-
[
International C. elegans Meeting,
1979]
-
[
International C. elegans Meeting,
1981]
-
[
International Worm Meeting,
2011]
The first step in analyzing whole genome sequence alignments is to detect variant sequences and associate them with genome annotations. Most genome sequence facilities have access to developers who run command line driven scripts to make this association. Our mission is to simplify this and make the annotation of SNP and Indel calls accessible to the average investigator. To this end we have launched Whole Genomes, a website where investigators can upload SNP-called files for custom annotations
(http://seqreport.omrf.org/genome: open to all on May 1, 2011). Administratively, the site design is flexible, allowing one to easily create annotation tables based on tab delimitated flat files like the GFF files distributed by Wormbase. Further, the site uses simple forms to establish persistent templates that describe the format for uploaded SNP files. All files are imported into a MySQL database and all comparisons are done via MySQL queries that offer a much more dynamic interaction with the data compared to a simple script driven approach. Users do not need to know anything about annotation files, templates, or MySQL to use the site.
Whole Genomes allows users to map SNPs to any combination of features in the annotation database, such as coding sequence, potential splice sites, untranslated regions, or microRNAs. For examples, a coding sequence query would report the specific amino acid changes for SNPs that fall within translatable sequence along with a metric of evolutionary conservation for that particular change. The site also allows the user to compare SNPs in two strains to identify both unique and common variations. In addition, if a user has minimal or no mapping information Whole Genomes can compare two allelic strains to find the gene that is affected in both. Each annotated SNP is associated with a unique "Download" link that lets users download the DNA sequence associated with the annotated feature. Finally, for any given SNP, the site will design PCR primers to isolate DNA for SNP verification.
-
[
East Asia Worm Meeting,
2004]
The anatomical data of synaptic connectivity of C. elegans has been degitized for research with computers. The set of files are entitled 'The database of Synaptic Connectivity of C. elegans for Computaiton' and electronicaly delivered to request. The data files describe all items involved in the paper of Albertson and Thomson (1976) and that of White et al. (1986). The policy we empolyed on creating the data base was that diagrams and tables in the original paper can be reconstructed uniquely up to topology from the degitized data. Since our database is equivalent to the anatomical data, quality of the latter can be investigated on analysing the former by computer. It has been found that the anatomical data is almost perfectly self-contained except a few inconsistent descriptions such that the neuron class PDE sends 61 synapses to the class DVA while the latter receives only 36 synapses from the former. This is an exceptionally extreme case of inconsistency and number of erroneously described synaptic contacts are several hundred among eight thousand contacts. In addition, it has been found that several inconsistent description can be corrected from consideration of topological nature of processes in a three dimensional space, which is also suggested by the database.
-
[
International C. elegans Meeting,
2001]
Two web sites have been established to allow easier access to nematode sequences from species other than C. elegans and C. briggsae ; WWW.NEMATODE.NET is maintained by the Genome Sequencing Center (GSC) at Washington University in collaboration with North Carolina State University, and WWW.NEMATODES.ORG is maintained by Mark Blaxter's lab at the University of Edinburgh. Useful features being built for NEMATODE.NET include the following - 1) Searches: All nematode expressed sequence tags (ESTs) generated at the GSC, currently 32,000 from 10 species, and NemaGene clusters built from these ESTs, are available for BLAST and text searching. Searches can be directed by species, library, or nematode clade in a way that is not possible using the NCBI EST database dbEST. 2) FTP: All EST project data can be downloaded for local analysis including FASTA files and sequence trace image files. 3) Trace Viewer: Fluorescent trace representations for each EST can be viewed. Traces can sometimes provide additional sequence information not included in the EST due to quality value cut-offs. 4) Project Updates: Information is available about libraries in construction and sequencing in progress as the project expands toward 235,000 ESTs. 5) Clone Requests: Details on clone availability and ordering procedure are provided. 6) Links: The site includes an up-to-date set of 300 links to information on human, animal, and plant parasitic nematodes. Further plans for NEMATODE.NET include linking of ESTs to their closest C. elegans homologues by DAS third-party curation of Wormbase. This work is funded by NIH-AI-46593, NSF-0077503, and a Merck / Helen Hay Whitney Foundation fellowship.
-
[
International C. elegans Meeting,
2001]
Although it is commonly stated that C. elegans is a soil nematode, hardly anyone has isolated it directly from soil extract, as opposed to from decomposing organic matter. Presumably, the dauer is the stage most likely to be encountered in soil, but it is nearly impossible to morphologically distinguish the dauer of C. elegans from that of other rhabditid species, especially when preserved in fixative and mounted in permanent slides. As a result, the ecology of C. elegans remains unknown: there are no primary data on its natural population dynamics, prevalence, dispersal or associations with phoretic vectors. PCR-based identification has now become quite easy, but is expensive to apply routinely in a survey situation, and limited in quantitative resolution. In order to study the species ecology of C. elegans and relatives, we have therefore set out to develop a protocol that allows us to combine morphological and molecular data from individual nematodes, and especially from cryptic stages such as the dauer. Our basic equipment consists of a microscope equipped with Differential Interference Contrast optics, with a thermal stage and with a video camera. The camera is connected to a personal computer equipped for Video Capture and Editing (VCE) with a generic capture card and non-linear editing software. Individual nematodes are immobilised by cooling on the microscope stage, and the morphology of different body regions is captured as videofiles on hard disk, while manually focusing through the specimen at highest magnification. The nematodes are then taken off the microscope, lysed in extraction buffer, used for PCR of ribosomal loci, and sequenced. Next, the obtained sequences are matched with known sequences, to determine the identity of each individual. Finally, the obtained identifications are used to compare the multifocal VCE files and search for morphological characters allowing consistent distinction between dauers from different species. We present the first ecological data obtained in this manner, from samples collected in central and southern California. The equipment used is similar to a stripped-down, low cost 3-D version of a 4-D microscope, consisting mostly of generic components that are widely available from various suppliers and easily configured with minimal expertise. The system is highly versatile, and can e.g. also be used for non-destructively capturing the detailed morphology of mutants, recording ephemeral staining patterns, exchanging data across the internet, teaching, and assembling a VCE reference archive. Each series of videofiles from one nematode basically represents a "virtual microscope slide", bypassing the need for permanent slides. The size and contents of the captured files can be optimized with VCE, and the resulting compressed files combine the ease of storage and distribution of still images, with the depth of information and representation of multifocal videofiles.
-
[
International Worm Meeting,
2015]
JBrowse is a next generation genome browsing tool that is part of the Generic Model Organism Database project (GMOD) and is being developed as a replacement for the Generic Genome Browser (GBrowse) which currently powers the genome browser at WormBase. JBrowse has several advantages as a genome browser, including a very fast user interface, with "Google Maps" style, on-demand rendering; local, in the browser rendering of many file formats (GFF, BigWig, BigBed, BAM, VCF) so that the files don't have to be uploaded to a server; combination tracks that allow users to combine data in tracks using arithmetic and set operations; and a highly customizable user interface. While JBrowse is not expected to replace GBrowse at WormBase any time soon, we are rolling JBrowse out to users now to try, use and give feedback on development directions. Please try out JBrowse athttp://jbrowse.wormbase.org/.
-
[
International Worm Meeting,
2003]
A major challenge facing researchers in biomedical sciences is extracting the vast amount of information available only in biological literature, most of it contained in individual papers. Manual extraction of information from scientific papers is tedious and slow. We therefore seek to design a web-based system that aids the C. elegans researcher and professional curator in retrieving and efficiently extracting information from papers and abstracts. We have started to devise an information extraction system, which consists of several elements. A preprocessing unit prepares and formats plain text files from the corpus of currently 1880 pdf-files of C. elegans articles and 15000 abstracts. The text is then tagged semantically according to an ontology we have developed. This ontology contains thirty three categories. They can be summarized as classes of biological interest (such as gene, phenotype and cell), of actions, facts or circumstances that relate two (biological) entities or describe one (such as physical association, regulation, and effect), as well as other (auxiliary) classes that are useful for the information extraction process. The ontology includes all terms from the Gene Ontology (GO) Consortium. The semantically marked-up text is presented in XML format, making it available to XML-processing software tools. The marked-up text will then be used for the retrieval and fact extraction of pre-specified types of relationships, events or entities, such as gene-gene interactions or GO-gene associations. A web-based user interface (www.textpresso.org) allows the researcher to formulate queries in a variety of ways: simple keyword searches, searches for a set of occurrences of categories in a sentence or publication as well as the extraction of specified facts. The researcher is able to view sentences, paragraphs and whole articles as well as bibliographical information to verify the returned output. The project currently focuses on C. elegans literature, however, an expansion to the literature of other model organisms should be straightforward. The project is part of WormBase (www.wormbase.org).
-
[
International Worm Meeting,
2007]
The Union Biometrica COPAS™ BioSorter™ has become an essential tool in our lab and is an integral part of the French C.elegans functional genomics platform (see abstract by Duverger et al.). It can be used for numerous applications including the quantification of fluorescent reporter gene expression, large-scale RNAi and genetic screens and combinatorial library drug screening. One challenge that we have faced is the management of data derived from these experiments. Currently, information retrieved from the BioSorter™ is stored on individual computers and the resulting files are not easily searchable. We are developing a database for the storage and integration of BioSorter™ data. This database will serve as a centralized repository and the user interface will facilitate data searching and retrieval. We have developed a first draft of the database data model according the specifications defined by lab members. Feedback from BioSorter™ users in C.elegans community is now being solicited through a web survey and will be used to refine the data model to meet the specifications of as many users as possible. Progress on this project will be discussed.
-
[
International C. elegans Meeting,
1999]
We are developing a JAVA based variation of the IMR's "4D Viewer" software package(1), that runs on both Macintosh and Windows 95/98/NT machines. The program imports 4D data sets created by the IMR's "4D Grabber" application and can also construct 3D stacks from sets of individual image files. The program allows the user to label cells in a 4D stack and construct rotatable 3D models that retain cell identifications. This function allows the user to rotate a previously analyzed 4D set so that it corresponds to the 3D orientation of a newly collected second data set; this aids in the identification of cells viewed from a different orientation. The program also simultaneously constructs fully editable lineage diagrams that are linked to the 3D models and the 4D image data. The 3D viewer provides depth fading, zooming, rotation and has tools for color coding cells and coupling cells together with lines. The program will be available free of charge after the meeting, and will be available for download on our website. (1)Thomas, C, P DeVries, J Hardin and J White (1996) Four-Dimensional Imaging: Computer Visualization of 3D Movements in Living Specimens. Science 273: 603-607.