Mac-Software und Onlinetools für Wissenschaftler

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Mac-Software und Onlinetools für Wissenschaftler

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Beitrag von polysom »

Mac-Software und Links für Biologie, Chemie, Medizin und andere Lebenswissenschaften

Hier eine Sammlung von Mac-Software für Wissenschaftler. Das ist eine aktualisierte und zusammengefasste Liste aus der Auflistung vom alten Forum mit einigen Ergänzungen. Ich habe die Liste in englisch gehalten, damit sie Wissenschaftlern weltweit nützlich sein kann. Es entstehen hier ständig neue Programme und verschwinden auch öfters mal wieder welche. Daher kann es sein, dass hier etwas fehlt oder, dass ein Link plötzlich nicht mehr geht.

Content:
1. Software for DNA, RNA and Cloning
2. Software for protein works and Western blotting
3. Software for Microscopy and Image processing
4. Software for Statistics and Math
5. Software for scientific writing
6. Miscellaneous Software
7. Scientific apps for iOS (iPhone / iPad)
8. Useful Links and Onlinetools
9. Links from Mac-Elch (from the old forum)





1. Software for DNA, RNA and Cloning

4Peaks
It says: The award winning 4Peaks helps molecular biologists to visualize and edit their DNA sequence trace files.
License: Freeware
http://nucleobytes.com/index.php/4peaks


Amplify
It says: Amplify is a freeware Macintosh program for simulating and testing polymerase chain reactions (PCRs). It can also be used as a tool for designing primers by evaluating candidates.
License: Freeware
http://engels.genetics.wisc.edu/amplify/


ApE
You can use it for viewing DNA sequence, translation, creating graphic restriction maps, saves graphics as encapsulated postscript or scalable vector graphics, virtual restriction digest and a lot more.
License: Freeware
http://biologylabs.utah.edu/jorgensen/wayned/ape/


Beacon Designer
It says: Beacon Designer™ automates the design of real time primers and probes. You can BLAST search sequences and search for template structures from within the program. Beacon Designer™ offers a comprehensive solution for mutation detection. Use Beacon Designer™ for optimal TaqMan® probes. And a lot more.
License: Commercial, free Trial
http://www.premierbiosoft.com/molecular ... index.html


Benchling
It says: Design, analyze, and share sequence data in the cloud.
License: Commercial, free online demo
https://benchling.com


BioSAVE
It says: BioSAVE (the E probably comes from Viewer somewhere) is a program for visualising DNA or protein sequences and annotations thereof.
License: Freeware, Source code available as Xcode project
http://www.mrc-lmb.cam.ac.uk/genomes/BioSAVE/


CLC Genomics Workbench
It says: CLC Genomics Workbench, for analyzing and visualizing next generation sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.
License: Commercial, free Trial
http://www.clcbio.com/products/clc-genomics-workbench/


CLC Sequence Viewer
It says: CLC Sequence Viewer creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options.
License: Commercial, free Trial
http://www.clcbio.com/products/clc-sequence-viewer/


Cloninghelp
It says: Free online software tools and information resources for molecular cloning.
License: Free online tools
http://www.cloninghelp.com


Clustal X
It says: Multiple alignment of nucleic acid and protein sequences.
License: Freeware
http://www.clustal.org/clustal2/


CodonCode Aligner
It says: CodonCode Aligner is a program for sequence assembly, contig editing, and mutation detection.
License: Commercial, free Trial
http://www.codoncode.com/aligner/


DNASTAR's Lasergene Cloning Suite
It says: Lasergene Cloning Suite software enables you to edit and annotate your sequences, create detailed circular or linear maps, perform automated virtual cloning using a variety of cloning methods, including Gateway multisite, TA, TOPO, and restriction cloning, and also provides all the tools you need for designing the best primer pairs for PCR, sequencing, and hybridization experiments.
License: Commercial, free Trial
http://www.dnastar.com/t-products-dnast ... oning.aspx


DNA Strider
It says: An intuitive and handy utility that helps its users to quickly get their data out and perform some basic DNA analysis functions.
License: Freeware
http://sourceforge.net/projects/dnastrider/


EnzymeX
It says: EnzymeX helps molecular biologists determine which restriction enzymes they should use to cut their DNA of interest, along with complete DNA sequence analysis and editing.
License: Freeware
http://nucleobytes.com/index.php/enzymex


FinchTV
It says: For the viewing of ABI and SCF chromatogram files.
License: Freeware
http://www.geospiza.com/finchtv/help/


GenBeans
It says: A highy interactive molecular biology software to analyze sequences.
License: Freeware, but based on Java
http://www.geneinfinity.org/genbeans/


Gene Construction Kit
It says: GCK allows easy manipulation of DNA sequences, either graphically or as sequence text. GCK eliminates tedious examination of DNA sequence data by automatically identifying open reading frames (ORF's), keeping track of sticky ends during cutting and pasting of restriction enzyme digestion fragments, assisting with PCR primer design, and enabling comprehensive annotation of DNA sequence features.
License: Commercial, free Trial
http://www.textco.com/gene-construction-kit.php


Geneious
Beautiful sequence alignment, assembly and analysis software for DNA and protein sequence alignment, genome browser, reference mapping and sequence assembly, Phylogenetic Tree Building and Viewing, molecular cloning, primer design, microsatellite genotyping and more.
License: Commercial, free Trial, based on Java
http://www.geneious.com


GeneStudio
It says: Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly interface.
License: Freeware, source code available
http://sourceforge.net/projects/genestudio/


Lasergene Genomics Suite
It says: Lasergene Genomics Suite provides all of the software you need for next-gen sequence assembly and analysis in a single, integrated package. We support all major next-gen sequencing technologies, making it simple to work with your data for any type of project, including de novo or reference-guided genome assemblies, targeted resequencing, metagenome and population assemblies, large-scale multi-sample SNP analysis, RNA-Seq, ChIP-Seq, and miRNA alignment and analysis, and more.
License: Commercial, free Trial
http://www.dnastar.com/t-products-dnast ... omics.aspx


MacVector
It says: MacVector is a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a variety of other functions.
License: Commercial, free Trial
http://macvector.com


OLIGO
It says: OLIGO Primer Analysis Software is the essential tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons. Based on the most up-to date nearest neighbor thermodynamic data, Oligo's search algorithms find optimal primers for PCR, including TaqMan, highly multiplexed, consensus or degenerate primers. Multiple file batch processing is possible. It is also an invaluable tool for site directed mutagenesis.
License: Commercial, free Trial
http://www.oligo.net


PlasmaDNA
It says: PlasmaDNA is a new, free DNA analysis and manipulation software. It is simple to learn and to use, and contains multiple features designed to help with the design of a successful cloning strategy, the generation of the sequences of new clones, the archiving of the cloning strategy.
License: Freeware
http://research.med.helsinki.fi/plasmadna/


Sequence Analysis
For analysing sequences
License: Freeware, but based on Java
http://informagen.com/SA/


Serial Cloner
It says: All the tools you need to analyze and manipulate your sequences are available in an all-in-one-window concept. Numerically select fragments, find restriction sites, ORF or any nucleotide or peptide sequence, calculate Tm of selected fragments, %GC or dynamically determine the translation your selection into peptide and calculate the MW using a compact interface.
License: Freeware
http://serialbasics.free.fr/Serial_Cloner.html


SnapGene
It says: SnapGene offers the fastest and easiest way to plan, visualize, and document your molecular biology procedures.
License: Commercial, free Trial and free Viewer
http://www.snapgene.com


Unipro UGENE
It says: Creating, editing and annotating nucleic acid and protein sequences. Multiple sequence alignment. Cloning in silico. Search for direct, inverted and tandem repeats in DNA sequences. Integrated Primer3 package for PCR primers design. Restriction analysis with integrated REBASE restriction enzyme database. And more.
License: Freeware, Source code available
http://ugene.unipro.ru


Vector NTI® Express
It says: Vector NTI® software is a completely integrated suite of sequence analysis and design tools that help you manage, view, analyze, transform, share, and publicize diverse types of molecular biology data, all within one graphically rich analysis environment.
License: Commercial, free Trial
http://www.lifetechnologies.com/de/de/h ... tware.html


WebDSV
The author: WebDSV is a free online DNA sequence editor and map/plasmid drawing program.
License: Free online tool
http://www.molbiotools.com/WebDSV/


XPlasMap
It says: It draws plasmid or linear DNA maps, showing features such as genes, multiple cloning sites, and restriction sites.
License: Freeware
http://www.iayork.com/XPlasMap/



2. Software for protein works and Western blotting

AUDENS
It says: AUDENS is a tool for automated de novo sequencing of peptides. It has a flexible preprocessing module which is designed to distinguish between signal and noise peaks.
License: Freeware, but based on Java
http://www.ti.inf.ethz.ch/pw/software/audens/


Gromacs
It says: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles..
License: Freeware, source code available
http://www.gromacs.org


ImageJ
You can perform densitometric analysis (analysing western blots) if you follow this method.
License: Freeware, but based on Java
http://imagej.nih.gov/ij/


ImageLab
Software for 1-D data analysis, for quantification of Western and Southern blots.
License: Commercial, can be downloaded free after registration and used in basic mode
http://www.bio-rad.com/de-de/product/image-lab-software


Image Studio Lite
It says: Free Western Blot Analysis Software.
License: Free, but registration required for download
http://www.licor.com/bio/products/softw ... index.html


iMol
It says: iMol is a free molecular visualization application for Mac OS X operating system.
License: Freeware, but last update was 2007
http://www.pirx.com/iMol/index.shtml


LabImage
It says: The LabImage Software Platform provides a unique approach for all bio-imaging needs from image analysis up to automation and device controlling. LabImage provides the world only Imaging Application Pool.
License: Commercial, free Trial
http://www.kapelan-bioimaging.com


Protein-ms
It says: Tools for mass spectrometry, especially for protein mass spectrometry and proteomics.
License: Freeware, Source code available.
http://sourceforge.net/projects/protms/


PyMOL
It says: PyMOL is a user-sponsored molecular visualization system on an open-source foundation.
License: Only old versions are free for academic use, new versions for paid subscribers only
http://www.pymol.org


Swiss-PdbViewer
It says: Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time.
License: Freeware
http://spdbv.vital-it.ch


UCSF Chimera
It says: UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.
License: Freeware
https://www.cgl.ucsf.edu/chimera/


VMD
It says: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
License: Freeware
http://www.ks.uiuc.edu/Research/vmd/



3. Software for Microscopy and Image processing

BioImageXD
It says: BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.
License: Freeware, Source code available
http://sourceforge.net/projects/bioimagexd/


CoLocalizer Pro
It says: CoLocalizer Pro is a quantitative colocalization analysis software. It calculates specialized coefficients to characterize colocalization of fluorescence markers objectively.
License: Commercial, free Trial
http://www.colocalizer.com/pro.html


Escape Medical Viewer
It says: EMV 5 is the latest version of Escape's medical (DICOM) viewer, anonymizer and converter. A native 64-bit Cocoa application, EMV 5 combines powerful features with intuitiveness, elegance and ease of use.
License: Commercial
https://escapetech.eu/dicom/emvmac.html


ImageJ
Wikipedia: ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health.
License: Freeware, but based on Java
http://imagej.nih.gov/ij/


Macnification
For capturing, organizing, editing and analyzing microscopic images of different file formats.
License: Commercial, free Trial
http://www.orbicule.com/macnification/


OMA
It says: The OMA program was developed by researchers as a way to investigate and post-process photometric images from CCD detectors used for laser-based imaging of reacting and nonreacting flows as well as some spectroscopic applications.
License: Freeware, Source code available
http://oma-x.org/omaWebPage/index.html



4. Software for Statistics and Math

G*Power
It says: G*Power is a tool to compute statistical power analyses for many different t tests, F tests, χ2 tests, z tests and some exact tests. G*Power can also be used to compute effect sizes and to display graphically the results of power analyses.
License: Free
http://www.gpower.hhu.de


GraphPad Prism
It says: GraphPad Prism combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization.
License: Commercial, free Trial
http://www.graphpad.com/scientific-software/prism/


GraphSketcher
For plotting and visualizing all kinds of data in many different ways.
License: Freeware, Source code available
http://www.omnigroup.com/blog/setting-o ... tcher-free


IGOR Pro
It says: IGOR Pro is an extraordinarily powerful and extensible scientific graphing, data analysis, image processing and programming software tool for scientists and engineers.
License: Commercial, free Trial
http://www.wavemetrics.com


Mathematica
Wikipedia: Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields, based on symbolic mathematics.
License: Commercial, free Trial
http://www.wolfram.com


Maple
Symbolic algebra and data analysis.
License: Commercial, free Trial
http://www.maplesoft.com


MATLAB
Wikipedia: MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment and fourth-generation programming language.
License: Commercial, free Trial
http://www.mathworks.com


Octave
It says: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation.
License: Freeware
http://www.octave.org


Orange
It says: Open source data visualization and analysis for novice and experts. Data mining through visual programming or Python scripting. Components for machine learning. Add-ons for bioinformatics and text mining. Packed with features for data analytics.
License: Freeware
http://orange.biolab.si


Plot2
It says: A scientific 2D plotting program for OS X.
License: Freeware
http://plot.micw.eu


pro Fit
It says: pro Fit is a macOS application for data/function analysis, plotting, and curve fitting. It is used by scientists, engineers and students to analyze their measurements and the mathematical models they use to describe them.
Licence: Free
http://www.quansoft.com


R
It says: R is a free software environment for statistical computing and graphics.
License: Freeware
http://www.r-project.org


Scilab
It says: Open source software for numerical computation.
License: Freeware, Source code available
http://www.scilab.org


Stata
it says: Stata is a complete, integrated software package that provides all your data science needs—data manipulation, visualization, statistics, and automated reporting.
Licence: Commercial
https://www.stata.com/products/



5. Software for scientific writing

Adobe InDesign
It says: From books and brochures to digital magazines and iPad apps, InDesign CC helps you create pixel-perfect page designs and typography. Easily adapt layouts for multiple page sizes, screen sizes, or orientations.
License: Commercial, Trial available
http://www.adobe.com/products/indesign.html


Bean
It says: Bean is a small, easy-to-use word processor that is designed to make writing convenient, efficient and comfortable.
License: Freeware
http://www.bean-osx.com/Bean.html


EndNote
It says: EndNote is the industry standard software tool for publishing and managing bibliographies, citations and references.
License: Commercial, Trial available
http://endnote.com


LaTeX
Wikipedia: LaTeX is a document preparation system and document markup language. It is the de facto standard for the communication and publication of scientific documents in many fields, including mathematics, physics, and computer science. LaTeX uses the TeX typesetting program for formatting its output, and is itself written in the TeX macro language.
Note: LaTeX is NOT an application, it is a markup language that you need to learn bevor you can work with it! And you need to install a LaTeX distribution AND an application.
License: Mostly Freeware, but also commercial sometimes
LaTeX Distribution: http://www.tug.org/mactex/ (includes TeXShop)
Applications:
TeXShop: http://pages.uoregon.edu/koch/texshop/texshop.html
iTeXMac: http://itexmac.sourceforge.net
LyX: http://www.lyx.org
Latexian: http://tacosw.com/latexian/


MathType
It says: MathType is a powerful interactive equation editor that lets you create mathematical notation for word processing, web pages, desktop publishing, presentations, elearning, and for TeX, LaTeX, and MathML documents.
License: Commercial, Trial available
http://www.dessci.com/en/products/mathtype/


Mellel
It says: Mellel is a fully featured, agile word processor for Mac OS X.
License: Commercial, Trial available
http://www.mellel.com


Ulysses
Very good creative writing text editor.
License: Commercial, Trial available
http://www.ulyssesapp.com



6. Miscellaneous Software

Arcadia
It says: Arcadia is a light-weight, cross-platform, C++ desktop application designed for visualizing biological networks such as metabolic pathways.
License: Freeware, Source code available
http://sourceforge.net/projects/arcadiapathways/


BD CellQuest Pro
Software for displaying and analyzing flow cytometry (FACS) data
License: Commercial
http://www.bd.com


BD FACStation
Software for displaying and analyzing flow cytometry (FACS) data. Software CD contains BD CellQuest Pro, BD FACSComp, BD Worklist Manager, BD Loader Manager, and BD Plate Manager applications.
License: Commercial
http://www.biocompare.com/12104-Equipme ... -Mac-OS-X/


CellDesigner
It says: CellDesigner is a modeling tool of biochemical networks with graphical user interface. It is designed to be SBW (Systems Biology Workbench) compliant, and support SBML (Systems Biology Markup Language) format.
License: Freeware
http://systems-biology.org/software/celldesigner/


ChemSpotlight
It says: ChemSpotlight is a Spotlight metadata importer plugin for Mac OS X, which reads common chemical file formats using the Open Babel chemistry library.
License: Freeware
http://chemspotlight.openmolecules.net


Cytostream
It says: A graphical user interface for the automated analysis of flow cytometry (FACS) data.
License: Commercial
https://code.google.com/p/cytostream/


EasyChem
It says: EasyChem is designed to draw chemical molecules in an intuitive way, with a very high quality. Exporting is done to various formats.
License: Freeware, Source code available
http://sourceforge.net/projects/easychem/


Edinburgh Pathway Editor
It says: Edinburgh Pathway Editor is a visual editor for Systems Biology. It allows you to draw Graphical Notations commonly used in Systems Biology.
License: Freeware, Source code available
http://epe.sourceforge.net/SourceForge/EPE.html


Escape Medical Viewer
EMV 4 is an elegant, robust and lightweight DICOM viewer, anonymizer and converter for MacOS. Can also be used for basic analysis of echocardiographic data.
License: Commercial, Trial available
http://www.escape.gr/dicom/emvmac.html


Heart Pro
imedicalapps.com: Heart Pro III app is a cardiac anatomy masterclass with uses for physicians and students alike. Heart Pro III allows a detailed look at the anatomy of the heart from a range of perspectives while including detailed anatomical information and a range of animations among other features.
License: Commercial
http://applications.3d4medical.com/heart_pro


iNMR
It says: iNMR can do all the things you expect from a traditional NMR program (and ten times more).
License: Commercial, Trial available
http://www.inmr.net


Lab Assistant
Digital Lab book. It says: Lab Assistant helps you organize your experiments. No scientist should be without this.
License: Freeware
http://nucleobytes.com/index.php/labassistant


MarvinBeans
It says: Powerful and fast sketching of molecules, queries and reactions. Characterizing molecules directly on the canvas. Visualizing attractive 2D & 3D structures accurately.
License: Freeware, but you need to register
http://www.chemaxon.com/download/marvin-suite/


MetaNeuron
It says: MetaNeuron is a free computer program that models the basic electrical properties of neurons. The program is intended for the beginning neuroscience student and requires no prior experience with computer simulations. Different aspects of neuronal behavior are highlighted in the six lessons presented in MetaNeuron.
License: Free
http://www.metaneuron.org


mMass
Open Source Mass Spectrometry Tool
License: Freeware, Source code available
http://www.mmass.org


MZmine 2
It says: A framework for differential analysis of mass spectrometry data.
License: Freeware, Source code available. Needs Java to run.
http://sourceforge.net/projects/mzmine/


OpenChrom
It says: OpenChrom is a tool for gas chromatography and mass spectrometry. The focus is to handle data files from different GC/MS and GC/FID systems and vendors. Its functionality and algorithms can be extended using a flexible plugin approach, based on Eclipse RCP.
License: Freeware, Source code available.
http://sourceforge.net/projects/openchrom/


OpenMS
It says: An open source framework for LC-MS based proteomics. OpenMS offers datastructures and algorithms for the processing of mass spectrometry data. The library is written in C++.
License: Freeware, Source code available.
http://sourceforge.net/projects/open-ms/


Papers
Is a reference management software for organizing scientific papers and citations. For a comparison of reference management software see this list.
License: Commercial, Trial available
http://www.papersapp.com/mac/


PhysioDesigner
It says: PhysioDesigner is an open platform that supports multilevel modeling of physiological systems in the field of integrated life sciences and systems biology, including physiology and neuroscience. Users can combine and build mathematical models of biological and physiological functions on PhysioDesigner.
License: Freeware
http://physiodesigner.org


Protein-ms
It says: Tools for mass spectrometry, especially for protein mass spectrometry and proteomics.
License: Freeware, Source code available.
http://sourceforge.net/projects/protms/


Sparky
It says: Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.
License: Freeware, Source code available
http://www.cgl.ucsf.edu/home/sparky/


Structural
It says: This handy little application calculates the molecular weight of a molecule from it’s empirical formula. It has over a hundred preset compounds, which can be added to.
License: Freeware
http://totlandweb.info/Applications/Structural/


Virtual Cell (VCell)
It says: The Virtual Cell is a software modeling environment for quantitative cell biological research. Users can create simple or complex multi-layered models with a Java web-based interface. Distinct biological and mathematical frameworks exist within a single graphical interface designed for experimental cell biologists or theoretical biophysicists..
License: Freeware, but you need to register
http://www.nrcam.uchc.edu/vcell_softwar ... urrent=two


VisANT
It says: Integrative Visual Analysis Tool for Biological Networks and Pathways.
License: Freeware, but based on Java
http://visant.bu.edu


XdrawChem
It says: XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft).
License: Free
https://www.woodsidelabs.com/chemistry/xdrawchem.php



7. Scientific apps for iOS (iPhone / iPad)

Abcam App
It says: The Abcam app features a suite of tools that are handy for any bench scientist. Time multiple experiments, use a molarity calculator or look up how to run a particular part of an application.
License: Free
https://itunes.apple.com/us/app/abcam/id591370165?mt=8


BioLegend Flow Cytometry Application
It says: This application provides you with important information about your Flow Cytometers and Fluorochromes. Now you can use BioLegend's Spectra Analyzer quickly and conveniently in the palm of your hand.
License: Free
https://itunes.apple.com/us/app/biolege ... 80717?mt=8


BioLegend Lab Tools
It says: This app is full of calculators and converters that should come in very hand in the lab or in the classroom.
License: Free
https://itunes.apple.com/us/app/biolege ... 19235?mt=8


Cell Imaging By Invitrogen Corporation
Is says: This mobile app is designed to help you find fluorescent dyes, reagents and protocols for cell biology related fluorescence microscopy applications.
License: Free
https://itunes.apple.com/us/app/cell-im ... 25632?mt=8


ChemSpider
It says: ChemSpider Mobile allows you to search the ChemSpider chemical database, provided by the Royal Society of Chemistry. Compounds can be searched by structure or by name, and browsed within the app.
License: Free
https://itunes.apple.com/us/app/chemspider/id458878661


CloningBench By Thermo Fisher Scientific
It says: The CloningBench mobile app is designed to provide you with useful and essential tools to help guide your cloning experiments.
License: Free
https://itunes.apple.com/us/app/cloning ... 17777?mt=8


EMD Millipore Interactive Histone Modifications
Is says: Through this interactive nucleosome experience, you can explore published histone modifications to obtain relevant bioinformatic data, supporting references, and available research reagents (such as antibodies, ChIP kits, and modifying enzymes) for histone modification and epigenetics research.
License: Free
https://itunes.apple.com/us/app/emd-mil ... 02957?mt=8
! Only available in the US Appstore !


Fluorescence SpectraViewer By Invitrogen Corporation
It says: Plot and compare spectra, check the spectral compatibility for many fluorophores and email the configuration to yourself or others in the lab in a clear printable format.
License: Free
https://itunes.apple.com/us/app/fluores ... 31826?mt=8


HPLC Calc by Sigma-Aldrich
It says: The HPLC Method Transfer Calculator does the following: Calculates conditions for transfer of an isocratic or gradient method from one HPLC column to another. Recommends flow rates for analytical columns.
License: Free
https://itunes.apple.com/us/app/hplc-ca ... 41172?mt=8


iMolview Lite
It says: iMolview Lite lets you browse and view in 3D protein and DNA structures from Protein Data Bank, and drug molecules from DrugBank.
License: Free
https://itunes.apple.com/us/app/imolvie ... 31121?mt=8


iOligo EazyPrimer
It says: iOligo EazyPrimer calculates basic PCR primer parameters and identifies secondary structures as you type your oligo’s sequence. The sequence's length cannot exceed 90 mers.
License: Free
https://itunes.apple.com/us/app/ioligo- ... ?l=en&mt=8


Light Lab By Carl Zeiss AG
It says: With Light Lab by Carl Zeiss Microscopy, you have a fully interactive spectra configuration tool for fluorescence microscopy at your hands. You easily check the spectral compatibility for over 500 fluorophores in the Spectra Viewer module, see the efficiencies in the Imaging Simulator, and email the configuration to yourself or others in the lab as pdf.
License: Free
https://itunes.apple.com/us/app/light-l ... 66212?mt=8


MIQE qPCR
It says: Get help from a special team of experts in qPCR while on the move. MIQE - qPCR helps you in reviewing scientific works and checking your own experiments, when qPCR is involved.
License: Free
https://itunes.apple.com/us/app/miqe-qp ... 50002?mt=8


NEB Tools
It says: Use Enzyme Finder to select a restriction enzyme by category or recognition sequence, or search by name to find information on any NEB enzyme.
License: Free
https://itunes.apple.com/us/app/neb-too ... 46827?mt=8


Promega Colony Counter
It says: Is the tedium of squinting over agar plates counting bacterial colonies getting to you? Take the plates out of the lab! No, not literally. Snap a picture with your phone and you can make counting an out-of-lab experience. The Colony Counter app gives you a count estimate you can then manually refine.
License: Free
https://itunes.apple.com/us/app/id620431249?mt=8


QIAGEN App
It says: QIAGEN’s application QIAGEN App is a great resource for iPhone and iPad users that helps to ease and simplify your daily work in the lab. Now with a great new design, this app provides simultaneous multiple lab timers, tables of many commonly used lab buffers and solutions, a variety of conversion and dilution calculators, and supportive multimedia presentations. The iPad app also includes packages for users of QIAcube, QIAgility, QIAxpert and Rotor-Gene Q providing protocol sheets, support documents, tutorials and updates.
License: Free
https://itunes.apple.com/us/app/qiagen- ... ggest=true


Real-time PCR By Thermo Fisher Scientific
It says: The application’s main feature is a real-time PCR handbook covering all aspects of real-time PCR from the basics of how the technology works to data analysis and interpretation
License: Free
https://itunes.apple.com/us/app/real-ti ... 57743?mt=8


Restriction Enzyme Tool By Promega Corporation
It says: Search for restriction enzymes by name, recognition sequence or overhang. Explore compatible enzymes for double digests quickly, without having to select each individually.
License: Free
https://itunes.apple.com/us/app/restric ... 03979?mt=8


Tydlig - Calculator Reimagined
It says: Tydlig is perfect for calculating everyday things like tips and discounts, showing the entire history and allowing you to change any number with instant updates. For deeper calculations real-time graphing is an excellent way to explore and visualize things like bank interest rates and trigonometric functions.
License: NOT Free
https://itunes.apple.com/us/app/tydlig- ... 06556?mt=8


WolframAlpha
It says: Remember the Star Trek computer? It's finally happening--with Wolfram|Alpha. Building on 25 years of development led by Stephen Wolfram, Wolfram|Alpha has rapidly become the world's definitive source for instant expert knowledge and computation.
License: NOT Free
https://itunes.apple.com/us/app/wolfram ... 89259?mt=8



8. Useful Links and Onlinetools

Mac in Chemistry
https://www.macinchem.org


Biological Macromolecular Resource
http://www.pdb.org/pdb/home/home.do


Orientations of Proteins in Membranes (OPM) database
http://opm.phar.umich.edu


Peptide Property Calculator
http://www.basic.northwestern.edu/bioto ... ncalc.html


DNA/RNA to protein translate tool
http://web.expasy.org/translate


Protein knowledgebase
http://www.uniprot.org


Collection of natural product syntheses
http://www.chem.wisc.edu/areas/reich/sy ... theses.htm


Online plasmid map drawing tool
http://www.bioinformatics.org/savvy


KEGG PATHWAY Database
http://www.genome.jp/kegg/pathway.html


Scientific picture archiv
http://www.sciencephoto.com


Biomedical literature search
http://www.ncbi.nlm.nih.gov/pubmed


Database System for Systematics and Taxonomy
http://www.biologie.uni-ulm.de/systax/


Oligonucleotide Properties Calculator
http://www.basic.northwestern.edu/bioto ... ocalc.html


Sequence Conversion tool
http://www-bimas.cit.nih.gov/molbio/readseq/


Different IDT SciTools® Web Tools
http://eu.idtdna.com/pages/scitools


Reverse Complement converts a DNA sequence into its reverse
http://www.bioinformatics.org/sms/rev_comp.html


Free online software tools and information resources for molecular cloning
http://www.cloninghelp.com


Online Interactive PDB Fast Viewer
http://www.molsoft.com/pdbv.html


BLAST Basic Local Alignment Search Tool
http://blast.ncbi.nlm.nih.gov/Blast.cgi


ProtParam - computation of various physical and chemical parameters for a protein
http://web.expasy.org/protparam/


Primer3: WWW primer tool
http://biotools.umassmed.edu/bioapps/primer3_www.cgi


Reactome pathway database
http://www.reactome.org


RestrictionMapper - online restriction mapping
http://www.restrictionmapper.org


Interactive Fluorescence SpectraViewer
http://www.lifetechnologies.com


Wavelength to RGB and HEX Calculator
http://rohanhill.com/tools/WaveToRGB/


Protein Hydrophobicity Plots
http://www.vivo.colostate.edu/molkit/hy ... index.html


Diana Lab Tools
http://diana.imis.athena-innovation.gr/ ... /index.php


http://sourceforge.net science applications
http://sourceforge.net/directory/science-engineering/


Free online DNA sequence editor and map/plasmid drawing program
http://www.molbiotools.com/WebDSV/







9. Nun noch eine Link-Liste, die MacElch bereitgestellt hat (aus dem alten Forum):


Allgemeines Interesse


Atomic Spectra Database des NIST (National Institute for Standards and Technology)
http://www.nist.gov/pml/data/asd.cfm

Enzyme Database - BRENDA
http://www.brenda-enzymes.info/

Function Annotation Server
http://www.doe-mbi.ucla.edu/Services/ProKnow/

The Dundee PRODRG Server
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/

Protein Topology home page
<http://www3.ebi.ac.uk/tops/> http://www3.ebi.ac.uk/tops/

Enzyme Structures Database
http://www.ebi.ac.uk/thornton-srv/databases/enzymes/

ESPript
http://espript.ibcp.fr/ESPript/ESPript/

ProFunc - Protein function from structure
http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/

InterPro: Home
http://www.ebi.ac.uk/interpro/

CRISP - A Database of Biomedical Research Funded By the National Institutes of Health (NIH)
<http://crisp.cit.nih.gov/> http://crisp.cit.nih.gov/

OVID
http://ovid.gwdg.de/

JOY
http://www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi

EBI SSM Home Page
http://www.ebi.ac.uk/msd-srv/ssm/

GeneDB
http://www.genedb.org/

Kristallographie:

Crystallography on OS X
http://chemistry.ucsc.edu/~wgscott/xtal/

MolProbity
http://kinemage.biochem.duke.edu/molprobity/

LABELIT
http://adder.lbl.gov/labelit/

TLS Motion Determination Home
http://skuld.bmsc.washington.edu/~tlsmd/index.html

Tcoffee
http://igs-server.cnrs-mrs.fr/Tcoffee/t ... /index.cgi

TEXTAL homepage
http://textal.tamu.edu:12321/webtex.html

HIC-Up
http://alpha2.bmc.uu.se/hicup/

Kristallographie-Programme:

Crystallography & NMR System
http://cns.csb.yale.edu/v1.1/

CCP4 Program Suite: refmac - dictionary - list of ligands
http://www.ccp4.ac.uk/dist/html/lib_list.html

Coot
http://www.ysbl.york.ac.uk/%7Eemsley/co ... anual.html http://www.ysbl.york.ac.uk/~emsley/coot/

XDS Package
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/

CCP4 Program Suite <cid:part1.06060901.04050205@u.washington.edu>
http://www.ccp4.ac.uk/

SnB Home Page
http://www.hwi.buffalo.edu/SnB/

SHELX Program Page
http://shelx.uni-ac.gwdg.de/SHELX/

EPMR
http://www.msg.ucsf.edu/local/programs/epmr/epmr.html

Uppsala Software Factory
http://alpha2.bmc.uu.se/~gerard/manuals/

The Elves Manual: Table of Contents
http://ucxray.berkeley.edu/~jamesh/elve ... index.html

PHENIX
http://phenix-online.org/download/documentation/phenix/

Robetta
http://robetta.bakerlab.org/queue.jsp

LIBELLULA
http://www.pdg.cnb.uam.es:8081/libellula.html
Benutzeravatar
mama
Beiträge: 1673
Registriert: Di 8. Feb 2022, 10:48

#2

Beitrag von mama »

Jesses, hast du dir eine Mühe gemacht! Toll!
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HJD
Beiträge: 3872
Registriert: Mo 7. Feb 2022, 18:24

#3

Beitrag von HJD »

Aber echt.
++
„Die Welt wird nicht bedroht von den Menschen, die böse sind, sondern von denen, die das Böse zulassen.“

Albert Einstein
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