CoffeeLint is a style checker that helps keep CoffeeScript code clean and consistent. CoffeeScript does a great job at insulating programmers from many of JavaScript's bad parts, but it won't help enforce a consistent style across a code base. CoffeeLint can help with that.

Domeo is an extensible web application enabling users to visually and efficiently create and share ontology-based stand-off annotation on HTML or XML document targets. The tool supports manual, fully automated, and semi-automated annotation with complete provenance records, as well as personal or community annotation with access authorization and control.

ImageOptim optimizes images — so they take up less disk space and load faster — by finding best compression parameters and by removing unnecessary comments and color profiles. It handles PNG, JPEG and GIF animations.

Great deep dive into the WebKit developer tools: #webinf #web #development #tools #html #css #javascript

dotjs is a Google Chrome extension that executes JavaScript files in ~/.js based on their filename.

Simple to use node.js HTTP / HTTPS client for fetching remote resources. Supports transparent gzip decoding via gzbz2.

The client sends GET requests for fetching the remote objects. You may send HEAD requests if you just need to check the availability of a remote resource. The error reporting is implemented with care. The module itself is used in production for background data processing of thousands of remote resources, therefore it is not your average HTTP / HTTPS node.js client. It is in use for both of the transfer modes: buffered responses or streamed to the disk responses. Most of the decisions that made their way into the http-get are based onto the experience of working with a large URL database where a lot of things can go wrong.

Provides general-purpose DITA map, topic, and domain specializations for the Publishing industry, as well as supporting processors (e.g., DITA Open Toolkit plugins).

Apache Stanbol (currently in incubation) is an open source modular software stack and reusable set of components for semantic content management.

Apache Stanbol components are meant to be accessed over RESTful interfaces to provide semantic services for content management. Thus, one application is to extend traditional content management systems with (internal or external) semantic services.

Track exceptions as they happen and diagnose them without user assistance.

This version accompanies the developement of RDFa 1.1 Core. As that document is not final yet, this service, and the underlying code, will change frequently until the development of RDFa 1.1 is finalized. The implementation may actually run ahead of the “official” version and implement the version in the editors’ draft already… Also, the package available for download may be out of sync with the code running this service.

RTextTools is a free, open source machine learning package for automatic text classification that makes it simple for both novice and advanced users to get started with supervised learning. The package includes nine algorithms for ensemble classification (svm, slda, boosting, bagging, random forests, glmnet, decision trees, neural networks, maximum entropy), comprehensive analytics, and thorough documentation.

Octopress is a framework designed by Brandon Mathis for Jekyll, the blog aware static site generator powering Github Pages. To start blogging with Jekyll, you have to write your own HTML templates, CSS, Javascripts and set up your configuration. But with Octopress All of that is already taken care of. Simply clone or fork Octopress, install dependencies and the theme, and you’re set.

The IPython Notebook consists of two related components:

An JSON based Notebook document format for recording and distributing Python code and rich text.
A web-based user interface for authoring and running notebook documents.

petl is a tentative Python module for extracting, transforming and loading tables of data.

pv - Pipe Viewer - is a terminal-based tool for monitoring the progress of data through a pipeline. It can be inserted into any normal pipeline between two processes to give a visual indication of how quickly data is passing through, how long it has taken, how near to completion it is, and an estimate of how long it will be until completion.

Welcome to Piazza—a place where students can come together to ask, answer, and explore under the guidance of their instructor. It'll save you time, and your students will love using it.

The Natural Language Software Registry (NLSR) is a concise summary of the capabilities and sources of a large amount of natural language processing (NLP) software available to the NLP community. It comprises academic, commercial and proprietary software with specifications and terms on which it can be acquired clearly indicated.

Anything To Triples (Any23) is a library, a Web service and a set of command line tools for extracting structured data in RDF format from a variety of Web documents.

Let me show you which steps have to be taken to generate a high-quality text mining application, ready to be used to annotate and to categorize any kind of text or documents covering nearly any domain. With our approach of thesaurus based text mining your documents can also be linked to the world of linked (open) data; enrich your documents with data from the LOD cloud!

Jason is a JSON viewer & editor for Mac OS X. It can open local documents as well as download JSON data via HTTP and, in case of invalid data, an error message is presented and the line containing the error is highlighted.

A static site generator built with Node.js, JSDOM, and Weld.

I will convert your Excel data into one of several web-friendly formats, including HTML, JSON and XML.

This plugin will allow you to use tools that were built to interact with Solr with ElasticSearch.

This is the REST service of CollateX. To call it, you can post witness data as specified below and get the collation result back in a number of formats.

A tool for document-supported history instruction.

As we work on DocumentCloud, we're constantly building pieces of infrastructure that could be useful for other organizations that work with similar kinds of data. We're releasing as we go by extracting useful components as standalone open source projects. Please follow our work if you're interested in what lies under the hood.

SCRIPTCOVER is a Chrome extension for Javascript coverage analysis.

It reports which Javascript statements/instructions from internal and external scripts have been executed (and how many times) while a web page loads and then when a user interacts with the page without any user modifications to the code.

Submit a series of strings or patterns and we will show you the urls on which they appear (in rank order).

RAD tool for Java.

The Closure tools help developers to build rich web applications with JavaScript that is both powerful and efficient.

FOX is a framework that integrates the Linked Data Cloud and makes uses of the diversity of NLP algorithms to extract RDF triples of high accuracy out of NL. In its current version, it integrates and merges the results of Named Entity Recognition, Keyword Extraction and Relation Extraction tools.

Many scientific disciplines are now data and information driven, and new scientific knowledge is often gained by scientists putting together data analysis and knowledge discovery ‘pipelines’. A related trend is that more and more scientific communities realize the benefits of sharing their data and computational services, and are thus contributing to a distributed data and computational community infrastructure (a.k.a. ‘the Grid’). However, this infrastructure is only a means to an end and ideally scientists should not be too concerned with its existence. The goal is for scientists to focus on development and use of what we call scientific workflows. These are networks of analytical steps that may involve, e.g., database access and querying steps, data analysis and mining steps, and many other steps including computationally intensive jobs on high-performance cluster computers. In this paper we describe characteristics of and requirements for scientific workflows as identified in a number of our application projects. We then elaborate on Kepler, a particular scientific workflow system, currently under development across a number of scientific data management projects. We describe some key features of Kepler and its underlying Ptolemy II system, planned extensions, and areas of future research. Kepler is a community-driven, open source project, and we always welcome related projects and new contributors to join.

The past decade has witnessed a growing trend in designing and using workflow systems with a focus on supporting the scientific research process in bioinformatics and other areas of life sciences. The aim of these systems is mainly to simplify access, control and orchestration of remote distributed scientific data sets using remote computational resources, such as EBI web services. In this paper we present the state of the art in the field by reviewing six such systems: Discovery Net, Taverna, Triana, Kepler, Yawl and BPEL. We provide a high-level framework for comparing the systems based on their control flow and data flow properties with a view of both informing future research in the area by academic researchers and facilitating the selection of the most appropriate system for a specific application task by practitioners.

With the advent of Grid and application technologies, scientists and engineers are building more and more complex applications to manage and process large data sets, and execute scientific experiments on distributed resources. Such application scenarios require means for composing and executing complex workflows. Therefore, many efforts have been made towards the development of workflow management systems for Grid computing. In this paper, we propose a taxonomy that characterizes and classifies various approaches for building and executing workflows on Grids. The taxonomy not only highlights the design and engineering similarities and differences of state-of-the-art in Grid workflow systems, but also identifies the areas that need further research.

A Scientific Workflow Systems is a specialized form of a workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or a workflow, in a scientific application.

List of scientific workflow tools from the Data Observation Network for Earth (DataONE)

A bioinformatics workflow management system is a specialized form of workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or a workflow, in a specific domain of science, bioinformatics.

A survey of existing (Python) libraries, frameworks, and tools for managing semi-automated workflows and pipelines of tasks. There are a number of loose, overlapping terms for these kinds of systems: BPM (business process management), workflow, pipeline, flowchart, state machine, visual programming, dataflow, flow-based programming, dependency management, task management, etc.

LinkedDataSail gathers RDF data incrementally, dereferencing URIs in response to queries.

KEA is an algorithm for extracting keyphrases from text documents. It can be either used for free indexing or for indexing with a controlled vocabulary.

Maui automatically identifies main topics in text documents. Depending on the task, topics are tags, keywords, keyphrases, vocabulary terms, descriptors, index terms or titles of Wikipedia articles.

Maui performs the following tasks:

term assignment with a controlled vocabulary (or thesaurus)
subject indexing
topic indexing with terms from Wikipedia
keyphrase extraction
terminology extraction
automatic tagging
It can also be used for terminology extraction and semi-automatic topic indexing.

Wikipedia Miner is a toolkit for navigating and making use of the structure and content of Wikipedia. It aims to make it easy for you to integrate Wikipedia's knowledge into your own applications, by:

providing simplified, object-oriented access to Wikipedia's structure and content.
measuring how terms and concepts in Wikipedia are connected to each other.
detecting and disambiguating Wikipedia topics when they are mentioned in documents.

Load SPARQL result table from an end-point as a data.frame

PDFMiner is a tool for extracting information from PDF documents. Unlike other PDF-related tools, it focuses entirely on getting and analyzing text data. PDFMiner allows one to obtain the exact location of text in a page, as well as other information such as fonts or lines. It includes a PDF converter that can transform PDF files into other text formats (such as HTML). It has an extensible PDF parser that can be used for other purposes than text analysis.

Wolfram|Alpha is a powerful tool for finding information about the universe at large, but sometimes we are interested in a much smaller universe: our families. Genealogical research is an increasingly popular hobby, and one which Wolfram|Alpha can make easier using features across several of its subject areas.

Accentuate.us uses statistics to predict where special characters are needed on a language-by-language basis.

The goal of this tool is to enable OData service authors to validate their implementation against the OData specification to ensure the service interoperates well with any OData client.

Pycco is a Python port of Docco: the original quick-and-dirty, hundred-line-long, literate-programming-style documentation generator. It produces HTML that displays your comments alongside your code. Comments are passed through Markdown, and code is passed through Pygments syntax highlighting.

This is incredibly awesome.

The NodeXL Template for Microsoft Excel 2007 is a free and open source extension to the widely used spreadsheet application that provides a range of basic network analysis and visualization features. NodeXL uses a highly structured workbook template that includes multiple worksheets to store all the information needed to represent a network graph. Network relationships (i.e., graph edges) are represented as an “edge list”, which contains all pairs of vertices that are connected in the network. Other worksheets contain information about each vertex (i.e., node) and cluster. Visualization features allow users to display a range of network graph representations and map data attributes to visual properties including shape, color, size, transparency, and location.

Underscore is a utility-belt library for JavaScript that provides a lot of the functional programming support that you would expect in Prototype.js (or Ruby), but without extending any of the built-in JavaScript objects. It's the tie to go along with jQuery's tux.

TiMBL is an open source software package implementing several memory-based learning algorithms, among which IB1-IG, an implementation of k-nearest neighbor classification with feature weighting suitable for symbolic feature spaces, and IGTree, a decision-tree approximation of IB1-IG. All implemented algorithms have in common that they store some representation of the training set explicitly in memory. During testing, new cases are classified by extrapolation from the most similar stored cases.

For the past decade, TiMBL has been mostly used in natural language processing as a machine learning classifier component, but its use extends to virtually any supervised machine learning domain. Due to its particular decision-tree-based implementation, TiMBL is in many cases far more efficient in classification than a standard k-nearest neighbor algorithm would be.

Traditional interactive information retrieval systems function by creating inverted lists, or term indexes. For every term in the vocabulary, a list is created that contains the documents in which that term occurs and its frequency within each document. Retrieval algorithms then use these term frequencies alongside other collection statistics to identify matching documents for a query.

Term-based search, however, is just one example of interactive information seeking. Other examples include offering suggestions of documents similar to ones already found, or identifying effective query expansion terms that the user might wish to use. More generally, these fall into several categories: query term suggestion, relevance feedback, and pseudo-relevance feedback.

We can combine the inverted index with the notion of retrievability to create an efficient query expansion algorithm that is useful for a number of applications, such as query expansion and relevance (and pseudo-relevance) feedback. We call this kind of index a reverted index because rather than mapping terms onto documents, it maps document ids onto queries that retrieved the associated documents.

A collection of the best open data sets and open-source tools for data science, wrapped in an easy-to-use REST/JSON API with command line, Python and Javascript interfaces. Available as a self-contained VM or EC2 AMI that you can deploy yourself.

Gunicorn 'Green Unicorn' is a Python WSGI HTTP Server for UNIX. It's a pre-fork worker model ported from Ruby's Unicorn project. The Gunicorn server is broadly compatible with various web frameworks, simply implemented, light on server resources, and fairly speedy.

Getting dots on maps, without legacy code or any baggage. Just that, to start. Dots on maps.

Lippmannian device is named after Lippmann, and provides a coarse means of showing actor partisanship.

The tool we’ve built is code-named Woodchipper. It allows the user to search and select text from participating collections and display them as a visualization which shows relationships among texts.

RStudio™ is a new integrated development environment (IDE) for R. RStudio combines an intuitive user interface with powerful coding tools to help you get the most out of R.

An intuitive, cross-platform graphical data analysis system. It uses menus and dialogs to guide the user efficiently through the data manipulation and analysis process, and has an excel like spreadsheet for easy data frame visualization and editing.

List of tools for doing research into the "natively digital".

Finding trending topics using Google Books n-grams data and Apache Hive on Elastic MapReduce

It is an Open Source (Apache 2), Distributed, RESTful, Search Engine built on top of Lucene.

A comparison of various Django-based wiki applications and projects.

The goal of the workshop was not to produce a white paper! Rather it was to identify a set of requirements, and a group of willing participants to develop a mandate, open source code and a set of deliverables to be used by scholars to accelerate data and knowledge sharing and discovery . Our starting point, and the only prerequisite to participating, was the belief that we need to move Beyond the PDF (meant to capture a common philosophy, not necessarily to be taken literally).

In a heady moment we might also describe our efforts as the desire to contribute to the development of a free and open digital printing press for the 21st century. A platform, when utilized, moves us beyond a static and disparate data and knowledge representation to a rich integrated content which grows and changes the more we learn. A system (content plus platform) from which a scholar can interact and once evaluated shows improved understanding and interest.

TemaTres is an open source vocabulary server, web application to manage and exploit vocabularies, thesauri, taxonomies and formal representations of knowledge.

It inserts a layout grid in web pages, allows you to hold it in place, and toggle between displaying it in the foreground or background.

Modular toolkit for Data Processing (MDP) is a Python data processing framework.

From the user's perspective, MDP is a collection of supervised and unsupervised learning algorithms and other data processing units that can be combined into data processing sequences and more complex feed-forward network architectures.

Stanford CoreNLP provides a set of natural language analysis tools which can take raw English language text input and give the base forms of words, their parts of speech, whether they are names of companies, people, etc., normalize dates, times, and numeric quantities, and mark up the structure of sentences in terms of phrases and word dependencies, and indicate which noun phrases refer to the same entities. It provides the foundational building blocks for higher level text understanding applications.

Stanford CoreNLP integrates all our NLP tools for the English language, including the part-of-speech (POS) tagger, the named entity recognizer (NER), the parser, and the coreference resolution system. The goal of this project is to enable people to quickly and painlessly get complete linguistic annotations of natural language texts. It is designed to be highly flexible and extensible, i.e., with a single option you can change which tools should be enabled and which should be disabled.

Maperitive is a FREE desktop application for drawing maps based on OpenStreetMap and GPS data. You can define what gets on the map and how it is painted. You can also export these maps into bitmaps and SVG files and print them.

tm (shorthand for Text Mining Infrastructure in R) provides a framework for text mining applications within R.

The tm package offers functionality for managing text documents, abstracts the process of document manipulation and eases the usage of heterogeneous text formats in R. The package has integrated database backend support to minimize memory demands. An advanced meta data management is implemented for collections of text documents to alleviate the usage of large and with meta data enriched document sets.

FlexPaper displays documents in your favorite browser using flash. Its way of reusing display containers makes it possible to view large documents and books.

The GEOLocate project is an effort to develop software and services for translating textual locality descriptions associated with biodiversity collections data into geographic coordinates.

MALLET is a Java-based package for statistical natural language processing, document classification, clustering, topic modeling, information extraction, and other machine learning applications to text.

lino is a free sticky & canvas service that requires nothing but a Web browser.

Chronos Timeline is designed specifically for needs in the humanities and social sciences to represent time-based data. Chronos allows scholars and students to dynamically present historical data in a flexible online environment. Switching easily between vertical and horizontal orientations, researchers can quickly scan large number of events, highlight and filter events based on subject matter or tags, and recontextualize historical data.

This little beautifier will reformat and reindent bookmarklets, ugly javascript, unpack scripts packed by the popular Dean Edward's packer, as well as deobfuscate scripts processed by javascriptobfuscator.com.

TileStache is a Python-based server application that can serve up map tiles based on rendered geographic data.

This user guide describes a Python package, PyMC, that allows users to efficiently code a probabilistic model and draw samples from its posterior distribution using Markov chain Monte Carlo techniques.