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FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context

Malte Mader, Ronald Simon, Sascha Steinbiss, Stefan Kurtz
2011 Journal of Clinical Bioinformatics  
Results: We have developed a web-based software FISH Oracle to visualize data from multiple array CGH experiments in a genomic context.  ...  FISH Oracle will be instrumental to identify candidate onco and tumor suppressor genes based on the frequency and genomic position of DNA copy number changes.  ...  Acknowledgements This work was supported by a grant from the Werner-Otto-Stiftung to SK and RS (# 6/73) and a grant from the Federal Ministry of Education and Research (BMBF), Germany to RS (# FKZ 01GS08189  ... 
doi:10.1186/2043-9113-1-20 pmid:21884636 pmcid:PMC3164613 fatcat:vjmj5wf6gba2vap3vpmce567t4

The UCSC Genome Browser database: update 2011

P. A. Fujita, B. Rhead, A. S. Zweig, A. S. Hinrichs, D. Karolchik, M. S. Cline, M. Goldman, G. P. Barber, H. Clawson, A. Coelho, M. Diekhans, T. R. Dreszer (+15 others)
2010 Nucleic Acids Research  
Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation  ...  As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data  ...  The final steps before public release are the creation of a BLAT server for sequence searches, and completion of descriptive web pages for the assembly and annotation tracks.  ... 
doi:10.1093/nar/gkq963 pmid:20959295 pmcid:PMC3242726 fatcat:fnemefhmkbc65bmwbfxqlp7lpm

Introduction to Bioinformatics [article]

Sabu M. Thampi
2009 arXiv   pre-print
Bioinformatics is a new discipline that addresses the need to manage and interpret the data that in the past decade was massively generated by genomic research.  ...  This discipline represents the convergence of genomics, biotechnology and information technology, and encompasses analysis and interpretation of data, modeling of biological phenomena, and development  ...  Once you've stored data in an accessible, flexible format, the next step is to extract what is important to you and visualize it.  ... 
arXiv:0911.4230v1 fatcat:4trytpwrw5apvkiejbwhiqmp6m

BioSilicoSystems – A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Sridhar Hariharaputran, Sridhar Hariharaputran
2010 Nature Precedings  
Apache Tomcat web server.  ...  Whenever a JavaServer page is opened in a web browser, a request is sent from the client to the server.  ...  Appendix I Appendix III As explained in the SBML web pages the following enzymatic reaction will be represented by SBML as <?xml version="1.0" encoding="UTF-8"?  ... 
doi:10.1038/npre.2010.5164 fatcat:72ufu6ycfba55gi6bvhatcld3e

BioSilicoSystems – A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Sridhar Hariharaputran, Sridhar Hariharaputran
2010 Nature Precedings  
Apache Tomcat web server.  ...  Whenever a JavaServer page is opened in a web browser, a request is sent from the client to the server.  ...  Appendix I Appendix III As explained in the SBML web pages the following enzymatic reaction will be represented by SBML as <?xml version="1.0" encoding="UTF-8"?  ... 
doi:10.1038/npre.2010.5164.1 fatcat:bo3ri2crajb5xk7kukxhe6affa

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
We will also assess the near isogenic panel in Japanese Rice Paddy fish for a number of molecular and whole body phenotypes.  ...  We also developed a Fourier-Shell-Correlation server and a tilt-pair-validation server, and added new types of images (e.g. rotationally averaged power spectra and central slices) to the visual-analysis  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

HGM 2010 Programme / Abstract

2010 The HUGO Journal  
The identification of an EYS mutation in a dog affected with retinal progressive atrophy would provide a useful model for establishing future therapies for retinitis pigmentosa.  ...  We would like to extend our utmost appreciation to them for all of their support.  ...  IMGT® gene data are provided on Ensembl Genome Browser (EBI) via a DAS server.  ... 
doi:10.1007/s11568-010-9143-0 fatcat:oykxd6u7snfi5o7m6tst7wi6yq

RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology

Michela Taufer, Ming-Ying Leung, Thamar Solorio, Abel Licon, David Mireles, Roberto Araiza, Kyle L. Johnson
2008 Parallel Computing  
The extensive sampling and predictions are made feasible in a short turnaround time because of the grid technology used.  ...  This paper presents RNAVLab (RNA Virtual Laboratory), a virtual laboratory for studying RNA secondary structures including pseudoknots that allows scientists to address this challenge.  ...  We would also like to thank the BBRC DNA Analysis Core Facility for services and facilities provided.  ... 
doi:10.1016/j.parco.2008.08.002 pmid:19885376 pmcid:PMC2714649 fatcat:axaiz75fyrcyxmzdz7nalji4ji

Physical Principles and Visual-OMP Software for Optimal PCR Design [chapter]

John SantaLucia
2007 Msphere  
The physical principles of DNA hybridization and folding are described within the context of how they are important for designing optimal PCRs.  ...  In addition, the thermodynamics of DNA-DNA duplex formation are quite different than that of DNA-RNA hybridization.  ...  Nouri Ben Zakour received financial support in the form of a PhD grant from the French Ministry of Research and Education. Designing Primers Using the Package GenoFrag  ... 
doi:10.1007/978-1-59745-528-2_1 pmid:17951788 fatcat:tghqvlsslzcspmi673q4m4q32m

The Fourth Paradigm – Data-Intensive Scientific Discovery [chapter]

Tony Hey
2012 Communications in Computer and Information Science  
The F o u r T H Data-In t e n s I v e scIen t I f I c DIs c o v e r y P a r a d i g m MiCroSoF T reSe arCH REDMOND, WASHINGTON  ...  very helpful discussion on a draft of this material. to all the contributors to this book for sharing their visions within the Fourth Paradigm.  ...  Acknowledgments My thanks to the participants at the April 24, 2009, Buckland-Lynch-Larsen "Friday Seminar" on information access at the University of California, Berkeley, School of Information for a  ... 
doi:10.1007/978-3-642-33299-9_1 fatcat:etue636ubrandga5corvkx3d7u

Digital Imaging Of Biological Type Specimens. A Manual Of Best Practice. Results From A Study Of The European Network For Biodiversity Information

C.L. Häuser, A. Steiner, J. Holstein, M.J. Scoble
2005 Zenodo  
Department of the NHM have generously engaged in discussion concerning the imaging fish specimens -we have benefited greatly from these discussions.  ...  Our thanks are also due to TINEKE PRINS and CEES ROOSELAAR at the ZMA Museum for their elaborate work on the collection data and the supply of type material, to GIDEON GIJSWIJT for hardware support at  ...  A copy of the database and files is fed to a separate file server that includes a web server for outside access.  ... 
doi:10.5281/zenodo.163941 fatcat:ukeeraeyzngpzm62qjcdsnk2ta

Global Data For Global Science

Multiple Authors
2015 Zenodo  
The Proceedings of the 1st ICSU World Data System Conference, held 3–6 September 2011 at Kyoto University, Japan, contains the papers submitted to the Data Science Journal.  ...  Watanabe and other members of WDS-SC for their arrangement in publishing a special issue on CODATA Data Science Journal, as a proceeding ACKNOWLEDGEMENTS The present work was done by using resources of  ...  of the European Commission. 5 ACKNOWLEDGEMENTS ACKNOWLEDGEMENTS The authors would like to express their special appreciation to a significant number of collaborators associated with the IPY activities  ... 
doi:10.5281/zenodo.34188 fatcat:dhoudwjt2bdjnmnq2e3jubmysa

ASSESSING THE GENETIC VARIABILITY OF GRAPE CLONES

S. Vezzulli, L. Leonardelli, U. Malossini, M. Stefanini, R. Velasco, C. Moser
2014 Acta Horticulturae  
Acknowledgments Research carried out with the financial contribution of the University of Bologna, Italy (STARCHitecture Project).  ...  P7.04 -Nutritional quality of einkorn wheat (Triticum monococcum L.) kernels Brandolini Andrea 1 , Hidalgo Alyssa 2 , Plizzari Luca 1 , Erba Daniela 2  ...  This feature and the possibility to store all data in a central and powerful relational database (SQL Server, Oracle, MySQL) allows the construction of large databases over long periods of time.  ... 
doi:10.17660/actahortic.2014.1046.48 fatcat:ockmijg55ne7bb46gbthiuewhe

Risks from Low Doses of Radiation: Continued

M. Goldman
1996 Science  
Faculty Position in Biophysics University of California, Los Angeles The Departments of Physics and Astronomy, Chemistry and Biochemistry and the Jules Stein Eye Institute invite applications for a senior  ...  Applicants should send a resume, a research statement, and names of at least three references to F. V.  ...  For consideration, submit TWO COPIES of a resume and publication listing (including the names, addresses and phone numbers of at least three people who will provide references) to: Postdoctoral Program  ... 
doi:10.1126/science.273.5275.561d fatcat:judbhnacbjgknmogqkklrjfo5y

Organizing institutions

2016 2016 10th International Conference on Software, Knowledge, Information Management & Applications (SKIMA)  
We thank the organizing committee for their commitment to the success of the event, the authors for their submissions and the program committee for their hard work. Acknowledgements.  ...  Acknowledgments The authors thank the Fundação Araucária of Paraná, Brazil and the Portuguese Fundação para a Ciência e Tecnologia through the financial support of INESC-ID funding under project PEst-OE  ...  In this context, a domain ontology is applied for imposing a rich and homogeneous structure to the visual descriptions of the domain objects that are the targets of this task.  ... 
doi:10.1109/skima.2016.7916183 fatcat:ctichxcphnhj7ci3h4lu662gbi
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