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organizations |
| 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.
Features:
- 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/
http://jwork.org/jport/pjp/ |
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
https://microscopetalk.wordpress.com/photomicrography/using-micam-with-tucsen-microscope-camera-configuration-calibration-and-measurement/
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/
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054072
https://biodesign.cc/2013/09/12/diy-automatic-colony-counter/ |
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/
http://openmrs.org/ |
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. |
|
knowledge, for open, free and low cost
computer software