A.12: Free apps for bioinformatics
- Page ID
- 45316
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Mike’s recommended free and/or open-source apps for bioinformatics on macOS or Windows 11 PCs.
Chrome OS users: If your device is Intel-based, then it is possible to install many of the apps (or equivalents) listed via activating LINUX on your device. This route is only advisable if you are willing and able to do some pretty serious installation work.
Statistics
R Core Team (2024). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Python programming language and libraries: panda, Numby, Scipy, Matplotlib, Biopython, PySB, and others
Mathematics software
GNU Octave, free and open source, uses similar programming syntax to MATLAB, https://octave.org/
SageMATH, python based, free and open source alternative to MATLAB and Wolfram Mathematica, https://www.sagemath.org/
Image, Drawing, Concept & Mind maps, Flow charts
Newt Editor, a free, web based, open source viewer and editor for biology pathways, https://newteditor.org/index.html
Draw.io, used to create work flows, mind maps, https://app.diagrams.net/
FreeCAD, open source “parametric 3D modeler”, https://www.freecad.org/
GIMP, GNU Image Manipulation Program, at https://www.gimp.org/
ImageJ2, JAVA-based, https://imagej.net/software/imagej2/
Krita, free and open source painting program, https://krita.org/en/
Preview, macos only
Screen recording, Video streaming
OBS Studio, at https://obsproject.com/
QuickTimePlayer, macos only
Office suite (compatible with Microsoft Word)
LibreOffice, at https://www.libreoffice.org/
Reference manager
Zotero, https://www.zotero.org/
Digital Notebook
Jupyter Lab and Notebooks, python based, web-based computational notebooks. In addition to python, Jupyter supports Julia and R Programming languages as well as Cytoscape, GNU Octave, SageMATH and other software. https://docs.jupyter.org/en/latest/index.html
OneNote, at https://www.onenote.com/
Bioinformatics tools
Bioconductor, at https://www.bioconductor.org/
Unipro UGENE, at http://ugene.net/
Cytoscape, at https://cytoscape.org/
MEGA, at https://www.megasoftware.net/
Coding IDE and code editor
Jupyter Lab
Visual Studio with Python application, Community edition, https://visualstudio.microsoft.com/vs/features/python/
Posit team (2024). RStudio: Integrated Development Environment for R. Posit Software, PBC, Boston, MA URL http://www.posit.co/.