https://www.bibsonomy.org/user/pitman/toolsBibSonomy RSS Feed for /user/pitman/toolsPDF (re)compression using JBIG2 for the EuDML project https://mir.fi.muni.cz/pdfRecompression/pitman2014-12-29T06:47:14+01:00eudml pdf tools <span itemprop="description">PDF (re)compression using JBIG2 for the EuDML project </span>PDF image rendering and OCR for the EuDML projecthttps://mir.fi.muni.cz/pdfToTextViaOCR/pitman2014-12-29T06:44:55+01:00eudml pdf tools <span itemprop="description">PDF image rendering and OCR for the EuDML project</span>Pipes is a powerful composition tool to aggregate, manipulate, and mashup content from around the web.http://pipes.yahoo.com/pipes/pitman2009-04-04T04:52:26+02:00aggregation tools service web feed mashup <span itemprop="description">Pipes is a powerful composition tool to aggregate, manipulate, and mashup content from around the web.</span>JIRA lets you prioritise, assign, track, report and audit your 'issues,' whatever they may be — from software bugs and help-desk tickets to project tasks and change requests. http://www.atlassian.com/software/jira/pitman2009-02-07T03:26:26+01:00issue management project software tools tracker <span itemprop="description">JIRA lets you prioritise, assign, track, report and audit your &#039;issues,&#039; whatever they may be — from software bugs and help-desk tickets to project tasks and change requests. </span>BibDesk is a bibliographic reference manager for Mac OS X. BibDesk is designed to help organize and use bibliographic databases in BibTeX .bib format. In addition to manual typing, BibDesk lets you drag & drop or cut & paste .bib files into the bibliographic database and automatically opens files downloaded from PubMed. BibDesk also keeps track of electronic copies of literature on your computer and allows for searching your database through several keys. BibDesk integrates well with TeX for creating citations and bibliographies. This integration includes a Citation search completion service, and drag & drop (cut & paste) support for adding citations to TeX files.http://bibdesk.sourceforge.net/pitman2009-01-17T20:35:59+01:00bibliography bibtex database latex reference research software tools <span itemprop="description">BibDesk is a bibliographic reference manager for Mac OS X. BibDesk is designed to help organize and use bibliographic databases in BibTeX .bib format. In addition to manual typing, BibDesk lets you drag &amp; drop or cut &amp; paste .bib files into the bibliographic database and automatically opens files downloaded from PubMed. BibDesk also keeps track of electronic copies of literature on your computer and allows for searching your database through several keys. BibDesk integrates well with TeX for creating citations and bibliographies. This integration includes a Citation search completion service, and drag &amp; drop (cut &amp; paste) support for adding citations to TeX files.</span>Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000204pitman2008-11-09T01:40:34+01:00bibliographic biology computational digital library tools web <span itemprop="description">Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.</span>The full details of the markup may be found on the reStructuredText page. This document is just intended as a reminder. http://docutils.sourceforge.net/docs/user/rst/quickref.htmlpitman2008-10-25T18:09:28+02:00library python reference structured text tools <span itemprop="description">The full details of the markup may be found on the reStructuredText page. This document is just intended as a reminder. </span>reStructuredText is an easy-to-read, what-you-see-is-what-you-get plaintext markup syntax and parser system. It is useful for in-line program documentation (such as Python docstrings), for quickly creating simple web pages, and for standalone documents. reStructuredText is designed for extensibility for specific application domains. The reStructuredText parser is a component of Docutils. reStructuredText is a revision and reinterpretation of the StructuredText and Setext lightweight markup systems.http://docutils.sourceforge.net/rst.htmlpitman2008-10-25T18:08:23+02:00programming python structured text tools web <span itemprop="description">reStructuredText is an easy-to-read, what-you-see-is-what-you-get plaintext markup syntax and parser system. It is useful for in-line program documentation (such as Python docstrings), for quickly creating simple web pages, and for standalone documents. reStructuredText is designed for extensibility for specific application domains. The reStructuredText parser is a component of Docutils. reStructuredText is a revision and reinterpretation of the StructuredText and Setext lightweight markup systems.</span>On this page First Author* explains and reviews new software, Internet tools, and databases designed to facilitate data retrieval and organisation. Follow the links on the right hand side for articles, which can be read on this page or downloaded free of charge by clicking on the PDF icons next to each title. For updates on new web tools and technology by month, see Deba tes. http://www.firstauthor.org/research_tools.htmlpitman2008-10-24T05:47:09+02:00review software tools <span itemprop="description">On this page First Author* explains and reviews new software, Internet tools, and databases designed to facilitate data retrieval and organisation. Follow the links on the right hand side for articles, which can be read on this page or downloaded free of charge by clicking on the PDF icons next to each title. For updates on new web tools and technology by month, see Deba tes. </span>SumoBrain is FREE! SumoBrain offers cross-collection searching, portfolios, alerts, and other collaboration tools, as well as bulk PDF download capabilities. Sumobrain caters to intellectual property professionals, attorneys, and users in the corporate world. While SumoBrain was conceived as a subscription service, we have decided to take the radical step of making SumoBrain completely free. As long as we can support its costs without subscription fees, it will remain free indefinitelyhttp://www.sumobrain.com/pitman2008-10-18T18:27:26+02:00collaboration free patent search tools <span itemprop="description">SumoBrain is FREE! SumoBrain offers cross-collection searching, portfolios, alerts, and other collaboration tools, as well as bulk PDF download capabilities. Sumobrain caters to intellectual property professionals, attorneys, and users in the corporate world. While SumoBrain was conceived as a subscription service, we have decided to take the radical step of making SumoBrain completely free. As long as we can support its costs without subscription fees, it will remain free indefinitely</span>http://www.mynetresearch.com/pitman2008-10-14T01:05:31+02:00collaborative community online research tools <a itemprop="url" data-versiondate="2008-10-14T01:05:31+02:00" href="http://www.mynetresearch.com/" rel="nofollow" class="description-link">http://www.mynetresearch.com/</a>Mathematics and Statisticshttp://mylibrary.library.nd.edu/demos/article-index/?cmd=term&id=21&start=0pitman2008-10-10T00:20:12+02:00library services tools <span itemprop="description">Mathematics and Statistics</span>OpenURL COinS: A Convention to Embed Bibliographic Metadata in HTMLhttp://ocoins.info/pitman2008-09-09T01:15:23+02:00html openurl tools <span itemprop="description">OpenURL COinS: A Convention to Embed Bibliographic Metadata in HTML</span>http://digg.com/pitman2008-09-04T19:27:09+02:00bookmarking social software tools <a itemprop="url" data-versiondate="2008-09-04T19:27:09+02:00" href="http://digg.com/" rel="nofollow" class="description-link">http://digg.com/</a>Encouraging and enabling the development of tools to facilitate the use of the DOI® System and DOI® names by end users is a priority of the International DOI Foundation. This page identifies tools that are currently available, with descriptions and links to their sources, and tools that are currently under development. More will be added as they become available. We welcome your comments to contact@doi.org.http://www.doi.org/tools.htmlpitman2008-08-21T02:57:37+02:00DOI system tools <span itemprop="description">Encouraging and enabling the development of tools to facilitate the use of the DOI® System and DOI® names by end users is a priority of the International DOI Foundation. This page identifies tools that are currently available, with descriptions and links to their sources, and tools that are currently under development. More will be added as they become available. We welcome your comments to contact@doi.org.</span>FriendFeed is a tool being used by scientists as a medium to discuss scientific research problems. FriendFeed allows users to set up what’s called a lifestream, aggregating stuff the user posts on the web.http://friendfeed.com/pitman2008-08-20T22:57:59+02:00community services social tools web web2.0 <span itemprop="description">FriendFeed is a tool being used by scientists as a medium to discuss scientific research problems. FriendFeed allows users to set up what’s called a lifestream, aggregating stuff the user posts on the web.</span>The simple way to create surveys. Intelligent survey software for primates of all species. SurveyMonkey has a single purpose: to enable anyone to create professional online surveys quickly and easily. http://www.surveymonkey.com/pitman2008-05-31T02:16:31+02:00research survey tools web <span itemprop="description">The simple way to create surveys. Intelligent survey software for primates of all species. SurveyMonkey has a single purpose: to enable anyone to create professional online surveys quickly and easily. </span>http://www.xml.com/pub/a/2004/07/14/onto.html?page=2pitman2008-05-19T18:05:21+02:002004 ontology owl rdf survey tools xml <a itemprop="url" data-versiondate="2008-05-19T18:05:21+02:00" href="http://www.xml.com/pub/a/2004/07/14/onto.html?page=2" rel="nofollow" class="description-link">http://www.xml.com/pub/a/2004/07/14/onto.html?page=2</a>Graph Visualization Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. Automatic graph drawing has many important applications in software engineering, database and web design, networking, and in visual interfaces for many other domains. Graphviz is open source graph visualization software. It has several main graph layout programs. See the gallery for some sample layouts. It also has web and interactive graphical interfaces, and auxiliary tools, libraries, and language bindings.http://www.graphviz.org/pitman2008-05-15T06:27:58+02:00graphics software tools visualization <span itemprop="description">Graph Visualization Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. Automatic graph drawing has many important applications in software engineering, database and web design, networking, and in visual interfaces for many other domains. Graphviz is open source graph visualization software. It has several main graph layout programs. See the gallery for some sample layouts. It also has web and interactive graphical interfaces, and auxiliary tools, libraries, and language bindings.</span>http://community.muohio.edu/blogs/darcusb/archives/2005/02/10/bleeding-edge-workflowpitman2008-04-23T23:56:44+02:00biblio latex tools workflow <a itemprop="url" data-versiondate="2008-04-23T23:56:44+02:00" href="http://community.muohio.edu/blogs/darcusb/archives/2005/02/10/bleeding-edge-workflow" rel="nofollow" class="description-link">http://community.muohio.edu/blogs/darcusb/archives/2005/02/10/bleeding-edge-workflow</a>