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[
International Worm Meeting,
2007]
Imagine being able to run WormBase on your own computer, unencumbered from server load at www.wormbase.org, network traffic, or even the need for a network connection. Run BLAST searches on your laptop enroute to your next presentation or explore expression patterns of your favorite gene family at the corner coffee shop. Maybe you have a private dataset that you would like to incorporate with WormBase to share within your lab or organization. Or perhaps you would like to set up a mirror site of WormBase as a community resource. All of these scenarios are easily possible with WormBase packages called "virtual machines". Virtual machines contain the entirety of WormBase and an operating system to hold everything together. In essence, this WormBase-customized operating system runs safely inside your Mac (Intel), Windows, or Linux computer using free software from VMWare. Virtual machines are now created for every WormBase release. Learn more about how to use these on the WormBase Wiki:
http://www.wormbase.org/wiki/index.php/Virtual_Machines Bring your laptop by this poster and we will install the most recent version of WormBase for you!
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[
International C. elegans Meeting,
1997]
We will describe a variety of interesting germline and somatic promoter activity patterns and make some suggestions as to how you might be able to engineer your gene to be expressed in any of all of these patterns.
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[
International Worm Meeting,
2021]
In keeping with the focus of this year's meeting on early career scientists, this poster aims to provide guidance and encouragement to new worm faculty in writing winning NSF Faculty Early Career Development (CAREER) proposals. The NSF-CAREER program is an exceptional funding opportunity for new investigators who are equally committed to outstanding research and education. The award is NSF-wide and thus is available to most areas of basic scientific research. If you are not yet tenured and looking to authentically integrate your research with education and/or outreach, this award is for you. Having served as a reviewer for these proposals, and currently in my last year of a CAREER award, I'd like to share some DOs and DONTs of proposal preparation and discuss ways to effectively integrate research and education/outreach components.
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[
Development & Evolution Meeting,
2008]
The pages of WormAtlas are getting a fresh look and organization.These changes will start from the front page and then be implemented throughout the Handbook and many other portions of the website.Here we will explain the principles of the new organization, and show you how to find your favorite features.This is the first major revamping of WormAtlas since its launch in 2002.We hope you will find the site simpler to navigate and we expect it will be more intuitive for beginners.As much as possible, these changes should not disrupt any previous weblinks you have established to your favorite pages.Inside the WormAtlas website, there will be several major changes. First will be an improved adult hermaphrodite handbook; it will include several completely revised chapters and a new one covering the nervous system. Second will be the launch of a handbook for anatomy of the worm embryo.Third will be the addition of more data to Slidable Worm.Lastly, we will be adding many new Neuron pages for the male nervous system in order to highlight new synaptic patterns emerging from the Wired Worm project conducted together with Scott Emmons. The WormImage website is expanding steadily.It now presents much more mutant data, particularly for genes affecting the nervous system.As before, we are relying heavily on MRC datasets, but we will continue to add more from the Riddle and Hall lab files.We encourage more laboratories to share your own best archival TEM and SEM images for this purpose.We are very grateful to many labs that have already contributed ideas, advice and experimental results that are featured on these websites.This work is supported by NIH RR12596.
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[
C.elegans Neuronal Development Meeting,
2008]
The pages of WormAtlas are getting a fresh look and organization. These changes will start from the front page and then be implemented throughout the Handbook and many other portions of the website. Here we will explain the principles of the new organization, and show you how to find your favorite features. This is the first major revamping of WormAtlas since its launch in 2002. We hope you will find the site simpler to navigate and we expect it will be more intuitive for beginners. As much as possible, these changes should not disrupt any previous weblinks you have established to your favorite pages. Inside the WormAtlas website, there will be several major changes. First will be an improved adult hermaphrodite handbook; it will include several completely revised chapters and a new one covering the nervous system. Second will be the launch of a handbook for anatomy of the worm embryo. Third will be the addition of more data to Slidable Worm. Lastly, we will be adding many new Neuron pages for the male nervous system in order to highlight new synaptic patterns emerging from the Wired Worm project conducted together with Scott Emmons. The WormImage website is expanding steadily. It now presents much more mutant data, particularly for genes affecting the nervous system. As before, we are relying heavily on MRC datasets, but we will continue to add more from the Riddle and Hall lab files. We encourage more laboratories to share your own best archival TEM and SEM images for this purpose. We are very grateful to many labs that have already contributed ideas, advice and experimental results that are featured on these websites. This work is supported by NIH RR12596.
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[
International C. elegans Meeting,
1999]
There are multiple ways of accessing the information from the genome project. First, you can search the genomic sequence on the blast server at either the Sanger Centre or GSC St Louis web site. The data sets searched on these servers are complete and updated every night. If you get a hit, you can retrieve the corresponding full sequence by web or ftp. Second, sequences are submitted to Genbank/EMBL. Finished sequence submissions contain some annotation including the gene predictions. Current unfinished sequence is also submitted to the HTG division of Genbank, so all sequences have an accession number, even if not finished. Finally, all the annotation information we have is made available via ACeDB, which also joins adjacent sequences and provides a wide variety of other information. The web version of ACeDB is most up to date. The state of the annotation and the specific information that is available will be described. Gene predictions are best efforts, and are liable to be wrong in the absence of supporting data. Please refer to them using the 'clone'.'number' identifier from ACeDB or Genbank, unless they have a three letter gene name. If you are responsible for assigning a gene name to a sequence, or identifying the sequence for a gene, please let us know. Please also email corrections to gene predictions or other information - these do result in fixes to our databases and hence ACeDB and Genbank. St Louis and Sanger each curate the sequence annotation for the parts of the genome they sequenced (email jspieth@watson.wustl.edu and worm@sanger.ac.uk) but information sent to either site will be forwarded to the other as required. ACeDB itself is built from the sequence annotation databases at each site, the current state of the physical map, and a database of genetic and literature information maintained in conjunction with the CGC (see abstract by Hodgkin et al.). We have also been developing a web interface to ACeDB (see abstract by Stein et al.). The Sanger Centre version of this web site uses a database that is rebuilt each week. As well as providing access by names of objects and text search, we have recently been exploring using the AltaVista search tool and interface to access the database. Other plans for ACeDB will also be discussed.
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[
International C. elegans Meeting,
1995]
The Caenorhabditis Genetics Center (CGC), supported by NIH NCRR, supplies Caenorhabditis strains and information to researchers. The St. Paul team is responsible for acquiring, maintaining and distributing worm stocks, generating and maintaining a C. elegans bibliography, and publishing the Worm Breeder's Gazette (WBG). The Cambridge team acts as a clearing house for C. elegans genetic nomenclature and maintains the genetic map. The CGC now has over 2150 different strains. We strive to have at least one allele of every published gene and all chromosome rearrangements, duplications and deficiencies. In addition, we have several strains of species closely related to C. elegans. Strains are available upon written request, which should include a brief statement of the intended use of the strains. Email requests (to stier@molbio.cbs.umn.edu) are satisfactory. The CGC bibliography currently includes over 2025 research articles and book chapters. The WBG is published 3 times each year and currently has over 675 subscribers. Various types of information from the CGC are available electronically. By gopher you can get current strain lists, the WBG subscriber directory, WBG Tables of Contents and the CGC bibliography. We can also email files to you. We like to be acknowledged in papers for providing strains. We also like to receive reprints of worm papers.
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[
International Worm Meeting,
2003]
Much pioneering genomic work, notably that from S. Kim's microarray facility and from J. Ahringer's RNAi library, relies on "GenePairs", a set of primers designed to amplify each C. elegans open reading frame. GenePairs were designed years ago, with an incompletely annotated genome, and many genes have changed since then. In particular, over one thousand GenePairs genes still had provisional names, which were quickly changed. Most analysis of these genes uses the GenePairs names to prevent ambiguity. In order to interpret some microarray data and to use some web resources, one needs to go from the current name of the gene to the GenePairs name or vice versa, which is not necessarily easy. For example, if you want to know what Wormbase has to say about Y59E9_116.A, which is an old GenePairs name for a gene, you might spend some time searching. A search of Wormbase turns up 13 matches, a few of which tell you that Y59E9_116.A is now called Y59E9AL.1, but most of which do not. In addition, since GenePairs were designed, many genes have been combined or split, usually because of cDNA sequencing. We have reannotated a list of genes from Stuart Kim's facility, so that we could easily "translate" from GenePairs to other databases. Data from the Stanford facility comes in tabular form. The table from Stanford has a column with a short description of the gene (from WormPD), a column with the genepairs name, and a column with alternate names. To that, we have added a column that has the current name of the gene, and several columns of brief functional annotations from Wormbase. In addition to the primary benefit of "translation", we have found several other benefits. First, the WormPD is no longer available to most C. elegans labs, which makes it hard to learn the rationale for the brief annotation. Second, some of the WormPD annotations are incorrect or incomplete. The Wormbase annotations are usually similar, sometimes better, sometimes worse, but with the database, genes that have differences in annotation can be identified and investigated. Third, the WormPD annotations are incompletesome genes have no description. Fourth, some GenePairs "genes" are now known to be more than one gene, which, of course, changes interpretation of results. Many, but unfortunately not all, of those are flagged in our database. In the hope that this database will be useful to others, we will present it (literally--you can pick up a CD) and describe its uses and limitations.
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[
C.elegans Neuronal Development Meeting,
2008]
Neuropeptides are packed into dense core vesicles (DCVs) and play critical roles in synaptic signaling. Before a DCV undergoes Ca-triggered exocytosis, it has to become fusion-competent through a so-called docking/priming step. Although a few molecules have been suggested to be involved in the docking/priming of DCVs, our understanding of the mechanism of this process is far from complete. Recently, we have developed high resolution functional assays to monitor the docking/priming process of DCVs in C. elegans neurons (Zhou et al., 2007, Neuron). Combining these techniques with the power of genetic manipulation in C. elegans model systems allows the illustration of sequential events in the docking/priming of DCVs at an unprecedented systematic level. I will summarize our recent progress towards a clearer picture of docking/priming of DCVs through analyzing the C. elegans mutants which are implicated to affect docking/priming.
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[
West Coast Worm Meeting,
2002]
C elegans is a filter-feeder: it takes in liquid with suspended particles (bacteria), then spits out the liquid, while trapping the particles. When one analyzes videotaped motions of bacteria or latex beads in the pharyngeal lumen, they seem to move backward with the liquid during the pharyngeal contraction, as you would expect. However, when the muscle relaxes, the liquid rushes forward and out the mouth, while the bacteria seem not to move very far anterior. The net result is that bacteria are transported posteriorly, toward the intestine. Unfortunately, the relaxation is very fast, only a few milliseconds, so that the detailed motions can't be seen. I decided to test whether I could simulate the transport of bacteria by simple hydrodynamic mechanisms.