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Box

Box allows you to store and share content online. Files and folders can be shared as web links, files and folders can be synced from the desktop. This means that files can be automatically backed up from multiple computers/devices, and stored on the Box server. It provides searching tools, and the ability to view files without downloading.

CiteULike is a free online web-based bibliography manager. It allows you to post, view, and organize scientific papers. Several journal services have one-click linking to CiteULike for saving references. This application also allows you to post links on a variety of social networking sites. Users can also search this site for publications that others have pulled into the site, and share reference lists publicly.

ColdFusion is both a platform and a language (ColdFusion Markup Language [CFML]) for enabling developers to build, deploy, and maintain Internet applications. ColdFusion is an Adobe product. ColdFusion is specifically designed to make it easier to connect HTML pages to a database and thereby create dynamically-generated web pages. Website content is managed in connection with a relational database and so can be generated on the fly.

Confluence is a commercial wiki product used by many universities, open source software efforts, etc. It is a product of Atlassian, and provides rich and flexible editing capabilities and a plugin environment to extend the features of the wiki. There is an extensive range of plugins. Many organizations use it for documentation, group collaboration, project or course sites, knowledge management, internal web sites, etc.

CrowdLabs is a system that supports community sharing, visualization and analysis of workflows using a philosophy employed by social web sites.

CrowdLabs features the ability to interact with the workflows through a Web browser. Workflow provenance is captured allowing scientists to publish their process as well as their results. For the latter, CrowdLabs generates links to the process that can be embedded in Wiki and HTML pages, as well as LaTeX documents.

DotNetNuke is a popular web content management system (or CMS) for Microsoft ASP.NET. The flexible DotNetNuke open source CMS platform also functions as a web application development framework. It is available in both a free Community Edition as well as cost basis Professional and Enterprise editions.

HUBzero is an open source platform that allows the creation of active web sites that support scientific collaboration and educational activities. It supports creating a group and inviting other users to join it, and delegating various group management roles. Researchers can upload files, tools, presentations, data, etc. It provides wiki and blog services. It supports social networking features such as content tagging, ratings. comments, citations, etc.

iMacros was designed to automate the most repetitious tasks on the web. With iMacros, you can quickly fill out web forms, remember passwords, create a webmail notifier, download information from other sites, scrape the Web (get data from multiple sites), and more. You can keep the macros on your computer for your own use, or share them with others by embedding them on your homepage, blog, company Intranet or any social bookmarking service.

Joomla! is an open source content management system (CMS). Joomla! provides a structured website that enables users to create and edit various types of web content without requiring in depth technical knowledge of web authoring or programming languages. Novice users can create web pages and add basic text and graphics to them with only a minimal introduction to the system; they can also take advantage of Joomla!

LifeDesks is intended for teams of taxonomists to facilitate easy and fast data sharing. Individuals or teams can create taxon-based checklists and taxon pages. Taxon pages may include descriptions, photographs, maps and bibliographies. The software will display the taxonomic hierarchy on the taxon page. There are options to tag objects with intellectual property rights using the Creative Commons licenses.

Mendeley is an bibliographic management tool. An optional local client, Mendeley Desktop, synchronizes with a standard Web-accessible interface. Users can enter new references, generate references from hard drive directories, or find references that others have already entered. References can be tagged as required. The emphasis is on social collaboration and sharing. Users can associate with each other and groups can be formed to developed shared collections.

myExperiment is a collaborative environment where scientists can safely publish their workflows and experiment plans, share them with groups and find those of others. It allows workflows, other digital objects and bundles (called Packs) to be swapped, sorted and searched like photos and videos on the Web.

Scratchpads is a social networking application for biodiversity research. It can by used by researchers to manage, share and publish taxonomic data online. The software has tools for managing:

UCINET is a comprehensive package for the analysis of social network data as well as other 1-mode and 2-mode data. Social network analysis methods include centrality measures, subgroup identification, role analysis, elementary graph theory, and permutation-based statistical analysis. In addition, the package has strong matrix analysis routines, such as matrix algebra and multivariate statistics.

Integrated with UCINET is the NetDraw program for drawing diagrams of social networks.

Webex is a proprietary web collaboration and meeting environment. WebEx allows users to host and join web video- and tele-conferences. WebEx requires client-side Java, a browser, and a plugin, but once installed, users can host and join meetings with a browser and no additional software. WebEx web conferencing allows any user to become the "presenter" can share an application or their entire desktop over the web with other meeting participants.

Zotero is an open source reference management software which manages bibliographic data and related research materials (such as PDFs). On many websites such as library catalogs, PubMed, Google Scholar, Google Books, Amazon.com, Wikipedia, and publisher's websites, Zotero shows an icon when a book, article, or other resource is being viewed. By clicking this icon, the full reference information can be saved to the Zotero library.

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