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A new plug-in software architecture applied for a portable molecular structure browser

Y Ueno, K Asai
<span title="">1997</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q33b3suvffclbkvfvrsg3ljwjm" style="color: black;">Proceedings. International Conference on Intelligent Systems for Molecular Biology</a> </i> &nbsp;
A molecular structure browser program was developed together with several plug-in modules on our programming library that maintains graphics portability and user interfaces.  ...  A new software configuration method using plug-in style components was established for the tool with the incremental development of software used in protein structural study.  ...  Availability Source code of prototype is available upon e-mail request for developers and our molecular structure browser will be released at ftp://ftp.etl.go.jp/pub/bioinfo.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9322057">pmid:9322057</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/32keg2kxlnevpalbkhrbwe7egu">fatcat:32keg2kxlnevpalbkhrbwe7egu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20151026151139/http://www.aaai.org/Papers/ISMB/1997/ISMB97-050.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0f/a6/0fa691b93f5ea0e62c93d764fc232738918b68d6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Integrating Application Programs for Bioinformatics Using a Web Browser

Yutaka Ueno, Kiyoshi Asai, Masanori Arita
<span title="">1999</span> <i title="Japanese Society for Bioinformatics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jf2bmhtlzjh4zjrkh3rivxd2sq" style="color: black;">Genome Informatics Series</a> </i> &nbsp;
Our framework also supports pluggable extension-modules for application programs by means of dynamic linking. A prototype system is implemented on our molecular structure-viewer program, MOSBY.  ...  When it is used as ahelper application to a Web browser, these messages will be sent from the browser by clicking a hyper-link in a Web document.  ...  Yutaka Akiyama for useful discussions, and Dr . Nobuyuki Otsu for continuous support and suggestions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.11234/gi1990.10.166">doi:10.11234/gi1990.10.166</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7vnw7zvmlvgrtczrbf2alrpnd4">fatcat:7vnw7zvmlvgrtczrbf2alrpnd4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220507194427/https://www.jstage.jst.go.jp/article/gi1990/10/0/10_0_166/_pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1c/c8/1cc8752cbe52d26dfbe7fcda8306ba189cc598af.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.11234/gi1990.10.166"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Molecules to maps: tools for visualization and interaction in support of computational biology

E. T. Kraemer, T. E. Ferrin
<span title="1998-10-01">1998</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
The volume of data produced by genome projects, X-ray crystallography, NMR spectroscopy, and electron and confocal microscopy present the bioinformatics community with new challenges for analyzing, understanding  ...  The plug-in architecture supports simple integration of new assessment tools into DINAMO, as well as its extension to include additional molecular graphics engines.  ...  to create reliable new application software in a timely manner.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/14.9.764">doi:10.1093/bioinformatics/14.9.764</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9918946">pmid:9918946</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x4feoxu7xzdafjl4a32qmlmn74">fatcat:x4feoxu7xzdafjl4a32qmlmn74</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20040527073117/http://bioinformatics.oupjournals.org:80/cgi/reprint/14/9/764.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0a/27/0a27bc4b3acc0cf8f62f5abf914df87a264c69a0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/14.9.764"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

A prototype molecular interactive collaborative environment (MICE)

P Bourne, M Gribskov, G Johnson, J Moreland, S Wavra, H Weissig
<span title="">1998</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/d4nr2uqysjfnpiksvyxq54p5bm" style="color: black;">Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing</a> </i> &nbsp;
Current work seeks to replace WebView with Netscape, Cosmoplayer, a standard VRML plug-in, and a Java-based console.  ...  MICE defines a Molecular Scene Description Language (MSDL) which allows scenes to be stored in a relational database (a molecular scene gallery) and queried.  ...  Current efforts are directed towards using Cosmoplayer™, a plug-in to the Netscape Navigator™ Web browser, and using Java beans to define the console to control the molecular scene.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9697176">pmid:9697176</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/msrbzqvm2jgzfac34jslbq7c7m">fatcat:msrbzqvm2jgzfac34jslbq7c7m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808203105/http://psb.stanford.edu/psb-online/proceedings/psb98/bourne.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/12/59/1259bdf9fe7505036d35974ca067617f81b5e563.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

A functional framework for Web-based information visualization systems

M. Bender, R. Klein, A. Disch, A. Ebert
<span title="">2000</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hjrujdrg7zaghbdsp5pdzq7cmm" style="color: black;">IEEE Transactions on Visualization and Computer Graphics</a> </i> &nbsp;
In this paper, we propose a functional developer's framework for general Webbased visualization systems which makes intelligent use of application specific software and hardware components on the server  ...  The obvious drawbacks of this development are highly dependent software systems, which are only available for a restricted number of users.  ...  The only assumptions for software on the client side is a Java-enabled Web browser and, if used, a VRML plug-in or Java 3D installed, respectively.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/2945.841118">doi:10.1109/2945.841118</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i4ln7x3hx5gyrec7df3ws2n3uq">fatcat:i4ln7x3hx5gyrec7df3ws2n3uq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060905190941/http://www.csc.lsu.edu/~karki/SV-05/04WV.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0c/77/0c774dd533f6ebaafbaa44cc77c43fa738f94b14.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/2945.841118"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Addressing the Future of Clinical Information Systems—Web-Based Multilayer Visualization

Chueh-Loo Poh, Richard I. Kitney, Rasu B. K. Shrestha
<span title="">2007</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/opxxmwcvy5fnnhqoc4wtvb4etm" style="color: black;">IEEE Transactions on Information Technology in Biomedicine</a> </i> &nbsp;
With the increasing importance of molecular and cellular biology, a new type of medicine, molecular based medicine, is now developing.  ...  This paper addresses some key issues relating to the development of new technology for clinical information systems (CIS) in relation to imaging and visualizing data.  ...  Weinberg and A. Bond for providing the cellular images used in our study.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/titb.2006.875680">doi:10.1109/titb.2006.875680</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17390983">pmid:17390983</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gtctgis2o5di3op7ulovck6p6u">fatcat:gtctgis2o5di3op7ulovck6p6u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829120630/http://www.bg.ic.ac.uk/research/r.kitney/paper3.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ed/53/ed5390103e81ce3f0382c0f11866a7bc65f1d7a0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/titb.2006.875680"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Molecular Dynamics Simulation of Biological Molecules. (2). Practice
生体分子の分子動力学シミュレーション (2) 応用

Yuto KOMEIJI, Sumie TAJIMA, Makoto HARAGUCHI, Nobuyuki TAKAHASHI, Masami UEBAYASI, Umpei NAGASHIMA
<span title="">2001</span> <i title="Society of Computer Chemistry Japan"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/w6tgytqbnngz5c6jtixpe65scq" style="color: black;">Journal of Chemical Software</a> </i> &nbsp;
Software, 6, 1-36 (2000) . [2] Ueno, Y., Asai, K., A new plug-in software architecture applied for a portable molecular structure browser, Proceedings, Intelligent systems for molecular biology, 5, 329  ...  In this review, the practical procedures of molecular dynamics simulations of a protein and DNA by using the software PEACH (Program for Energetic Analysis of bioCHemical molecules) are described.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2477/jchemsoft.7.1">doi:10.2477/jchemsoft.7.1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xezob5o2fjckro3zaoxqwcb6ry">fatcat:xezob5o2fjckro3zaoxqwcb6ry</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190505230611/https://www.jstage.jst.go.jp/article/jchemsoft/7/1/7_1_1/_pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3a/79/3a79e886523759dbb00eb6ad39be91015e3cab07.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2477/jchemsoft.7.1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

openBEB: open biological experiment browser for correlative measurements

Chandrasekhar Ramakrishnan, Andrej Bieri, Nora Sauter, Sophie Roizard, Philippe Ringler, Shirley A Müller, Kenneth N Goldie, Kaloyan Enimanev, Henning Stahlberg, Bernd Rinn, Thomas Braun
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
The open architecture of openBEB enables the fast integration of plug-ins, e.g., for data acquisition or visualization.  ...  Results: We have developed openBEB (open Biological Experiment Browser), a software framework for data acquisition, coordination, annotation and synchronization with database solutions such as openBIS.  ...  Acknowledgements We thank Stefan Arnold, Christoph von Arx, Benjamin Bircher, Dominic Giss, Simon Kemmerling (C-CINA, University Basel) for testing the openBEB software.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-15-84">doi:10.1186/1471-2105-15-84</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24666611">pmid:24666611</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3987129/">pmcid:PMC3987129</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/33lyusgpjncuddbrqipz2u5ugm">fatcat:33lyusgpjncuddbrqipz2u5ugm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808022836/https://link.springer.com/content/pdf/10.1186%2F1471-2105-15-84.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ce/e4/cee4fcd625236f299ff7e9c943b3d4a50ee80025.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-15-84"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3987129" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

Björn Menten, Filip Pattyn, Katleen De Preter, Piet Robbrecht, Evi Michels, Karen Buysse, Geert Mortier, Anne De Paepe, Steven van Vooren, Joris Vermeesch, Yves Moreau, Bart De Moor (+3 others)
<span title="2005-05-23">2005</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser.  ...  One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment.  ...  The easy plug-in architecture makes it possible for each user to add custom algorithms for data analysis and visualization and share these with the user community.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-6-124">doi:10.1186/1471-2105-6-124</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15910681">pmid:15910681</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1173083/">pmcid:PMC1173083</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/o23fqjhs2vafnfykt5w3hyif7e">fatcat:o23fqjhs2vafnfykt5w3hyif7e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426132055/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-6-124" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8e/02/8e02a5485b06f3ee28517375a31a93477051379a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-6-124"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1173083" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Stylesheet transformations for interactive visualization

Nicholas F. Polys
<span title="">2003</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6jpbkn7xf5cdtoo7r7dr2vqkhq" style="color: black;">Proceeding of the eighth international conference on 3D web technology - Web3D &#39;03</a> </i> &nbsp;
Standards design approaches offer a number of advantages: data durability, data interoperability, and an ecology of tools to be deployed for production and delivery.  ...  This paper describes and evaluates such techniques to transform structured data such as Chemical Markup Language (CML) to different forms and contexts for Web3D delivery using Extensible Stylesheet Transformations  ...  These techniques are usually described for use with the common and capable web browser plug-ins [1, 11, 12] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/636593.636606">doi:10.1145/636593.636606</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/vrml/Polys03.html">dblp:conf/vrml/Polys03</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/io23eh26jbagfagqw2lt4mwyy4">fatcat:io23eh26jbagfagqw2lt4mwyy4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829134255/http://www.web3d.org/x3d/content/examples/Basic/ChemistryMarkupLanguage/Polys.StylesheetTransformationsInteractiveVisualization.Web3d2003Symposium.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/92/03/920318ad539fb2401e325e015bdec3345fdd12ec.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/636593.636606"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

Stylesheet transformations for interactive visualization

Nicholas F. Polys
<span title="">2003</span> <i title="ACM Press"> Proceeding of the eighth international conference on 3D web technology - Web3D &#39;03 </i> &nbsp;
Standards design approaches offer a number of advantages: data durability, data interoperability, and an ecology of tools to be deployed for production and delivery.  ...  This paper describes and evaluates such techniques to transform structured data such as Chemical Markup Language (CML) to different forms and contexts for Web3D delivery using Extensible Stylesheet Transformations  ...  These techniques are usually described for use with the common and capable web browser plug-ins [1, 11, 12] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/636604.636606">doi:10.1145/636604.636606</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eezvcwvrpjf57f3e4ew2wdjg74">fatcat:eezvcwvrpjf57f3e4ew2wdjg74</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829134255/http://www.web3d.org/x3d/content/examples/Basic/ChemistryMarkupLanguage/Polys.StylesheetTransformationsInteractiveVisualization.Web3d2003Symposium.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/92/03/920318ad539fb2401e325e015bdec3345fdd12ec.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/636604.636606"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

UNICORE 6 — Recent and Future Advancements

Achim Streit, Piotr Bala, Alexander Beck-Ratzka, Krzysztof Benedyczak, Sandra Bergmann, Rebecca Breu, Jason Milad Daivandy, Bastian Demuth, Anastasia Eifer, André Giesler, Björn Hagemeier, Sonja Holl (+13 others)
<span title="2010-09-21">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6qikrj3t35bxbeh2amndymlvxu" style="color: black;">Annales des télécommunications</a> </i> &nbsp;
Gaussian98 and it's latest version Gaussian09 is designed to predict energies, molecular structures, vibrational frequencies and numerous molecular properties for a broad range of molecular systems in  ...  Finally, the Eclipse platform has a very sophisticated plug-in mechanism: every software component in an Eclipse-based client is a plug-in, each of which adding a welldefined range of functions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s12243-010-0195-x">doi:10.1007/s12243-010-0195-x</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bq574f2darhibnx5g5dkhfqf2q">fatcat:bq574f2darhibnx5g5dkhfqf2q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809091941/http://juser.fz-juelich.de/record/136184/files/J%C2%A9%C6%A1l_4319_Streit.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ea/7b/ea7b3c5e2c7735dd0a62406236127d5aa04cce0d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s12243-010-0195-x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

PHENIX: building new software for automated crystallographic structure determination

Paul D. Adams, Ralf W. Grosse-Kunstleve, Li-Wei Hung, Thomas R. Ioerger, Airlie J. McCoy, Nigel W. Moriarty, Randy J. Read, James C. Sacchettini, Nicholas K. Sauter, Thomas C. Terwilliger
<span title="2002-10-21">2002</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6inoqqfovnhtledhw3uuo322xa" style="color: black;">Acta Crystallographica Section D: Biological Crystallography</a> </i> &nbsp;
This new software will provide the necessary algorithms to proceed from reduced intensity data to a re®ned molecular model and to facilitate structure solution for both the novice and expert crystallographer  ...  A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is therefore being developed.  ...  A graphical representation of a molecule imported in PHENIX for a molecular-replacement translation search.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444902016657">doi:10.1107/s0907444902016657</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12393927">pmid:12393927</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tabjmto6zjcqbnvzktwg3xvzvq">fatcat:tabjmto6zjcqbnvzktwg3xvzvq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725023256/http://journals.iucr.org/d/issues/2002/11/00/ba5027/ba5027.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ff/40/ff40044f597fac2f29faab86bc446fd846c9cbe9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444902016657"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Application portals: practice and experience

Mary Thomas, Maytal Dahan, Kurt Mueller, Steve Mock, Cathie Mills, Ray Regno
<span title="">2002</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/o454xj4tdjfllm3oragfkdrffi" style="color: black;">Concurrency and Computation</a> </i> &nbsp;
In this paper, we describe our experiences gained in building Grid portals and developing software for the Grid.  ...  Finally, we discuss the new and emerging architecture system that being studied based on the web services architecture.  ...  In addition, The authors would like to acknowledge the San Diego Supercomputer Center and the NSF funded NPACI program for their support (both with resources and staff) and for allowing the portals project  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cpe.694">doi:10.1002/cpe.694</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pfjlwdzrx5avnhgflhyizuxfra">fatcat:pfjlwdzrx5avnhgflhyizuxfra</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809012857/http://aspen.ucs.indiana.edu/gce/C557hotpage/CPE_App_Portals.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/53/77/53778632e3bec6c3f8105dd720dc1bca5156648d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cpe.694"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Self-Repairing Computers

Armando Fox, David Patterson
<span title="">2003</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/buhpjyagg5hqhh72uxskzgenve" style="color: black;">Scientific American</a> </i> &nbsp;
In this article, we review several of our activities in these areas: service architectures for Chemical Informatics; Web 2.0 approaches for managing real-time data from online experiments; management and  ...  We conclude with a discussion of further research opportunities in the application of Web 2.0 to e-Science.  ...  The PubChem database is a collection of nearly 10 million molecular structures along with bioassay results for 549 assays.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/scientificamerican0603-54">doi:10.1038/scientificamerican0603-54</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vaanc2oiyjc2tc7bus6wkfoine">fatcat:vaanc2oiyjc2tc7bus6wkfoine</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20071216032129/http://grids.ucs.indiana.edu/ptliupages/publications/INGRIDFinal.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8d/71/8d71ed7b9bc0d54b984855f0d219201774ac0dd7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/scientificamerican0603-54"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>
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