THE GYPSY DATABASE (GyDB) OF MOBILE GENTIC ELEMENTS:
The GyDB project is owned and operated by Biotech Vana S.L., Plaza José Maria Orense Nº 7-83, 46022 Valencia, Spain, with the collaboration and permission of the University of Valencia to use the URL http://gydb.uv.es. The GyDB furthers the scientific objective of excellence in research, services, and education by making available worldwide an online platform with a focus on the evolutionary history, taxonomy and molecular diversity of mobile genetic elements.
CONTRIBUTIONS:
Biotechvana is glad to share the GyDB with all authors interested in mobile genetic elements and in to improving the database background. Authors interested in collaborating are invited to contribute any material concerning mobile genetic elements. We are also glad to engage with other international biodatabases in all varieties of collaborations concerning mobile genetic elements. For more information, please see the sections below or contact Carlos Llorens, Biotechvana editor.
TERMS AND CONDITIONS:
The GyDB is a long-term research project that aims to investigate, the non-redundant diversity, evolution and phylogenetic relationships of mobile genetic elements and related nonviral proteins. The project has two components, Research and Database Services. Research is published as is standard in international journals; Database Services consist in the infrastructure of web sites and servers freely available in the database. The material supplied at the GyDB is distributed under the terms of the CREATIVE COMMONS ATTRIBUTION LICENSE, which allows unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. There is no restriction imposed by Biotechvana on the use of this scenario, excepting the following:
- Use of the GyDB for any illegal purpose, or in any manner that could exceed authorized access, damage, disable, overload, or harm the operation of this site or any other party's use of the Biotechvana Web sites, is strictly prohibited.
- Limitations of copyright are imposed on photographs and/or other material provided by other contributors. The GyDB incorporates images of biological organisms we believe are helpful in facilitating an improved perspective concerning biodiversity and relationships among mobile genetic elements and hosts. The GyDB makes this material available for informative purposes only, and does not redistribute the images. Transmission or reproduction of protected items beyond that allowed by fair use as defined in the copyright laws requires the permission of the copyright owners. Under these terms, we authorize you to retrieve those images of which we are owners (see "Acknowledgments" below). If you are interested in any other image courtesy of other authors, you should contact the copyright owner
We are both authors and contributors. We are glad to accept results and discussions from other authors disputing or in favor of our conclusions. However, a priori, all the discussions, results, and supplementary material should concern published or (at least) peer-reviewed material. This means that, despite all, we are receptive to well-sustained unpublished information capable to improve the background of the project. By our side, we try to only consider sequences whose full-length genome is publicly available. If you would like to contribute information on a new mobile genetic element, you do not need to provide us the sequence; you may submit it, as is customary, to the NCBI genbank or any other database, give it a name, and notice us the genbank accession assigned to the sequence. We will then create a file of this mobile genetic element and you will be properly cited. Later, the sequence will be processed in three ways: it will be included in a BLAST database that may be publicly consulted, and we will phylogenetically analyze the different protein domains encoded by this sequence to which we assign a monophyletic group. Finally, we will create or re-built a collection of hidden markov model (HMM) profiles considering your element in each consensus constructed, the collection of HMM profiles will be publicly available at the HMM server at GyDB.
BIOTECHVANA COMPLEMENTS:
We distribute the GyDB package of web sites, MySQL databases and programming algorithms at Biotechvana Bioinformatics under the terms of the COMMON PUBLIC LICENSE to be run on personal computers (PCs) and intranets. We do not anticipate imposing limitations on either the use or modification of the source code in order to personalize the database or create your own database. However, bear in mind that designed programming algorithms, commercial name, anagrams, layout, source code, and design (collectively, the "Content") are trademarks or items copyright of Biotechvana and that all rights are reserved. This means that we allow you to create your own database, using the GyDB as a template but we do not allow you to reproduce, redistribute, transmit, publish, and/or sell the GyDB itself without our prior permission (see, however, "Transposable Project and Further Improvements" below). Authors interested in consulting the in-progress collection of multiple alignments HMM-profiles and majority-rule consensus sequences on which we have based the database of HMM profiles available at the HMM server, may access this collection (in collective, the GyDB collection) as a part or section of the BB collection.
TRANSPOSABLE PROJECT AND FURTHER IMPROVEMENTS:
The GyDB project pursues the fascinating goal of analyzing the non-redundant diversity of mobile genetic elements in the context of the Tree of Life. The idea of a long-term research project shared with other authors by way of the Internet is very attractive to us. With this in mind, we retain the perspective that the project may be itself transposable from one research group into another. Eventual contributions to the GyDB are free, but we will please to share the project with all interested researchers who are open to formally entering this investigation. The terms and conditions of this agreement are outlined more extensively in the GYDB PARTNERSHIP.
LINKS:
Links to other web sites are provided by the GyDB in good faith and for informational purposes only. Biotechvana disclaims any responsibility for the materials contained in any web site linked to the GyDB project.
PRIVACY POLICY:
Simply visiting the GyDB does not publicly expose your identity unless you choose to provide this information, in order to participate in the project (via our data submission form). In this case, personal information will be used only for administrative purposes and will be kept confidential. It will not be released to other databases for any type of illegitimate use.
MEDICAL QUESTIONS:
The GyDB project does not provide specific medical advice. Personal questions for diagnosis must be addressed to qualified professionals.
COOKIES:
A cookie is a small data file that web sites commonly write to a site visitor's hard drive when the site is visited. The GyDB will set a temporary session cookie (PHPSESSID) whenever you visit the site. The cookie and the information concerning your session will be automatically eliminated shortly after you close your browser. It is not stored long-term on your computer. You may deny the cookie, but keep in mind that doing so prevents use of our cookie-dependent features.
DISCLAIMER:
Access to the GyDB is available free of charge
for ordinary use in the course of research. Wwe try to make available only peer reviewed information (this includes our own results and research). However, the information supplied in the GyDB online project is being provided freely, and no kind of agreement or contract is created between you and Biotechvana beyond the CREATIVE COMMONS ATTRIBUTION LICENSE. Biotechvana makes efforts to keep the GyDB available twenty-four hours a day and seven days a week, but does not guarantee that the service will be uninterrupted or error-free, or that the service will be free of viruses or other harmful components. Biotechvana does not give any kind of warranty nor assume any kind of liability or responsibility for the services, incidences or results reported or involving the GyDB (despite of our efforts to improve their accuracy, completeness, quality or others). Please make sure that you understand that the information provided here is being provided freely, and no liability is accepted by Biotechvana, partners, sponsors, and/or contributors concerning the use of the database, this is your choice. By accessing or using the GyDB in any way, including services, or solely browsing the site, you agree to and are bound by the terms of use described in this document.
INTERACTIVE POLICY:
Given that the GyDB Project is in its beginning stages, we will make every effort to review this policy in light of its evolution and the commentary we receive; please check the latest version. We anticipate accepting senior revisers who will adapt and modify the current privacy policy in light of new requirements, and who will engage efforts with other databases within the field. If you have any questions explicitly concerning privacy, please see the section Privacy policy of Biotechvana.
ACKNOWLEDGMENTS:
In the Iteration II (in preparation) of this project we are grateful to:
- Pavel Neumann, Institute of Plant Molecular Biology, Czech Republic, for useful revision of Ogre LTR retrotransposon
- Teo Chee How, Unit of Genetic and Molecular Biology. University of Malaya, Malaysia for useful revision and update of Monkey LTR retrotransposon
- Eric W. Ganko, Department of Bioinformatics, Biology Dept. UNC-Chapel-Hill, for useful corrections and information about C. elegans-like Mag and Cer2-3 LTR retroelements
- Claudia Copeland, Department of Bioinformatics, University of Leipzig, for useful information about the Boudicca LTR retrotransposon
- All contributors in Version I
In the iteration I of this project we are grateful to:
- University of Valencia for support and permission to use the URL http://gydb.uv.es with research and education purposes, and by providing fundings for publication charges.
- Alfredo Martinez, Department of Plant Patology, University of Georgia, for contributing an image of Fusarium sp.
- Wikipedia, the free encyclopedia from where we have picked up the image of Takifugu rubripes, Copyright of the user Chris 73, and free available under the dual terms of the Wikipedia Commons image and the Creative Commons licenses.
- Jean-Jacques Eckert and Patrick Bertrand of Recif France, for contributing an image of Tripneustes gratilla.
- Joaquin Panadero, our friend and Biotechvana partner of the Centro Nacional de Biotecnologia (CNB), for his collaboration in this project and contributing the images of Madrill sp., Primates sp., Saccharomyces cerevisiae, Mus musculus, Mandrillus sphinx, Saccaromyces exiguus, and Cricetelus, griseus.
- Pierre J.G.M. de Wit of Laboratory of Phytopathology, Wageningen University (www.php.wur.nl/uk), for contributing an image of Cladosporium fulvum by way of Alejandro Perez of the Universidad de Malaga.
- Alberto Urbaneja of "Instituto Valenciano de Investigaciones Agrarias" (IVIA), for contributing an image of Ceratitis capitata.
- Valmir Duarte of Faculdade de Agronomia, UFRGS, Porto Alegre, for contributing an image of Colletotrichum gloeosporioides.
- Duncan van Vliet of the Web site "www.onderwaterwereld.net", for contributing an image of Ciona intestinalis.
- Hugh D. Wilson of TAMU herbarium, Texas A&M University, for contributing an image of Zea diploperennis.
- "Aquaria Central" for contributing an image of Stizostedion vitreum.
- Marcel Lecomte, for contributing an image of Pyrenophora graminea, by way of the Web site "Skynet.be".
- Tom Volk of the University of Wisconsin-La Crosse, for contributing an image of Tricholoma magnivelare, the american matsutake mushroom.
- Michael Schleicher of the Ludwig-Maximilians-Universitaet, for contributing an image of Dictyostelium discoideum, host of the Gypsy-like Skipper retrotransposon.
- The Web site "www.knoch1.de", for making online available a comprehensive database of images of plant organisms from which we have picked up the images of Arabidopsis thaliana and Nicotiana tomentosiformis for educational and research purposes, following the on-line permission of the copyright owner.
- Chris Glenn of JC Raulston Arboretum, for contributing an image of Phascolarctos cinereus with permission of the copyright owner, Bryce Lane, Department of Horticultural Science, NC State University.
- David Pearce of the Web site "primates.com", for contributing an image of Hylobates syndactylus.
- Jaap van Tuyl of Wageningen University and Research Center, for contributing an image of Lilium henryi by way of the
Lilium information page.
- Alan Hill of Hopwood Hall College, for contributing an image of Pan paniscus by way of the "ZipCodeZoo.com" Web site project.
- Marc Hauser of the Cognitive Evolution Laboratory of Harvard University, for contributing an image of Cercopithecus aethiops tantalus.
- Juan Bibiloni of "Jardín Botánico Mundani" in Mallorca, for contributing an image of Sorghum bicolor.
- David Stand of BayScience Foundation, for contributing an image of Macaca mulatta by way of the "ZipCodeZoo.com" Web site project.
- J. Michael Miller of the Science National Center for Zoonotic, Vector-borne, and Enteric Diseases, of Coordinating Center for Infectious Diseases (CCID), Atlanta, for contributing an image of Schistosoma japonicum.
-
Richard J Howard of DuPont Experimental Station, for contributing an image of Magnaporthe grisea reprinted, with permission, from the Annual Review of Microbiology, Volume 50 © 1996 by Annual Reviews (www.annualreviews.org).
- Tim.J. Goodwin of the University of Otago, for useful information and comments concerning the DIRS1 lineage of retrotransposons within the context of the elaboration of the Three Kings Hypothesis manuscript.
- Ralf J. Sommer of the Max Planck Institute for Developmental Biology, for contributing an image of Caenorhabditis elegans.
- Alex Wild, author of the insect photography Web site "myrmecos.net", for contributing an image of Tribolium castaneum.
- Rita Bernhardt, Lehrstuhl für Biochemie, Universität des Saarlandes, for contributing an image of
Schizosaccharomyces pombe.
- John H. Wahlert et al. of Baruch College, City University of New York, for contributing an image of
Clonorchis sinensis.
- Cal Vornberger, nature photographer, for contributing an image of Meleagris gallopavo by way of the Animal Diversity Web of the University of Michigan Museum of Zoology.
- Ralph Cavaliere of Gettysburg College for contributing an image of Aspergillus nidulans.
- Our friends Enrique Donat and Cristina Campos for contributing the images of Pinus sp., Ovis sp., and Gallus gallus.
- Margarita López of SESBE (Sociedad Española de Biología Evolutiva) for contributing two images of Capra pyrenaica copyright of Jorge Aguilar Bosch.
- Rachel Epstein, our friend and Biotechvana partner of Washington University, for all English revisions.
- Maria Consuelo Palacios for her collaboration in this project.
- Javi Ortiz, Isaac Fernandez and Bernardo Celda for technical support at the Servicio Central de Soporte a la Investigacion Experimental (SCSIE) of the University of Valencia.
- Our friend and Biotechvana partner Miguel Vicente Ripollés of the Ausias March Institute of Valencia, for coordinate the collaboration of Virtudes Planelles, Fran Frechina, Jordi Cervera, Pablo Sabater, and Emilio Javaloyas.Our thanks to all them, also.
- Peter Balint-Kurti from the United States Agricultural Research Service, for useful information of the Monkey LTR retrotransposon.
- Howard Laten of Loyola University of Chicago, for useful information of the Diaspora LTR retrotransposon.
- Andreas Trepte of Max-Planck-Institute, for contributing an image of Drosophila melanogaster.
- Thomas Kaufman of Flybase, for contributing the images of Drosophila virilis and Drosophila ananassae.
- Sarah LaRose of the Virtual Museum of Canada, for contributing an image of Alternaria alternata copyright of George Barron.
- CEEI of Valencia for supporting us at the start of this project.
- We have been awarded the NOVA 2006 by IMPIVA and Conselleria d`Empresa, Universitat I Cìencia of Valencia.
- The BB platform and the GyDB project have been partly supported by European Union funding grants IMCBTA/2005/45, IMIDTD/2006/158 and IMIDTD/2007/33 from IMPIVA and by grant BFU2005-00503 from Ministerio de Educación y Ciencia to Andres Moya.
Last revised: April 16, 2008
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