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Software Tools

BLAST (Basic Local Alignment Search Tool)

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between genetic sequences, comparing nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterized genes. Alternative implementations include AB-BLAST (formerly known as WU-BLAST), FSA-BLAST, and ScalaBLAST.

Additional Information: Tags: bioinformatics,phylogenetics,sequence alignment Contributor: Cost: Free
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Bitbucket is a free hosting site for open-source computer program source code. Bitbucket supports version control, offsite backup, and access by multiple authenticated users.

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Tags: programming,provenance,repository,social networking Contributor: EB, TB Cost: Free
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BibDesk allows the user to edit and manage bibliographies. It helps keep track of both the bibliographic information and the associated files or web links.

BibDesk helps simplify using a bibliography in other applications and is suited for LaTeX users.

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Tags: bibliography,catalog,metadata Contributor: JB, RL Cost: Free
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Bayesian Evolutionary Analysis Sampling Trees (BEAST) is a program for Bayesian Markov Chain Monte Carlo (MCMC) analysis of molecular sequences. It is oriented towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST averages over tree space, so that each tree is weighted proportional to its posterior probability.

Additional Information:

Lemey P, Rambaut A, Drummond AJ & Suchard MA (2009) PLoS Computational Biology 5, e1000520.
Drummond AJ & Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7, 214.
Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307-1320.

Tags: evolution,phylogenetics Contributor: RK, JP Cost: Free
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Basecamp Collaboration Apps

Signals offers a suite of web-based collaboration applications. All applications are mobile-optimized.

Basecamp - Project Management

  • Project organization, task management
  • Milestone tracking
  • File storage/sharing

Highrise - Contact Management

  • Tracking of proposals/contracts/drafts
  • Contact list management
  • Task management

Backpack - File/Information Sharing

  • Document management, file storage
  • Management of documentation
  • Logistical coordination/organization

Campfire - Collaborative Chat Room Space

  • Chat room space with history tracking
  • Conference calling capability
  • Image/graphic sharing during collaboration
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Cost varies based on usage. There are initial, free levels of service, but higher numbers of users and data in the system will lead to increasing levels of cost. A single sign-on can be used across applications.

Tags: collaboration,repository,social networking Contributor: AS, SL Cost: Free
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Asymptote is a vector graphics language that can be used for technical drawing.

Being a language, it gives ultimate control to the user. Typesetting of labels and equations is done by LaTeX, which produces high-quality PostScript output. It provides a portable standard for typesetting mathematical figures and generates output in PostScript, PDF, SVG, or 3D PRC vector graphics.

Additional Information: Tags: graphics,mathematics,visualization Contributor: RS, RD Cost: Free
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Archon is an open source, Web-based archive management system for archivists and manuscript curators that automatically publishes archival descriptive information and digital archival objects.

Archon users do not need to encode a finding aid, input a catalog record, or program a stylesheet. Archon operates through scripts that automatically make data elements in the system searchable and browsable on a repository website. Information can be input or edited using simple web forms. Archon automatically uploads the information, publishes the website, and generates EAD and MARC records.

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Tags: database,metadata,preserve,web services Contributor: BS, RL Cost: Free
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Archivists' Toolkit

The Archivists' Toolkit is an open-source data management system that provides support for the management of archives. This tool is aimed at archival repositories that store various kinds of data, especially text and image data. The tool supports accessioning and describing archival materials, establishing names and subjects associated with archives, managing locations of the materials, and exporting EAD finding aids, MARCXML records, and METS, MODS and Dublin Core records.

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Tags: data storage,metadata Contributor: RL, BS Cost: Free
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Archivematica is a comprehensive digital preservation system. Archivematica uses a micro-services design pattern to provide an integrated suite of tools that allows users to process digital objects from ingest to access in compliance with the ISO-OAIS functional model.

Users monitor and control the micro-services via a web-based dashboard. Archivematica uses a range of best practices and metadata standards. Archivematica implements media type preservation plans based on an analysis of the significant characteristics of file formats.

Additional Information:
Tags: preserve Contributor: TC, BS Cost: Free
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ArcGIS Desktop

ArcGIS Desktop is a collection of software products for building complete geographic information systems (GIS). produced by Esri. ArcGIS Desktop 9 provides an integrated GIS, combining object-oriented and traditional file-based data models with a set of tools to create and work with geographic data. The following three applications comprise the ArcGIS Desktop software suite:

  • ArcMap (mapping and data manipulation): ArcMap is a map-authoring application
  • ArcCatalog (data management): shared ArcGIS application that allows you to organize and access all GIS information (e.g., maps, globes, datasets, models, metadata, and services). Includes tools for browsing and finding geographic information; recording, viewing, and managing metadata; viewing datasets; and defining the schema structure of the object-based geographic datasets.
  • ArcToolbox (data conversion, modeling, and spatial analysis): includes tools to do geographic feature overlay, feature selection and analysis, topology processing, and data conversion resulting in an output dataset. The geoprocessing framework allows you to use each geoprocessing function in a variety of ways. The tools can be used directly from a dialog, executed via command line, combined with other processes in visual models using Model Builder, or used in advanced scripts.
Additional Information: Tags: analyze,GIS,map,visualization Contributor: Cost: Cost-basis
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