuring a high-level programming language, primarily intended for numerical computations. Octave helps in solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with MATLAB. It may also be used as a batch-oriented language. Octave is one of the major free alternatives to MATLAB, others being FreeMat and Scilab. Scilab, however, puts less emphasis on (bidirectional) syntactic compatibility with MATLAB than Octave does.
OpenCFU 9.1 various systems http://opencfu.sourceforge.net/
Counting colonies on agar plates is a widely used method in microbiology. OpenCFU software that should facilitate (and render more reproducible) the enumeration of colony forming unit (CFU). You can simply run the program on your computer and input pictures of plated bacterial colonies (or other cells).
OpenEpi 9.1 various systems http://www.openepi.com/ http://unix.freetzi.com/epi/Menu/OE_Menu.htm OpenEpi is a free, web-based, open source, operating system-independent series of programs for use in epidemiology, biostatistics, public health, and medicine, providing a number of epidemiologic and statistical tools for summary data. OpenEpi was developed in JavaScript and HTML, and can be run in modern web browsers. The program can be run from the OpenEpi website or downloaded and run without a web connection. The source code and documentation is downloadable and freely available for use by other investigators. OpenEpi has been reviewed, both by media organizations and in research journals.
OpenMRS 9.1 various systems https://sourceforge.net/projects/openmrs/
OpenMRS is a community-developed, open source, enterprise electronic medical record system. Our mission is to improve health care delivery in resource-constrained environments by coordinating a global community to creates and support this software.
Orange (software) 9.1 various systems http://orange.biolab.si/ Orange is a component-based visual programming software package for data visualization, machine learning, data mining and data analysis. Orange components are called widgets and they range from simple data visualization, subset selection and preprocessing, to empirical evaluation of learning algorithms and predictive modeling. Visual programming is implemented through an interface in which workflows are created by linking predefined or user-designed widgets, while advanced users can use Orange as a Python library for data manipulation and widget alteration
PSPP 4.1 Unix https://www.gnu.org/software/pspp/ https://www.freshports.org/math/pspp/ PSPP is a free software application for analysis of sampled data, intended as a free alternative for IBM SPSS Statistics. It has a graphical user interface and conventional command-line interface. It is written in C and uses GNU Scientific Library for its mathematical routines. This software provides a comprehensive set of capabilities including frequencies, cross-tabs comparison of means (t-tests and one-way ANOVA); linear regression, logistic regression, reliability (Cronbach's alpha, not failure or Weibull), and re-ordering data, non-parametric tests, factor analysis, cluster analysis, principal components analysis, chi-square analysis and more.
Nota: the version 1.0 is stable
R 9.1 various systems https://www.r-project.org/ https://www.freshports.org/math/R/ R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency. The R distribution contains functionality for a large number of statistical procedures. Among these are: linear and generalized linear models, nonlinear regression models, time series analysis, classical parametric and nonparametric tests, clustering and smoothing. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations. Additional modules ("add-on packages") are available for a variety of specific purposes.
RapidMiner 9.1 various systems http://rapidminer.com/ "Lightning Fast Unified Data Science Platform"
RapidMiner is a data science software platform developed by the company of the same name that provides an integrated environment for data preparation, machine learning, deep learning, text mining, and predictive analytics. It is used for business and commercial applications as well as for research, education, training, rapid prototyping, and application development and supports all steps of the machine learning process including data preparation, results visualization, model validation and optimization. RapidMiner is developed on an open core model. One smaller free version is available too.
RStudio 9.1 various systems https://www.rstudio.org/ https://www.freshports.org/devel/RStudio/ RStudio es un entorno de desarrollo integrado (IDE) para el lenguaje de programación R, dedicado a la computación estadística y gráficos. Incluye una consola, editor de sintaxis que apoya la ejecución de código, así como herramientas para el trazado, la depuración y la gestión del espacio de trabajo.
SageMath - SAGE 4.1 Unix http://www.sagemath.org/ https://www.freshports.org/math/sage/ SageMath (previously SAGE, "System for Algebra and Geometry Experimentation"[) is a computer algebra system with features covering many aspects of mathematics, including algebra, combinatorics, graph theory, numerical analysis, number theory, calculus and statistics. Sage is a free open-source mathematics software system licensed under the GPL. It combines the power of many existing open-source packages into a common Python-based interface. Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.
SciLab 4.1 Unix http://www.scilab.org/ https://scilab.io/ https://www.freshports.org/math/scilab/ Scilab is an open source, cross-platform numerical computational package and a high-level, numerically oriented programming language. It can be used for signal processing, statistical analysis, image enhancement, fluid dynamics simulations, numerical optimization, and modeling, simulation of explicit and implicit dynamical systems and (if the corresponding toolbox is installed) symbolic manipulations.

Scilab is one of the two major open-source alternatives to MATLAB, the other one being GNU Octave. Scilab is similar enough to MATLAB that some book authors (who use it) argue that it is easy to transfer skills between the two systems.[5] Scilab however puts less emphasis on (bidirectional) syntactic compatibility with MATLAB than Octave does.
SciPy 9.1 various systems http://www.scipy.org/ SciPy es una biblioteca open source de herramientas y algoritmos matemáticos para Python que nació a partir de la colección original de Travis Oliphant que consistía de módulos de extensión para Python, lanzada en 1999 bajo el nombre de Multipack. SciPy contiene módulos para optimización, álgebra lineal, integración, interpolación, funciones especiales, FFT, procesamiento de señales y de imagen, resolución de ODEs y otras tareas para la ciencia e ingeniería. Está dirigida al mismo tipo de usuarios que los de aplicaciones como MATLAB, GNU Octave, y Scilab.
SOFA 9.1 various systems http://www.sofastatistics.com/ SOFA - Statistics Open For All, The user-friendly, open-source statistics,
analysis, and reporting package.
Spark 4.1 Unix http://spark.apache.org/
for FreeBSD: http://www.freshports.org/devel/spark/
Apache Spark is a fast and general-purpose cluster-computing framework. Originally developed at the University of California, Berkeley's AMPLab, the Spark codebase was later donated to the Apache Software Foundation, which has maintained it since. Spark provides an interface for programming entire clusters with implicit data parallelism and fault-tolerance. It provides high-level APIs in Java, Scala and Python, and an optimized engine that supports general execution graphs. It also supports a rich set of higher-level tools including Spark SQL for SQL and structured data processing, MLlib for machine learning, GraphX for graph processing, and Spark Streaming.
Statcato 9.1 various systems http://www.statcato.org/ https://sourceforge.net/projects/statcato/
Lab & Book: http://www.statcato.org/statcato/index.php/tutorials/lab-activities
Statcato is a Java software application for elementary statistics. Its features include data and graph generation, probability distributions, descriptive statistics, confidence intervals, hypothesis tests, correlation, regression, and analysis of var.
Features: - probability distributions (probability density, cumulative probability, inverse cumulative probability); - descriptive statistics (e.g. mean, sum, standard deviation, coefficient of variation, quartiles, skewness, kurtosis, etc.); - confidence intervals, hypothesis tests, correlation and regression, multinomial experiments, ANOVA.
The International Genome Sample Resource 9.9 no operating system http://www.internationalgenome.org/ The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set.
Unipro UGENE 4.1 Unix http://ugene.net/ Unipro UGENE is multiplatform, open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze, and visualize their data. UGENE integrates widely used bioinformatics tools within one common user interface. UGENE toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees, and 3D structures. On FreeBSD the total software-stack is suported. More information: http://ugene.net/downloads/UniproUGENE_UserManual.pdf
VMD, visual molecular dynamics 9.1 various systems http://www.ks.uiuc.edu/Research/vmd/
for FreeBSD http://www.freshports.org/science/vmd/
VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
Zotero 9.1 various systems https://www.zotero.org/ Zotero is a free and open-source reference management software to manage bibliographic data and related research materials (such as PDF files). Notable features include web browser integration, online syncing, generation of in-text citations, footnotes and bibliographies, as well as integration with the word processors Microsoft Word, LibreOffice, and OpenOffice.
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