<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/8481?offset=0 https://bioinformaticsonline.com/pages/view/2261/best-book-titles-for-learning-bionformatics Tue, 13 Aug 2013 17:31:51 -0500 https://bioinformaticsonline.com/pages/view/2261/best-book-titles-for-learning-bionformatics <![CDATA[Best book Titles for Learning Bionformatics]]> Nothing can add to our intellect more than reading a book.  In books, we can experience new things that we would not normally be able to experience. It is proved that books can change our lives and other people’s lives. Reading can make us more intelligent, updated, imaginative. Without reading we wouldn’t know anything that we know today. There are several book, online and offile to read and I can't mentioned all of them here in the list. Therefore, I mentioned some bioinformatics and its related books in subgroups. Hope you will like the list. 

Sequence Analysis and General Bioinformatics

  • BLAST, Ian Korf, Mark Yandell, Joseph Bedell, 2003, O'Reilly
  • Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl Leon, 2003, O'Reilly
  • Bioinformatics for Geneticists, Michael Barnes, Ian C Gray (Editors), 2003, John Wiley & Sons
  • Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley & Sons
  • Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press
  • Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall
  • Evolutionary Computation in Bioinformatics, Gary B. Fogel, David W. Corne (Editors), 2002, Morgan Kaufmann
  • Introduction to Bioinformatics, Arthur M. Lesk, 2002, Oxford University Press
  • Instant Notes in Bioinformatics, D.R. Westhead, J. H. Parish, R.M. Twyman, 2002, Bios Scientific Pub
  • Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L. Raymer, Elaine Nicpon Marieb, 2002, Benjamin/Cummings
  • Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley & Sons
  • Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao Jiang, Ying Xu, Michael Zhang (Editors), 2002, MIT Press
  • Hidden Markov Models for Bioinformatics, Timo Koski, Timo Koskinen, 2001, Kluwer Academic Publishers
  • Bioinformatics: From Genomes to Drugs, Thomas Lengauer (Editor), 2001, John Wiley & Sons
  • Statistical Methods in Bioinformatics: An Introduction (Statistics for Biology and Health), Warren Ewens, Gregory Grant, 2001, Springer Verlag
  • Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition, Andreas D. Baxevanis, B. F. Francis Ouellette, 2001, Wiley-Interscience
  • Bioinformatics: The Machine Learning Approach, Second Edition (Adaptive Computation and Machine Learning), Pierre Baldi, Soren Brunak, Sren Brunak, 2001, MIT Press
  • Introduction to Bioinformatics, T eresa Attwood, David Parry-Smith, 2001, Prentice Hall
  • Bioinformatics: A Primer, Charles Staben, 2001, Jones & Bartlett Pub
  • Data Analysis and Classification for Bioinformatics, Arun Jagota, 2000, AKJ Academics
  • Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor Laboratory Press
  • Bioinformatics: A Biologist's Guide to Biocomputing and the Internet, Stuart M. Brown, 2000, Eaton Pub Co
  • Bioinformatics: Sequence, Structure and Databanks: A Practical Approach (The Practical Approach Series, 236), Des Higgins (Editor), Willie Taylor (Editor), 2000, Oxford Univ Press
  • Neural Networks and Genome Informatics, Cathy H. Wu, Jerry W. McLarty, 2000, Elsevier Science
  • Computational Molecular Biology: An Introduction (Wiley Series in Mathematical and Computational Biology), Peter Clote and Rolf Backofen, 2000, John Wiley & Sons
  • Computational Molecular Biology: An Algorithmic Approach, Pavel A. Pevzner, 2000, MIT Press
  • Post-Genome Informatics, Minoru Kanehisa, 2000, Oxford Univ Press
  • Mathematical and Computational Biology: Computational Morphogenesis, Hierarchical Complexity, and Digital Evolution, Chrystopher L. Nehaniv, 1999, American Mathematical Society
  • Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications, Jason T. L. Wang, Bruce A. Shapiro, Dennis Elliott Shasha (Editors), 1999, Oxford Univ Press
  • Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, David Sankoff and Joseph Kruskal (Editors), 1999, Cambridge University Press
  • Bioinformatics Basics: Applications in Biological Science and Medicine, Hooman Rashidi, 1999, CRC Press
  • Bioinformatics: Methods and Protocols (Methods in Molecular Biology, Vol 132), Stephen Misener and Stephen A. Krawetz (Editors),1999, Humana Press
  • Bioinformatics: Databases and Systems, Stanley Letovsky (Editor),1999, Kluwer Academic Publishers
  • Computational Molecular Biology, P. Green, 1998, Blackwell Science Inc.
  • Computational Methods in Molecular Biology (New Comprehensive Biochemistry, V. 32), Steven L. Salzberg, David B. Searls, Simon Kasif (Editors), 1998, Elsevier Science Ltd.
  • Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Richard Durbin, S. Eddy, A. Krogh, G. Mitchison, 1998, Cambridge University Press
  • Guide to Human Genome Computing, M. J. Bishop (Editor), 1998, Academic Press
  • Introduction to Computational Molecular Biology, Joao Meidanis, Joao C. Setabal, 1997, PWS Pub. Co.
  • Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Dan Gusfield, 1997, Cambridge University Press
  • Sequence Data Analysis Guidebook, Simon R. Swindell (Editor), 1997, Humana Press
  • High Performance Computational Methods for Biological Sequence Analysis, Tieng K. Yap, Ophir Frieder, Robert L. Martino, 1996, Kluwer Academic Pub.
  • Computer Methods for Macromolecular Sequence Analysis, Methods in Enzymology, volume 266, Russell F. Doolittle (Editor), 1996, Academic Press
  • DNA and Protein Sequence Analysis: A Practical Approach (Practical Approach Series , No 171), 1996, M. J. Bishop and C. J. Rawlings (Editors), 1996, IRL Press
  • Molecular Bioinformatics: Algorithms and Applications, Steffen Schulze-Kremer, 1995, Walter De Gruyter
  • Introduction to Computational Biology - Maps, sequences and genomes, Michael S. Waterman, 1995, Chapman & Hall
  • Computer Analysis of Sequence Data, Annette M. Griffin and Hugh G. Griffin (Editors), 1994, Humana Press
  • Artificial Intelligence and Molecular Biology, Lawrence Hunter (Editor), 1993, AAAI Press
  • Sequence Analysis Primer, Michael Gribskov and John Devereux (Editors), 1992, Oxford University Press
  • Mathematical Methods of Analysis of Biopolymer Sequences (Dimacs Series in Discrete Mathematics and Theoretical Computer Science ; Volume 8), S. G. Gindikin, 1992, American Mathematical Society
  • Mathematical Methods for DNA Sequences, Michael S. Waterman (Editor), 1989, CRC Press

Programming Books for Bioinformatics

  • Mastering Perl for Bioinformatics, James D. Tisdall, 2003, O'Reilly
  • Genomic Perl: From Bioinformatics Basics to Working Code, Rex A. Dwyer, 2002, Cambridge University Press
  • Beginning Perl for Bioinformatics, James Tisdall, 2001, O'Reilly
  • Developing Bioinformatics Computer Skills, Cynthia Gibas, Per Jambeck, 2001, O'Reilly

General Genomics

  • Functional Microbial Genomics (Volume 33), Brendan Wren, Nick Dorrell, 2003, Academic Press
  • Discovering Genomics, Proteomics, and Bioinformatics, A. Malcolm Campbell, Laurie J. Heyer, 2002, Benjamin/Cummings
  • Genomes, Terence A. Brown, 2002, John Wiley & Sons
  • Essentials of Medical Genomics, Stuart M. Brown , 2002, John Wiley & Sons
  • A Primer of Genome Science, Greg Gibson, Spencer V. Muse, 2002, Sinauer Associates
  • Pathogen Genomics: Impact on Human Health, Karen Joy, Phd Shaw (Editors), 2002, Humana Press
  • Genomics, John E. Antonopoulos, 2000, Xlibris Corporation
  • Genomics and Proteomics: Functional and Computational Aspects, Sandor Suhai (Editor), 2000, Plenum Pub Corp
  • Functional Genomics: A Practical Approach (The Practical Approach Series, 235), S. Hunt and F. Livesey (Editors), 2000, Oxford Univ Press
  • Human Molecular Genetics, Andrew P. Read, Tom Strachan 1999, BIOS Scientific Publishers Ltd.
  • Genomics: The Science and Technology Behind the Human Genome Project, Charles R. Cantor and Cassandra L. Smith, 1999, John Wiley & Sons
  • Cells: A Laboratory Manual, 3 volumes, David L. Spector, Robert D. Goldman, Leslie A. Leinwand, 1998, Cold Spring Harbor Laboratory Press
  • Genome Analysis: A Laboratory Manual, 4 volumes, Bruce Birren, et al. (Editors), 1997, Cold Spring Harbor Laboratory Press
  • The Human Genome Project, N. G. Cooper (Editor), 1994, University Science Books

Comparative Genomics

  • Handbook of Comparative Genomics: Principles and Methodology, Cecilia Saccone, Graziano Pesole, 2003, Wiley-Liss
  • Sequence - Evolution - Function: Computational Approaches in Comparative Genomics, Eugene V. Koonin, Michael Y. Galperin, 2002, Kluwer Academic Publishers
  • Comparative Genomics - Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, David Sankoff and Joseph H. Nadeau, 2000, Kluwer Academic Pub
  • Comparative Genomics, Melody Clark (Editor), 2000, Kluwer Academic Pub

Proteomics

  • Proteins and Proteomics: A Laboratory Manual, Richard J. Simpson (Editor), Cold Spring Harbor Laboratory
  • Proteomics in Practice: A Laboratory Manual of Proteome Analysis , Reiner Westermeier, Tom Naven, 2002, John Wiley & Sons
  • Posttranslational Modifications of Proteins: Tools for Functional Proteomics (Methods in Molecular Biology, Vol 194) , Christoph Kannicht (Editor), 2002, Humana Press
  • Peptide Arrays on Membrane Supports: Synthesis and Applications (Springer Lab Manual), Joachim Koch, Michael Mahler (Editors), 2002, Springer Verlag
  • Proteomics , Timothy Palzkill, 2002, Kluwer Academic Publishers
  • Introduction to Proteomics: Tools for the New Biology , Daniel C. Liebler (Editor), 2001, Humana Press
  • Proteome Research: Mass Spectrometry (Principles and Practice) , P. James (Editor), 2001, Springer Verlag
  • Interpreting Protein Mass Spectra: A Comprehensive Resource , A. Peter Snyder, 2000, American Chemical Society
  • Protein Sequencing and Identification Using Tandem Mass Spectrometry , Michael Kinter, Nicholas E. Sherman, 2000, Wiley-Interscience
  • From Genome to Proteome: Advances in the Practice and Application of Proteomics, Michael J. Dunn (Editor), 2000, Vch Verlagsgesellschaft Mbh
  • Proteomics: From Protein Sequence to Function, S. Pennington (Editor), M. Dunn (Editor), 2000, Springer Verlag
  • Proteome Research: Two-Dimensional Gel Electrophoresis and Detection Methods (Principles and Practice), T. Rabilloud (Editor), 2000, Springer Verlag
  • Proteome and Protein Analysis, R. M. Kamp, D. Kyriakidis, th Choli-Papadopoulou (Editor), 1999, Springer Verlag
  • Proteome Research: New Frontiers in Functional Genomics, M. R. Wilkins, et al. (Editors), 1997, Springer Verlag

Protein Structure

  • Structural Bioinformatics, Philip E. Bourne, Helge Weissig (Editors), 2003, John Wiley & Sons
  • Protein Structure Prediction: Bioinfomatic Approach, I.F. Tsigelny, 2002, International University Line
  • Introduction to Protein Architecture: The Structural Biology of Proteins, Arthur M. Lesk, 2001, Oxford University Press
  • Protein Structure Prediction: Methods and Protocols, David M. Webster (Editor), 2000, Humana Press
  • Introduction to Protein Structure, Carl-Ivar Branden, John Tooze, 1999, Garland Publishing
  • Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Alan Fersht, 1999, Freeman

Pharmacogenomics

  • Pharmacogenomics: Social, Ethical, and Clinical Dimensions, Mark A. Rothstein (Editor), 2003, Wiley-Liss
  • Pharmacogenomics: The Search for Individualized Therapies, Julio Licinio, Ma-Li Wong (Editors), 2002, John Wiley & Sons
  • Pharmacogenomics, Werner Kalow, Urs A. Meyer, Rachel Tyndale (Editors), 2001, Marcel Dekker
  • Pharmacogenetics and Pharmcogenomics: Recent Conceptual and Technical Advances (Pharmacology, Volume 61, Number 3, 2000), Elliot S. Vesell (Editor), 2000, S. Karger Publishing
  • Pharmacogenetics, Wendell Weber, 1997, Oxford University Press

DNA Microarrays

  • Statistical Analysis of Gene Expression Microarray Data, T. P. Speed (Editor), 2003, CRC Press
  • Microarray Gene Expression Data Analysis: A Beginner's Guide, Helen C. Causton, John Quackenbush, Alvis Brazma, 2003, Blackwell Publishers
  • The Analysis of Gene Expression Data (Statistics for Biology and Health), G. Parmigiani, E. S. Garrett, R. A. Irizarry, S. Zeger , Graeme Clark (Editors), 2003, Springer Verlag
  • A Practical Approach to Microarray Data Analysis, Daniel P. Berrar, Werner Dubitzky, Martin Granzow (Editors), 2002, Kluwer Academic Publishers
  • DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling, Pierre Baldi, G. Wesley Hatfield, 2002, Cambridge University Press
  • DNA Microarrays: A Molecular Cloning Manual, David Bowtell, Joseph Sambrook (Editors), 2002, Cold Spring Harbor Laboratory
  • DNA Array Image Analysis: Nuts & Bolts, Gerda Kamberova, Shishir Shah, 2002, DNA Press
  • Microarray Analysis, Mark Schena, 2002, John Wiley & Sons
  • A Biologist's Guide to Analysis of DNA Microarray Data, Steen Knudsen, 2002, John Wiley & Sons
  • Microarrays for an Integrative Genomics (Computational Molecular Biology), Isaac S. Kohane, Alvin Kho, Atul J. Butte, 2002, MIT Press
  • Microarrays for the Neurosciences: An Essential Guide (Cellular and Molecular Neuroscience), Daniel H. Geschwind, Jeffrey P. Gregg (Editors), 2002, MIT Press
  • DNA Microarrays: Gene Expression Applications, Bertrand Jordan (Editor), 2001, Springer Verlag
  • DNA Arrays: Methods and Protocols (Methods in Molecular Biology, Volume 170), Jang B. Rampal (Editor), 2001, Humana Press
  • DNA Arrays: Technologies and Experimental Strategies, Elena V. Grigorenko (Editor), 2001, CRC Press
  • Microarray Biochip Technology, Mark Schena (Editor), 2000, Eaton Pub
  • Expression Genetics: Accelerated and High-Throughput Methods (Biotechniques Update Series), Michael McClelland (Editor), Arthur B. Pardee (Editor), 1999, Eaton Pub
  • DNA Microarrays: A Practical Approach (Practical Approach Series 205), Mark Schena (Editor), 1999, Oxford Univ Press
  • cDNA Preparation and Characterization (Methods in Enzymology Volume 303), S.M. Weissman (Editor), 1999, Academic Press

Systems Biology, Genetic and Biochemical Network

  • Handbook of Graphs and Networks : From the Genome to the Internet, Stefan Bornholdt, Heinz Georg Schuster (Editors), 2003, Vch Verlagsgesellschaft Mbh
  • Computational Cell Biology, Christopher Fall, Eric Marland, John Wagner, John Tyson (Editors), 2002, Springer Verlag
  • Gene Regulation and Metabolism: Post-Genomic Computational Approaches (Computational Molecular Biology), Julio Collado-Vides, Ralf Hofestadt (Editors), 2002, MIT Press
  • Foundations of Systems Biology, Hiroaki Kitano (Editor), 2001, MIT Press
  • Genomic Regulatory Systems: Development and Evolution, Eric H. Davidson , 2001, Academic Press
  • Genes & Signals, Mark Ptashne, Alexander Gann, 2001, Cold Spring Harbor Laboratory
  • Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology), James M. Bower and Hamid Bolouri (Editors), 2001, MIT Press
  • Protein-Protein Interactions: A Molecular Cloning Manual, Erica Golemis (Editor), 2001, Cold Spring Harbor Laboratory
  • Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists, Eberhard O. Voit, 2000, Cambridge University Press
  • Mathematical Physiology, James P. Keener, James Sneyd, 1998, Springer Verlag

 

DNA Sequencing

  • DNA Sequencing: From Experimental Methods to Bioinformatics (Introduction to Biotechniques Series), Luke Alphey, 1997, Springer Verlag
  • Automated DNA sequencing and analysis, Adams M.D., Fields C., Venter J.C. (Editors), 1994, Academic Press

 

Apart from above mentioned books, you can also find some useful books links at following mentioned URLs:

 

http://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713

http://www.amazon.com/Bioinformatics-Genes-Proteins-Computers-Advanced/dp/1859960545

http://www.amazon.com/Introduction-Bioinformatics-Algorithms-Computational-Molecular/dp/0262101068

http://books.google.no/books?id=pxSM7R1sdeQC&dq=Pierre+baldi+%2B+bioinformatics&printsec=frontcover&source=bn&hl=en&ei=IoGRS6uCIJT-NYLA8Z0N&sa=X&oi=book_result&ct=result&redir_esc=y#v=onepage&q&f=false

http://www.amazon.com/Statistical-Methods-Bioinformatics-Introduction-Statistics/dp/0387400826

 

If you think your favourite books are not listed then please write it down in comment section for the benefits of other users. Feel free to add many more books in comment section. 

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/12944/orione-%E2%80%93-a-web-based-framework-for-ngs-analysis-in-microbiology Wed, 23 Jul 2014 06:43:03 -0500 https://bioinformaticsonline.com/bookmarks/view/12944/orione-%E2%80%93-a-web-based-framework-for-ngs-analysis-in-microbiology <![CDATA[Orione – a web-based framework for NGS analysis in microbiology]]> End-to-end NGS microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult due to a lack of interoperability, reproducibility, and transparency. To overcome these limitations researchers at CRS4, Italy have developed Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for NGS microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics.

Reference

Cuccuru G1, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, Uva P, Zanetti G, Fotia G. (2014) Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics [Epub ahead of print]. [article]

Address of the bookmark: http://orione.crs4.it/

]]> Martin Jones https://bioinformaticsonline.com/bookmarks/view/26927/phylographer-graph-visualization-tool Wed, 06 Apr 2016 19:06:48 -0500 https://bioinformaticsonline.com/bookmarks/view/26927/phylographer-graph-visualization-tool <![CDATA[PhyloGrapher - Graph Visualization Tool]]> PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements).PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it is possible to use PhyloGrapher to visualize any type of relations between elements. 

More at http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html

Address of the bookmark: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html

]]> Jitendra Prajapati https://bioinformaticsonline.com/bookmarks/view/27477/cytoscape Mon, 23 May 2016 02:32:00 -0500 https://bioinformaticsonline.com/bookmarks/view/27477/cytoscape <![CDATA[Cytoscape]]> Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

Address of the bookmark: http://www.cytoscape.org/

]]> Anjana https://bioinformaticsonline.com/news/view/28199/genome-workbench-2107 Fri, 01 Jul 2016 12:09:59 -0500 https://bioinformaticsonline.com/news/view/28199/genome-workbench-2107 <![CDATA[Genome Workbench 2.10.7]]> Genome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.

For the full list of features, improvements and fixes, see the release notes:https://ncbi.nlm.nih.gov/tools/gbench/releasenotes

New Features

  • BLAST Tool: added support for local custom BLAST databases
  • Graphical Sequence View: added log scaling option for graph tracks
  • Generic Table View: new tutorial added

Bug Fixes and Improvements

  • Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
  • Tree View: layout updated to better accommodate nodes of different sizes
  • Table Import Dialog (MacOS): fixed issue with table visibility
  • Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
  • Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
  • Graphical Sequence View: fixed protein coloration methods
  • Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
  • Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
  • Search View: ORF Finder – fixed incorrect protein lengths
  • Fixed bug with not opening project file (.gbp) on a click
  • Fixed issues in GVF import
  • Fixed BLAST Search tool against NCBI databases not working
  • Fixed tblastn (protein BLAST) not working in standalone mode
  • Fixed GTF export failure
]]> Gudiya Pal https://bioinformaticsonline.com/bookmarks/view/28855/vcfr Fri, 19 Aug 2016 07:38:24 -0500 https://bioinformaticsonline.com/bookmarks/view/28855/vcfr <![CDATA[vcfR]]> Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in the vignette ‘vcf data.’ These files are typically intended to be post-processed (i.e., filtered) as an attempt to remove false positives or otherwise problematic sites. The R package vcfR provides tools to facilitate this filtering as well as to visualize the effects of choices made during this process.

Address of the bookmark: https://cran.r-project.org/web/packages/vcfR/vignettes/visualization_1.html

]]> Archana Malhotra https://bioinformaticsonline.com/bookmarks/view/31714/krona Wed, 22 Mar 2017 04:47:35 -0500 https://bioinformaticsonline.com/bookmarks/view/31714/krona <![CDATA[Krona]]> Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive charts are self-contained and can be viewed with any modern web browser (see Browser support).

image

Address of the bookmark: https://github.com/marbl/Krona/wiki

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35896/phylographer-graph-visualization-tool Wed, 07 Mar 2018 18:11:25 -0600 https://bioinformaticsonline.com/bookmarks/view/35896/phylographer-graph-visualization-tool <![CDATA[PhyloGrapher - Graph Visualization Tool]]> PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it is possible to use PhyloGrapher to visualize any type of relations between elements. 

https://www.youtube.com/watch?v=WgufqYMHCvM

Address of the bookmark: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36368/d3-javascript-for-visualization Mon, 23 Apr 2018 08:42:22 -0500 https://bioinformaticsonline.com/bookmarks/view/36368/d3-javascript-for-visualization <![CDATA[D3 javascript for visualization !]]> Welcome to the D3 gallery! More examples are available on bl.ocks.org/mbostock. If you want to share an example and don't have your own hosting, consider using Gist and bl.ocks.org. If you want to share or view live examples try vida.io.

Address of the bookmark: https://github.com/d3/d3/wiki/Gallery

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37982/raven-a-software-suite-for-matlab-that-allows-for-semi-automated-reconstruction-of-genome-scale-models Wed, 24 Oct 2018 22:38:05 -0500 https://bioinformaticsonline.com/bookmarks/view/37982/raven-a-software-suite-for-matlab-that-allows-for-semi-automated-reconstruction-of-genome-scale-models <![CDATA[RAVEN: a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models]]> The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Address of the bookmark: https://github.com/SysBioChalmers/RAVEN

]]> Jit