Nature Methods: Visualization

Check out this month's table of contents in  Nature Methods. It contains a series of five commissioned Reviews discuss the challenges of visualizing biological data and the visualization tools available to biologists working with genomes, alignments and phylogenies, macromolecular structures, images and systems biology data.

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Foreword

Supplement on visualizing biological data - pS1

Daniel Evanko

doi:10.1038/nmeth0310-S1

Full Text - Supplement on visualizing biological data | PDF (188 KB) - Supplement on visualizing biological data

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Commentary

Visualizing biological data—now and in the future - ppS2 - S4

Seán I O'Donoghue, Anne-Claude Gavin, Nils Gehlenborg, David S Goodsell, Jean-Karim Hériché, Cydney B Nielsen, Chris North, Arthur J Olson, James B Procter, David W Shattuck, Thomas Walter & Bang Wong

doi:10.1038/nmeth.f.301

Methods and tools for visualizing biological data have improved considerably over the last decades, but they are still inadequate for some high-throughput data sets. For most users, a key challenge is to benefit from the deluge of data without being overwhelmed by it. This challenge is still largely unfulfilled and will require the development of truly integrated and highly useable tools.

Abstract - Visualizing biological data[mdash]now and in the future | Full Text - Visualizing biological data—now and in the future | PDF (336 KB) - Visualizing biological data—now and in the future

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Reviews

Visualizing genomes: techniques and challenges - ppS5 - S15

Cydney B Nielsen, Michael Cantor, Inna Dubchak, David Gordon & Ting Wang

doi:10.1038/nmeth.1422

Abstract - Visualizing genomes: techniques and challenges | Full Text - Visualizing genomes: techniques and challenges | PDF (993 KB) - Visualizing genomes: techniques and challenges | Supplementary information

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Visualization of multiple alignments, phylogenies and gene family evolution - ppS16 - S25

James B Procter, Julie Thompson, Ivica Letunic, Chris Creevey, Fabrice Jossinet & Geoffrey J Barton

doi:10.1038/nmeth.1434

Abstract - Visualization of multiple alignments, phylogenies and gene family evolution | Full Text - Visualization of multiple alignments, phylogenies and gene family evolution | PDF (867 KB) - Visualization of multiple alignments, phylogenies and gene family evolution | Supplementary information

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Visualization of image data from cells to organisms - ppS26 - S41

Thomas Walter, David W Shattuck, Richard Baldock, Mark E Bastin, Anne E Carpenter, Suzanne Duce, Jan Ellenberg, Adam Fraser, Nicholas Hamilton, Steve Pieper, Mark A Ragan, Jurgen E Schneider, Pavel Tomancak & Jean-Karim Hériché

doi:10.1038/nmeth.1431

Abstract - Visualization of image data from cells to organisms | Full Text - Visualization of image data from cells to organisms | PDF (1,682 KB) - Visualization of image data from cells to organisms

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Visualization of macromolecular structures - ppS42 - S55

Seán I O'Donoghue, David S Goodsell, Achilleas S Frangakis, Fabrice Jossinet, Roman A Laskowski, Michael Nilges, Helen R Saibil, Andrea Schafferhans, Rebecca C Wade, Eric Westhof & Arthur J Olson

doi:10.1038/nmeth.1427

Abstract - Visualization of macromolecular structures | Full Text - Visualization of macromolecular structures | PDF (2,317 KB) - Visualization of macromolecular structures | Supplementary information

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Visualization of omics data for systems biology - ppS56 - S68

Nils Gehlenborg, Seán I O'Donoghue, Nitin S Baliga, Alexander Goesmann, Matthew A Hibbs, Hiroaki Kitano, Oliver Kohlbacher, Heiko Neuweger, Reinhard Schneider, Dan Tenenbaum & Anne-Claude Gavin

doi:10.1038/nmeth.1436

Abstract - Visualization of omics data for systems biology | Full Text - Visualization of omics data for systems biology | PDF (1,469 KB) - Visualization of omics data for systems biology | Supplementary information