David H Hall et al. (2002) East Coast Worm Meeting "Wormatlas: A web-based behavioral and structural atlas of C. elegans"

David H Hall, Maurice Volaski, Michael Zhang, Constantinos Polydorou, Thomas Boulin, Zeynep F Altun

[East Coast Worm Meeting, 2002]

We have recently launched the prototype of Wormatlas (www.wormatlas.org). This atlas is designed to serve the scientific community with the main goal of bringing all the anatomical information pertinent to C. elegans within one readily accessible and easy to use web site. By creating extensive links to the WormBase as well as the C. elegansWWW server, we are aiming to provide users with seamless links between these databases. We hope to create the most comprehensive and complete online anatomy atlas for any genetic model organism. Wormatlas is designed to have two main sections, Index and Guides, with multiple chapters within each section. The Index section will contain the Handbook, Slidable Worm, Literature Archive, Cell Identifications, Neuron Data, Glossary, and Methods. The main goal of the Handbook is to provide a relatively simplified, image-supported and curated information about the general and specific anatomy of C. elegans.The images included in the Handbook will be annotated scanning and transmission electron (TEM) micrographs, computer-drawn images as well as DIC and fluorescent micrographs. The Slidable Worm is designed to provide 600-1200 annotated and nonannotated versions of TEM cross-sections of the animal available for viewing by the users with the help of a newly designed JAVA applet interface. The images will come from the original images from the MRC/LMB archive, from the MIT archive (courtesy of E. Hartwieg and R. H. Horvitz), from our Caltech/AECOM archives, and possibly others. The Literature Archive will provide on-line copies of landmark articles and treatises about the anatomy of the nematode. These HTML format articles include multiple web links to other sites in Wormatlas and WormBase to strengthen their interactivity for the structures mentioned. The Glossary aims to provide a comprehensive list of all nomenclature used to describe any cell structure in the nematode. Cell Identification and Neuron Data are planned to provide enough detail on features of single cells, esp. neurons, to aid researchers in recognizing and studying individual cells by their 3D shapes and positions, comparing TEM, DIC and GFP information, and by providing links to curated data on their gene expression patterns. Finally, Anatomical Methods will provide an up to date summary of the different modalities that are currently used in cell identification and tissue pathology studies. This website is designed to accommodate the vast amount of structural, behavioral and gene expression data that has appeared since publication of The Mind of a Worm in a dynamic and easily updatable medium. This curated information can be viewed in individual neuron pages as well as neuron data appendices. In the future, we want to develop interactive user interfaces to visualize behavioral circuitries and perhaps neurophysiology information as they become available. The second section of Wormatlas provides guides for optimal usage of the information included in the first section. It offers general information relevant to C. elegans as well as specific usage directions for Wormatlas. For instance, we have created a color coding system in which the main structural elements of the animal have each been assigned a specific color from the web-safe color palette. The uniform color code will help viewers to perceive anatomical relationships and tissue symmetries even without any symbolic annotation. Our close collaboration with WormBase researchers has helped to create a common display language, in data sharing, and in development of a shared Gene Ontology vocabulary. Wormatlas is being created to serve the scientific community and as such, we greatly appreciate your input, data sharing, suggestions and criticisms that help improve the web site. We are actively seeking peer review as each new chapter is readied for release.

David H Hall et al. (2002) Mid-west Worm Meeting "Wormatlas: A web-based behavioral and structural atlas of C. elegans"

David H Hall, Zeynep F Altun, Constantinos Polydorou, Thomas Boulin, Maurice Volaski, Michael Zhang

[Mid-west Worm Meeting, 2002]

We have recently launched the prototype of Wormatlas (www.wormatlas.org). This atlas is designed to serve the scientific community with the main goal of bringing all the anatomical information pertinent to C. elegans within one readily accessible and easy to use web site. By creating extensive links to the WormBase as well as the C. elegansWWW server, we are aiming to provide users with seamless links between these databases. We hope to create the most comprehensive and complete online anatomy atlas for any genetic model organism. Wormatlas is designed to have two main sections, Index and Guides, with multiple chapters within each section. The Index section will contain the Handbook, Slidable Worm, Literature Archive, Cell Identifications, Neuron Data, Glossary, and Methods. The main goal of the Handbook is to provide a relatively simplified, image-supported and curated information about the general and specific anatomy of C. elegans.The images included in the Handbook will be annotated scanning and transmission electron (TEM) micrographs, computer-drawn images as well as DIC and fluorescent micrographs. The Slidable Worm is designed to provide 600-1200 annotated and nonannotated versions of TEM cross-sections of the animal available for viewing by the users with the help of a newly designed JAVA applet interface. The images will come from the original images from the MRC/LMB archive, from the MIT archive (courtesy of E. Hartwieg and R. H. Horvitz), from our Caltech/AECOM archives, and possibly others. The Literature Archive will provide on-line copies of landmark articles and treatises about the anatomy of the nematode. These HTML format articles include multiple web links to other sites in Wormatlas and WormBase to strengthen their interactivity for the structures mentioned. The Glossary aims to provide a comprehensive list of all nomenclature used to describe any cell structure in the nematode. Cell Identification and Neuron Data are planned to provide enough detail on features of single cells, esp. neurons, to aid researchers in recognizing and studying individual cells by their 3D shapes and positions, comparing TEM, DIC and GFP information, and by providing links to curated data on their gene expression patterns. Finally, Anatomical Methods will provide an up to date summary of the different modalities that are currently used in cell identification and tissue pathology studies. This website is designed to accommodate the vast amount of structural, behavioral and gene expression data that has appeared since publication of The Mind of a Worm in a dynamic and easily updatable medium. This curated information can be viewed in individual neuron pages as well as neuron data appendices. In the future, we want to develop interactive user interfaces to visualize behavioral circuitries and perhaps neurophysiology information as they become available.

David H Hall et al. (2002) West Coast Worm Meeting "Wormatlas: A web-based behavioral and structural atlas of C. elegans"

Thomas Boulin, Zeynep F Altun, Michael Zhang, Maurice Volaski, Constantinos Polydorou, David H Hall

[West Coast Worm Meeting, 2002]

We have recently launched the prototype of Wormatlas (www.wormatlas.org). This atlas is designed to serve the scientific community with the main goal of bringing all the anatomical information pertinent to C. elegans within one readily accessible and easy to use web site. By creating extensive links to the WormBase as well as the C. elegans WWW server, we are aiming to provide users with seamless links between these databases. We hope to create the most comprehensive and complete online anatomy atlas for any genetic model organism.