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 IU Trident Indiana University

Open Source Software

One of the critical ways in which PTI and IU impacts and enables scientific research at IU, in the State of Indiana, and the nation as a whole through the distribution of open source software. Such software also aids the development of the Indiana economy. These open source software products often are used to the benefit of the private sector in Indiana and the nation as a whole. The production of open source software also enhances IU's competitiveness for federal grant funding, aiding PTI and IU in bringing competitively awarded federal research monies into Indiana and creating new high quality jobs in Indiana.

The production of open source software also enhances the value of Indiana University's scholarly output, since the use of open source software facilitates reproduce ability and testability of scientific research.

A list of open source software products produced and currently distributed by PTI and its affiliated organizations is given below:

PTI Research Centers

Last Updated 11/05/15

Software Name URL Description PTI Center
Curbee https://github.com/Data-to-Insight-Center/sead2/tree/master/sead-api Suite of microservices applied to research objects to enhance (curate) them for publication. Minimally, it includes validation and packaging, but can be extended to any services needed for quality curation. Data 2 Insight
SEAD Matchmaker https://github.com/Data-to-Insight-Center/sead2/tree/master/sead-matchmaker Recommendation engine that acts as matchmaker between people, data, and repositories to identify the most appropriate repositories for publication and publishing of research data objects. Data 2 Insight
SEAD-IU Cloud https://github.com/Data-to-Insight-Center/sead2/tree/master/sda-agent Storage and publication option for SEAD users that relies on IU Scholarly Data Archive and its robust distributed storage with two copies of data made by default. Data 2 Insight
Komadu https://github.com/Data-to-Insight-Center/komadu Provenance collection tool that can be added to an existing cyberinfrastructure for the purpose of collecting and visualizing data lineage (e.g., dataset derivation, versioning and so on).  Data 2 Insight
HathiTrust Research Center secure commons https://github.com/htrc Suite of services provisioning computational analysis to the nearly 14 million digitized books (70% in copyright) in the HathiTrust digital library. Data 2 Insight
HTRC Data Capsules https://github.com/htrc/HTRC-DataCapsules Secure environment for text analysis at scale of sensitive digitized content.  Data 2 Insight
Avalon Media System http://avalonmediasystem.org/ Open source system for providing online access to audio and video collections Data 2 Insight
PhotoCat2 https://github.com/iudlp/photocat2 Image cataloging tool Data 2 Insight
Variations 6.3 http://variations.sourceforge.net/ Digital music library system (update) Data 2 Insight
Variations FRBR Source Release http://vfrbr.info/ Experimental discovery system for music metadata Data 2 Insight
Kuali OLE 1.6 http://www.kuali.org/download Open Library Environment Data 2 Insight
RIS2N3 https://github.com/dgcliff/RIS2N3 Converts RIS citation format to N3 format for loading into VIVO. Data 2 Insight
Phoebus http://damsl.cs.indiana.edu/projects/phoebus Data movement service Data 2 Insight
XSP http://damsl.cs.indiana.edu/projects/phoebus/xsp.php Network library Data 2 Insight
Karma http://d2i.indiana.edu/provenance_karma The Karma tool is a standalone tool that can be added to existing cyberinfrastructure for purposes of collection and representation of provenance data. Karma utilizes a modular architecture that permits support for multiple instrumentation plugins that make it usable in different architectural settings. Data 2 Insight
NetKarma http://d2i.indiana.edu/provenance_netkarma NetKarma allows researchers to see the exact state of the network and store configuration of the experiment and its slice. THe provenance of the data will be stored and visualized through a data portal. The provenance data can be used by the researcher to analyze their data, allow for the suspension and resumption of an experiment and provide a single reference to find the details and data collected in an experiment. Data 2 Insight
NetKarma plugin to Cytoscape   http://d2i.indiana.edu/provenance_netkarma   Provides visualization of metadata   Data 2 Insight
Sigiri http://d2i.indiana.edu/sigiri Sigiri Job Scheduler provides a simple abstraction for interaction with heterogeneous resource managers spanning grid and cloud computing, and features that make the tool useful for the midscale physical or natural scientist. Data 2 Insight
XMC Cat http://d2i.indiana.edu/xmccat XMC Cat is a metadata catalog that stores rich metadata describing data objects that are themselves stored in files, storage repositories, or on the web. Data 2 Insight

PTI Service and Cyberinfrastructure Centers

Software Name URL Description PTI Center
Open Science Grid middleware http://software.grid.iu.edu
http://repo.grid.iu.edu
Middleware (communication) software for Open Science Grid Research Technologies
XLiveCD http://xlivecd.indiana.edu/ Open source system to allow Microsoft Windows users to access Linux X-term applications and graphics Research Technologies
Apache Rave http://rave.apache.org Open Social and W3C Widget-compliant Web portal software for building Science Gateways and component-based, standard compliant social networking sites. Rave is a collaboration between Hippo Software, SURFNet, Mitre Corp, and the IU Science Gateway Group. Research Technologies
Apache Airavata http://airavata.apache.org Tools for building scientific workflows and science gateways, wrapping scientific applications as secure network services, delivering distributed messages for collaborating applications, and registering online services and workflows. Research Technologies
Apache Airavata PGA https://github.com/apache/airavata-php-gateway Apache Airavata PHP reference implementation Research Technologies
SciGaP https://github.com/SciGaP/ The SciGaP project develops science gateways as a service using Apache Airavata and related software. Research Technologies
GeoGateway https://github.com/GeoGateway/ GeoGateway is a data product search and analysis gateway for scientific discovery, field use, and disaster response Research Technologies
Lustre UID/GID Mapping and Shared Key code   Contribution to Lustre base open source distribution allows secure use of Lustre file system over wide area networks Research Technologies
Trinity http://trinityrnaseq.sourceforge.net RNA sequence assembly NCGAS
mlRho http://www.ncbi.nlm.nih.gov/pubmed/20331786 Population mutation rates NCGAS
CAFE http://www.indiana.edu/~hahnlab/software.html Computational analysis of (gene) family evolution NCGAS
Heterogeneity test http://www.indiana.edu/~hahnlab/software.html Coalescent test for differences in allele frequency distributions NCGAS
Perlymorphism http://www.indiana.edu/~hahnlab/software.html A suite of population genetics tools for large DNA sequence datasets NCGAS

Inactive / Historical Open Source Software from PTI

Software Name URL Description PTI Center
GeneIndex http://sourceforge.net/projects/geneindex/ Seeks words of various lengths specified by users NCGAS
fastDNAml http://iubio.bio.indiana.edu/soft/molbio/evolve/fastdnaml/fastDNAml.html Maximum likelihood inference of evolutionary trees NCGAS
Life Sciences DataBase Parsers Software to input data into IBM DiscoveryLink NCGAS
PENELOPE-MPI Open source but not distributed in US without permission from government. Parallel (supercomputer) software for studying radiation transport used in planning chemotherapy for brain cancer Research Technologies
Pubsonline http://sourceforge.net/projects/iupubsonline/ Open source bibliographic management Research Technologies
SMBL (Simple Message Broker Library) http://sourceforge.net/projects/smbl/ Tool for message passing interface programming with distributed systems Research Technologies
High Performance Storage Systems (HPSS) connector for the Java framework   Contribution to HPSS base distribution to enable access via Java applets Research Technologies
Twister http://www.iterativemapreduce.org/ Twister is a software tool that supports faster execution of many data mining applications implemented as MapReduce programs. The tool extends the functionality of MapReduce, a distributed programming technique patented by Google for large-scale data processing in datacenter environments. Twister allows MapReduce to achieve higher performance, perform faster data transfers, and reduce the time it takes to process vast sets of data for data mining and machine learning applications. Digital Science Center
Fault Tolerant Hybrid Information Service (FTHPIS) http://www.opengrids.org/hybrid/index.html FTHPIS is a hybrid grid information service supporting both the scalability of large amounts of relatively slowly varying data and a high performance rapidly updated information service for dynamic regions. This generic implementation supports two information service implementations: ExtendedUDDI and WS-Context Digital Science Center
mpiJava http://www.hpjava.org/mpiJava.html mpiJava is an object-oriented Java interface to the standard Message Passing Interface for parallel programming (MPI). It provides the functionality of MPI for programmers wishing to write parallel programs in the Java programming language. It is implemented as a set of Java wrappers to various native MPI packages. Digital Science Center
Global-MMCS http://www.globalmmcs.org/ The Global-MMCS Project tries to build a collaboration system, which integrates various services including videoconference, instant messaging and streaming, support multiple videoconferencing technologies and heterogeneous collaboration environments. Digital Science Center
NaradaBrokering http://grids.ucs.indiana.edu/ptliupages/projects/narada/ NaradaBrokering is a content distribution infrastructure, and enables the development of secure, failure-resilient Systems. Digital Science Center
Carousel http://grids.ucs.indiana.edu/ptliupages/projects/carousel/software.htm Community Grid for PDA project developed an environment supporting ubiquitous accessing to Community Grid systems from various small wireless devices such as Smartphone. Digital Science Center
HPJava http://grids.ucs.indiana.edu/ptliupages/projects/HPJava/index.html HPJava is an environment for scientific and parallel programming using Java. It is based on an extended version of the Java language. Digital Science Center
Klatsch https://github.com/truthy/klatsch The purpose of the Klatsch framework is to provide an easy-to-program, flexibleinterface for exploring and analyzing feeds of social media data. Digital Science Center