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 | |||
| Software Name | URL | Description | PTI Center |
|---|---|---|---|
| Boost versions 1.51 and 1.52 | http://www.boost.org/ | Contains Boost Graph Library and other libraries developed by OSL/CREST | CREST |
| Transfer Entropy Toolbox | http://code.google.com/p/transfer-entropy-toolbox | MATLAB scripts and C/C++ code for transfer entropy | CREST |
| CompuCell3D v. 3.6.1 | http://www.compucell3d.org | Simulation of multi-cell developmental biology. | CREST |
| ConceptClang | http://zalewski.indefero.net/p/clang | Simulation of multi-cell developmental biology | CREST |
| CorePy | http://www.corepy.org/ | “CorePy is a Python package for developing assembly-level applications on x86, Cell BE and PowerPC processors | CREST |
| Open MPI, MTT and SLURM | http://www.open-mpi.org/ | Message Passing Interface library objects, resource manage utilities | CREST |
| Open MPI version 1.5 | http://www.open-mpi.org/software/ompi/v1.5/ | Stable release of the Open MPI project | CREST |
| OSCAR 6.0.5 (April 7, 2010) | http://svn.oscar.openclustergroup.org/trac/oscar/blog/oscar-6.0.5 | Open Source Cluster Application Resources | CREST |
| Netgauge | http://www.unixer.de/research/netgauge/ | Netgauge is a high-precision network parameter measurement tool. | CREST |
| Graph 500 | http://www.graph500.org/ | Software for the #1 and #2 Graph 500 entries for June 2011, and the #4 and #5 ones for November 2011. | CREST |
| ORCS | http://www.unixer.de/research/orcs/ | An Oblivious Routing Congestion Simulator | CREST |
| LogGPSim | http://www.unixer.de/research/LogGOPSim/ | LogGOPSim [1] is a simulator for parallel applications and algorithms that uses the LogGOPS (or LogP, LogGP, or LogGPS) network model to simulate the execution of parallel algorithms and full applications. | CREST |
| MPIParMETIS | http://www.unixer.de/research/mpitopo/mpiparmetis/ | MPIParMETIS is a prototypic library which assists developers of parallel applications to use the scalable graph topology interface in MPI-2.2 | CREST |
| VTK | http://www.vtk.org | Visualization Toolkit | CREST |
| PhotoCat2 | https://github.com/iudlp/photocat2 | Image cataloging tool | Data 2 Insight |
| Variations 6.2 | 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 0.6 | 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 |
| 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 |
| Phoebus | http://damsl.cs.indiana.edu/projects/phoebus | Data movement service | Data 2 Insight |
| Sigiri | http://d2i.indiana.edu/sigiri | With the maturation of Grid computing facilities and recent explosion of cloud computing data centers, mid-scale computational science has more options than ever before to satisfy computational needs. But heterogeneity brings complexity. We propose a simple abstraction for interaction with heterogeneous resource managers spanning grid and cloud computing, and on features that make the tool useful for the mid-scale physical or natural scientist. Key strengths of the abstraction are its support for multiple standard job specification languages, preservation of direct user interaction with the service, removing the delay that can come through layers of services, and the predictable behaviour under heavy loads. | 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. It is an open source web service written in Java that utilizes the Axis2 web service engine and Apache Tomcat. Its features include adaptability to domain schemata through configuration instead of code changes, support for automatic capture of metadata through the use of curation plugins, and search and browse capabilities through a web-based GUI that is dynamically generated from a domain schema. This allows XMC Cat to be deployed in different scientific and educational domains without requiring new code to be written. | Data 2 Insight |
| 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, flexible interface for exploring and analyzing feeds of social media data. | Digital Science Center |
| Service and Cyberinfrastructure Centers | |||
| Open Science Grid middleware | http://software.grid.iu.edu http://repo.grid.iu.edu | Middleware (communication) software for Open Science Grid> | Research Technologies |
| 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 | http://hpss.org | Contribution to HPSS base distribution to enable access via Java applets | Research Technologies |
| Lustre UID/GID Mapping Kernel Module | http://opensfs.org | Contribution to Lustre base open source distribution – allows secure use of Lustre file system over wide area networks |
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 |
| Tree3D | 3D viewer for viewing phylogenetic (evolutionary) trees | Research Technologies | |
| Apache Rave | http://incubator.apache.org/rave/ | 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.org | Tools for building scientific workflows, wrapping scientific applications as secure network services, delivering distributed messages for collaborating applications, and registering online services and workflows. | Research Technologies |
| 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 | Available on request, http://ncgas.org/contact | Software to input data into IBM DiscoveryLink | NCGAS |
| Trinity | http://trinityrnaseq.sourceforge.net | RNA sequence assembly | NCGAS |
| mlRho | http://www.ncbi.nlm.nih.gov/pubmed/20331786 | Population mutation rates | NCGAS |
| CAFÉ | http://sites.bio.indiana.edu/~hahnlab/Software.html | Computational analysis of (gene) family evolution | NCGAS |
| Heterogeneity test | http://sites.bio.indiana.edu/~hahnlab/Software.html | Coalescent test for differences in allele frequency distributions | NCGAS |
| Perlymorphism | http://sites.bio.indiana.edu/~hahnlab/Software.html | A suite of population genetics tools for large DNA sequence datasets | NCGAS |
