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Software Tools


MetaMorph is an industry standard image analysis suite and capture platform.

The MetaMorph software suite supports a wide array of microscopes, cameras, and precision stages used in bioresearch. The software provides acquisition, processing, and analysis features that allow researchers to build custom imaging systems for solving experimental problems in cellular imaging.

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Tags: analyze,image Contributor: FF, JB Cost: Cost-basis
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Metacat is a flexible, open source metadata catalog and data repository that targets scientific data, particularly from ecology and environmental science. Metacat accepts XML as a common syntax for representing the large number of metadata content standards that are relevant to ecology and other sciences. Thus, Metacat is a generic XML database that allows storage, query, and retrieval of arbitrary XML documents without prior knowledge of the XML schema.

Metacat is designed and implemented as a Java servlet application that utilizes a relational database management system to store XML and associated meta-level information. Installation of Metacat recommends the use of Apache Tomcat for servlet management and PostgreSQL as the underlying RDBMS, although other configurations are possible. Metacat provides a rich client Application Programming Interface (API) and supports a variety of languages, including Java, Python, and Perl.

Metacat is being used extensively throughout the world to manage environmental data. It is a key infrastructure component for the NCEAS data catalog, the Knowledge Network for Biocomplexity (KNB) data catalog, and for the DataONE system, among others.

Additional Information:
  • Berkley, C., M. Jones, J. Bojilova, and D. Higgins, 2001. Metacat: A schema-independent XML database system. 13th Intl. Conference on Scientific and Statistical Database Management: 171.
  • Jones, M.B., C. Berkley, J. Bojilova, M. Schildhauer, 2001. Managing scientific metadata, IEEE Internet Computing 5(5): 59-68.
  • Metacat Administrator's Guide (http://knb.ecoinformatics.org/software/dist/MetacatAdministratorGuide.pdf)
Tags: catalog,EML,metadata,repository,XML Contributor: Cost: Free
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Mesquite is a modular software system for evolutionary analysis, designed to help biologists analyze comparative data about organisms. Although its emphasis is on phylogenetic analysis, some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. The analyses include:

  • Reconstruction of ancestral states (parsimony, likelihood)
  • Tests of process of character evolution, including correlation
  • Analysis of speciation and extinction rates
  • Simulation of character evolution (categorical, DNA, continuous)
  • Parametric bootstrapping (integration with programs such as PAUP* and NONA)
  • Morphometrics (PCA, CVA, geometric morphometrics)
  • Coalescence (simulations, other calculations)
  • Tree comparisons and simulations (tree similarity, Markov speciation models)

Mesquite is not primarily designed to infer phylogenetic trees, but rather for diverse analyses using already inferred trees.

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Example use: Tyler, Kevin M.; Wagner, Gerd K.; Wu, Qiong; Huber, Katharina T., Functional Significance May Underlie the Taxonomic Utility of Single Amino Acid Substitutions in Conserved Proteins,2010, Journal of Molecular Evolution (70:4), DOI: 10.1007/s00239-010-9338-y

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Merritt Repository Service

Merritt is a repository service and curation environment for storage and preservation of digital objects, provided by the California Digital Library. Merritt can be used to manage, archive, and share content. It can provide significant features for a digital object:

  • permanent storage
  • access via persistent URLs
  • tools for long term management
  • easy-to-use interface for deposits and udpates

Merritt is built upon micro-services, which are independent yet interoperable set of functions that together, combine to form the technical infrastructure of a digital preservation repository. These micro-services are meant to be small and modular, and easy to develop, deploy, maintain, and if needed, replace. The complex function of a digital repository emerges from the interaction of the micro-services. More background, and specifications of individual micro-services, can be found at the Curation wiki:

The Merritt Repository Service is provided by the University of California Curation Center (UC3), part of the California Digital Library. The primary audience for the service is the students, staff and faculty memberss of the University of California (UC), and is also available to researchers and organizations outside of UC. UC researchers are using Merritt to fulfill data management and sharing requirements for NSF and NIH grants.

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Tags: data management plan,data storage,repository Contributor: PW, KC Cost: Cost-basis
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MERMAid (Metadata Enterprise Resource Management Aid)

The Metadata Enterprise Resource Management Aid (MERMAid) is a tool to develop, validate, manage and publish metadata records via secure internet access. It allows users and data providers to establish unlimited metadata databases to organize their metadata records as they choose (i.e. by program, project, data type, personnel). Some of the key features in MERMAid include (1) user-defined roles and permissions at the metadata management and database levels; (2) change tracking; and (3) enhanced validation. Also, your existing FGDC compliant metadata (in XML format) can be ingested into and managed through MERMAid.

MERMAid was developed by the National Coastal Data Development Center (NCDDC).

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Related Tools: Metavist, NPS Metadata Editor

Tags: editor,geospatial,metadata Contributor: Cost: Free
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Mercury metadata search & data retrieval

Mercury is a web-based system to search for metadata and retrieve associated data. Mercury provides a single portal to information contained in disparate data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfaces then allow the users to perform simple, fielded, spatial and temporal searches across these metadata sources. Mercury supports various metadata standards including XML, Z39.50, FGDC, Dublin-Core, Darwin-Core, EML, and ISO-19115.

Additional Information: Tags: discover,FGDC,metadata,XML Contributor: Cost: Free
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Mercury Metadata Editor

Mercury is a web-based system to search for metadata and retrieve associated data sets. The Mercury Metadata Editor creates a subset of standard FGDC metadata, along with data documentation that can be used in the Mercury search tool. The Mercury Metadata Editor:

  • Allows users to enter contextual metadata that is specifically designed for use in the Mercury search tool.
  • Creates a standard format for metadata (XML)
  • Has picklists for standard terms Using the on-line Mercury Metadata Editor tool to create and edit contextual metadata requires no programming expertise.
Additional Information: Tags: FGDC,metadata editor Contributor: Cost: Free
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Mercurial (Hg)

Mercurial is a free, distributed source control management tool and is used for version control of files. Mercurial is distributed, giving each developer a local copy of the entire development history.

  • It works independently of network access or a central server.
  • Committing, branching and merging are fast and cheap.
  • You can generate diffs between revisions, or jump back in time within seconds and is suitable for large projects.
  • Mercurial is platform independent. Most of Mercurial is written in Python, with a small part in portable C for performance reasons.
  • The functionality of Mercurial can be expanded with extensions, which can change the workings of the basic commands, add new commands and access all the core functions of Mercurial.
  • The basic interface is easy to use, easy to learn and hard to break.
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Tags: computing,data storage,repository,version control Contributor: MS, MG Cost: Free
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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. Browser plug-in allows capture of reference information from just about any web page, and Mendeley has an API and plug-ins for word processors such as Open Office. PDFs can be uploaded from your local system, and citations can be generated and lists exported. Many online journals have one-click function to add a reference to your Mendeley library. There are limits on how many groups can be managed in the free-version.

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Tags: bibliography,citation,metadata,social networking,web 2.0 Contributor: CP, BS Cost: Free
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MediaWiki is a free web-based software application written in PHP with a backend database. It was developed by the Wikimedia Foundation and it also runs projects such as Wikispecies and WikiMediaCommons. It is the wiki tool used for WikiPedia. There are numerous extensions available for adding capabilities to MediaWiki (see http://www.mediawiki.org/wiki/Category:Extensions).

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Tags: catalog,data integration Contributor: Cost: Free
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