Download JAR files tagged by well with all dependencies

This Lutra submodule provides a common framework that other submodules in Lutra use and extend. It includes an implementation of OTTR's data model with classes for templates, instances, types, etc.; a system for handling results and error messages; core interfaces and abstract classes for streamed pipelines for parsing and writing templates and instances; as well as implementation of the TemplateStore, a container for templates, with algorithms for checking correctness of templates and expanding and checking correctness of instances. Lutra is the reference implementation of the OTTR framework. For more information about OTTR, see http://ottr.xyz.

scala-tptp-parser is a library for parsing the input languages of the TPTP infrastructure for knowledge representation and reasoning. The package contains a data structure for the abstract syntax tree (AST) of the parsed input as well as the parser for the different language of the TPTP, see http://tptp.org for details. In particular, parser are available for: - THF (TH0/TH1): Monomorphic and polymorphic higher-order logic, - TFF (TF0/TF1): Monomorphic and polymorphic typed first-order logic, including extended TFF (TFX), - FOF: Untyped first-order logic, - TCF: Typed clause-normal form, - CNF: (Untyped) clause-normal form, and - TPI: TPTP Process Instruction language. The parser was initially based on v7.4.0.3 of the TPTP syntax BNF (http://tptp.org/TPTP/SyntaxBNF.html), but is continuously updated to keep track of TPTP language updates.

All Roads Lead to ROME. ROME is a set of Atom/RSS Java utilities that make it easy to work in Java with most syndication formats. Today it accepts all flavors of RSS (0.90, 0.91, 0.92, 0.93, 0.94, 1.0 and 2.0), Atom 0.3 and Atom 1.0 feeds. Rome includes a set of parsers and generators for the various flavors of feeds, as well as converters to convert from one format to another. The parsers can give you back Java objects that are either specific for the format you want to work with, or a generic normalized SyndFeed object that lets you work on with the data without bothering about the underlying format.

This project is a resource for the JCoRe Linnaeus Annotator. The dictionaries contained herein are used for the recognition of concrete species names in text, e.g. "human", "mouse", "n. furzeri", "c. elegans" etc as well as species hints, i.e. indirect clues to a species like the word "patient" which most likely refers to a human. Additionally to such rather clear proxies, this project also includes a small dictionary containing maximum-frequency-proxies for genus expressions like "Drosophila" which will be mapped to "D. melanogaster". For the task of only finding concrete species names in text, there is the project jcore-linnaeus-species-ae-species-dict.

This project has a lot of business classes to work with genes and related named entities. Genes are part of a GeneDocument and may have gold IDs as well as mapped/predicted IDs. Another large part are species because most (all?) gene ID databases are species specific. So there are also classes or members to represent species mentions and the assignment of species IDs (taxonomy IDs) to genes. There is little to no business logic herein. This project is only useful as building block in other projects dealing with species assignment, gene ID mapping or similar efforts.

The chart-fx charting library is an extension in the spirit of Oracle's XYChart and performance/time-proven JDataViewer charting functionalities. Emphasis was put on plotting performance for both large number of data points and real-time displays, as well as scientific accuracies leading to error bar/surface plots, and other scientific plotting features (parameter measurements, fitting, multiple axes, zoom, ...). The library also contains a small set of math routines that can operate directly on the DataSet primitive for fitting, computing spectra, linear algebra, FIR/IIR filtering, and other functionalities common to signal processing.

A scalable, concurrent, in-memory Key Value (KV) map. Oak implements a concurrent Key-Value map that can keep all keys and values off-heap. This enables working with bigger heap sizes than JVM's managed heap. OakMap implements an API similar to the industry standard Java8 ConcurrentNavigableMap API. It provides strong (atomic) semantics for read, write, and read-modify-write, as well as (non-atomic) range query (scan) operations, both forward and backward. OakMap is optimized for big keys and values, in particular, for incremental maintenance of objects (update in-place). It is faster and scales better with additional CPU cores than the popular Java ConcurrentNavigableMap ConcurrentSkipListMap