Open-source tools for enhancing full-text searching of OPACs Use of Koha, Greenstone and Fedora

Purpose - There are many library automation packages available as open-source software, comprising two modules: staff-client module and online public access catalogue (OPAC). Although the OPAC of these library automation packages provides advanced features of searching and retrieval of bibliographic records, none of them facilitate full-text searching. Most of the available open-source digital library software facilitates indexing and searching of full-text documents in different formats. This paper makes an effort to enable full-text search features in the widely used open-source library automation package Koha, by integrating it with two open-source digital library software packages, Greenstone Digital Library Software (GSDL) and Fedora Generic Search Service (FGSS), independently. Design/methodology/approach - The implementation is done by making use of the Search and Retrieval by URL (SRU) feature available in Koha, GSDL and FGSS. The full-text documents are indexed both in Koha and GSDL and FGSS. Findings - Full-text searching capability in Koha is achieved by integrating either GSDL or FGSS into Koha and by passing an SRU request to GSDL or FGSS from Koha. The full-text documents are indexed both in the library automation package (Koha) and digital library software (GSDL, FGSS) Originality/value - This is the first implementation enabling the full-text search feature in a library automation software by integrating it into digital library software.

Geographic Resources Decision Support System – an Open Source GIS

Fully structured and matured open source spatial and temporal analysis technology seems to be the official carrier of the future for planning of the natural resources especially in the developing nations. This technology has gained enormous momentum because of technical superiority, affordability and ability to join expertise from all sections of the society. Sustainable development of a region depends on the integrated planning approaches adopted in decision making which requires timely and accurate spatial data. With the increased developmental programmes, the need for appropriate decision support system has increased in order to analyse and visualise the decisions associated with spatial and temporal aspects of natural resources. In this regard Geographic Information System (GIS) along with remote sensing data support the applications that involve spatial and temporal analysis on digital thematic maps and the remotely sensed images. Open source GIS would help in wide scale applications involving decisions at various hierarchical levels (for example from village panchayat to planning commission) on economic viability, social acceptance apart from technical feasibility. GRASS (Geographic Resources Analysis Support System, http://wgbis.ces.iisc.ernet.in/grass) is an open source GIS that works on Linux platform (freeware), but most of the applications are in command line argument, necessitating a user friendly and cost effective graphical user interface (GUI). Keeping these aspects in mind, Geographic Resources Decision Support System (GRDSS) has been developed with functionality such as raster, topological vector, image processing, statistical analysis, geographical analysis, graphics production, etc. This operates through a GUI developed in Tcltk (Tool command language / Tool kit) under Linux as well as with a shell in X-Windows. GRDSS include options such as Import /Export of different data formats, Display, Digital Image processing, Map editing, Raster Analysis, Vector Analysis, Point Analysis, Spatial Query, which are required for regional planning such as watershed Analysis, Landscape Analysis etc. This is customised to Indian context with an option to extract individual band from the IRS (Indian Remote Sensing Satellites) data, which is in BIL (Band Interleaved by Lines) format. The integration of PostgreSQL (a freeware) in GRDSS aids as an efficient database management system.

Open source drug discovery- A new paradigm of collaborative research in tuberculosis drug development

It is being realized that the traditional closed-door and market driven approaches for drug discovery may not be the best suited model for the diseases of the developing world such as tuberculosis and malaria, because most patients suffering from these diseases have poor paying capacity. To ensure that new drugs are created for patients suffering from these diseases, it is necessary to formulate an alternate paradigm of drug discovery process. The current model constrained by limitations for collaboration and for sharing of resources with confidentiality hampers the opportunities for bringing expertise from diverse fields. These limitations hinder the possibilities of lowering the cost of drug discovery. The Open Source Drug Discovery project initiated by Council of Scientific and Industrial Research, India has adopted an open source model to power wide participation across geographical borders. Open Source Drug Discovery emphasizes integrative science through collaboration, open-sharing, taking up multi-faceted approaches and accruing benefits from advances on different fronts of new drug discovery. Because the open source model is based on community participation, it has the potential to self-sustain continuous development by generating a storehouse of alternatives towards continued pursuit for new drug discovery. Since the inventions are community generated, the new chemical entities developed by Open Source Drug Discovery will be taken up for clinical trial in a non-exclusive manner by participation of multiple companies with majority funding from Open Source Drug Discovery. This will ensure availability of drugs through a lower cost community driven drug discovery process for diseases afflicting people with poor paying capacity. Hopefully what LINUX the World Wide Web have done for the information technology, Open Source Drug Discovery will do for drug discovery. (C) 2011 Elsevier Ltd. All rights reserved.

Foot-mounted INS for everybody - an open-source embedded implementation

We present an open-source, realtime, embedded implementation of a foot-mounted, zero-velocity-update-aided inertial navigation system. The implementation includes both hardware design and software, uses off-the-shelf components and assembly methods, and features a standard USB interface. The software is written in C and can easily be modified to run user implemented algorithms. The hardware design and the software are released under permissive open-source licenses and production files, source code, documentation, and further resources are available at www.openshoe.org. The reproduction cost for a single unit is below $800, with the inertial measurement unit making up the bulk ($700). The form factor of the implementation is small enough for it to be integrated in the sole of a shoe. A performance evaluation of the system shows a position errors for short trajectories (<;100 [m]) of ± 0.2-1% of the traveled distance, depending on the shape of trajectory.

An open source massively parallel solver for Richards equation: Mechanistic modelling of water fluxes at the watershed scale

In this paper we present a massively parallel open source solver for Richards equation, named the RichardsFOAM solver. This solver has been developed in the framework of the open source generalist computational fluid dynamics tool box OpenFOAM (R) and is capable to deal with large scale problems in both space and time. The source code for RichardsFOAM may be downloaded from the CPC program library website. It exhibits good parallel performances (up to similar to 90% parallel efficiency with 1024 processors both in strong and weak scaling), and the conditions required for obtaining such performances are analysed and discussed. These performances enable the mechanistic modelling of water fluxes at the scale of experimental watersheds (up to few square kilometres of surface area), and on time scales of decades to a century. Such a solver can be useful in various applications, such as environmental engineering for long term transport of pollutants in soils, water engineering for assessing the impact of land settlement on water resources, or in the study of weathering processes on the watersheds. (C) 2014 Elsevier B.V. All rights reserved.

A do-it-yourself (DIY) switched mode power conversion laboratory

In the education of physical sciences, the role of the laboratory cannot be overemphasised. It is the laboratory exercises which enable the student to assimilate the theoretical basis, verify the same through bench-top experiments, and internalize the subject discipline to acquire mastery of the same. However the resources essential to put together such an environment is substantial. As a result, the students go through a curriculum which is wanting in this respect. This paper presents a low cost alternative to impart such an experience to the student aimed at the subject of switched mode power conversion. The resources are based on an open source circuit simulator (Sequel) developed at IIT Mumbai, and inexpensive construction kits developed at IISc Bangalore. The Sequel programme developed by IIT Mumbai, is a circuit simulation program under linux operating system distributed free of charge. The construction kits developed at IISc Bangalore, is fully documented for anyone to assemble these circuit which minimal equipment such as soldering iron, multimeter, power supply etc. This paper puts together a simple forward dc to dc converter as a vehicle to introduce the programming under sequel to evaluate the transient performance and small signal dynamic model of the same. Bench tests on the assembled construction kit may be done by the student for study of operation, transient performance and closed loop stability margins etc.

Field Flow Sensitive Pointer and Escape Analysis for Java Using Heap Array SSA

Context sensitive pointer analyses based on Whaley and Lam’s bddbddb system have been shown to scale to large Java programs. We provide a technique to incorporate flow sensitivity for Java fields into one such analysis and obtain an escape analysis based on it. First, we express an intraprocedural field flow sensitive analysis, using Fink et al.’s Heap Array SSA form in Datalog. We then extend this analysis interprocedurally by introducing two new φ functions for Heap Array SSA Form and adding deduction rules corresponding to them. Adding a few more rules gives us an escape analysis. We describe two types of field flow sensitivity: partial (PFFS) and full (FFFS), the former without strong updates to fields and the latter with strong updates. We compare these analyses with two different (field flow insensitive) versions of Whaley-Lam analysis: one of which is flow sensitive for locals (FS) and the other, flow insensitive for locals (FIS). We have implemented this analysis on the bddbddb system while using the SOOT open source framework as a front end. We have run our analysis on a set of 15 Java programs. Our experimental results show that the time taken by our field flow sensitive analyses is comparable to that of the field flow insensitive versions while doing much better in some cases. Our PFFS analysis achieves average reductions of about 23% and 30% in the size of the points-to sets at load and store statements respectively and discovers 71% more “caller-captured” objects than FIS.

Accelerating frequency-domain diffuse optical tomographic image reconstruction using graphics processing units

Diffuse optical tomographic image reconstruction uses advanced numerical models that are computationally costly to be implemented in the real time. The graphics processing units (GPUs) offer desktop massive parallelization that can accelerate these computations. An open-source GPU-accelerated linear algebra library package is used to compute the most intensive matrix-matrix calculations and matrix decompositions that are used in solving the system of linear equations. These open-source functions were integrated into the existing frequency-domain diffuse optical image reconstruction algorithms to evaluate the acceleration capability of the GPUs (NVIDIA Tesla C 1060) with increasing reconstruction problem sizes. These studies indicate that single precision computations are sufficient for diffuse optical tomographic image reconstruction. The acceleration per iteration can be up to 40, using GPUs compared to traditional CPUs in case of three-dimensional reconstruction, where the reconstruction problem is more underdetermined, making the GPUs more attractive in the clinical settings. The current limitation of these GPUs in the available onboard memory (4 GB) that restricts the reconstruction of a large set of optical parameters, more than 13, 377. (C) 2010 Society of Photo-Optical Instrumentation Engineers. DOI: 10.1117/1.3506216]

Points-to Analysis as a System of Linear Equations

We propose a novel formulation of the points-to analysis as a system of linear equations. With this, the efficiency of the points-to analysis can be significantly improved by leveraging the advances in solution procedures for solving the systems of linear equations. However, such a formulation is non-trivial and becomes challenging due to various facts, namely, multiple pointer indirections, address-of operators and multiple assignments to the same variable. Further, the problem is exacerbated by the need to keep the transformed equations linear. Despite this, we successfully model all the pointer operations. We propose a novel inclusion-based context-sensitive points-to analysis algorithm based on prime factorization, which can model all the pointer operations. Experimental evaluation on SPEC 2000 benchmarks and two large open source programs reveals that our approach is competitive to the state-of-the-art algorithms. With an average memory requirement of mere 21MB, our context-sensitive points-to analysis algorithm analyzes each benchmark in 55 seconds on an average.

A Case Study in Matching Service Descriptions to Implementations in an Existing System

A number of companies are trying to migrate large monolithic software systems to Service Oriented Architectures. A common approach to do this is to first identify and describe desired services (i.e., create a model), and then to locate portions of code within the existing system that implement the described services. In this paper we describe a detailed case study we undertook to match a model to an open-source business application. We describe the systematic methodology we used, the results of the exercise, as well as several observations that throw light on the nature of this problem. We also suggest and validate heuristics that are likely to be useful in partially automating the process of matching service descriptions to implementations.

Dynamic path profile aided recompilation in a JAVA just-in-time compiler

Just-in-Time (JIT) compilers for Java can be augmented by making use of runtime profile information to produce better quality code and hence achieve higher performance. In a JIT compilation environment, the profile information obtained can be readily exploited in the same run to aid recompilation and optimization of frequently executed (hot) methods. This paper discusses a low overhead path profiling scheme for dynamically profiling AT produced native code. The profile information is used in recompilation during a subsequent invocation of the hot method. During recompilation tree regions along the hot paths are enlarged and instruction scheduling at the superblock level is performed. We have used the open source LaTTe AT compiler framework for our implementation. Our results on a SPARC platform for SPEC JVM98 benchmarks indicate that (i) there is a significant reduction in the number of tree regions along the hot paths, and (ii) profile aided recompilation in LaTTe achieves performance comparable to that of adaptive LaTTe in spite of retranslation and profiling overheads.

Integrating CDS/ISIS Databases with Greenstone Digital Library Software (GSDL)

CDS/ISIS is an advanced non-numerical information storage and retrieval software developed by UNESCO since 1985 to satisfy the need expressed by many institutions, especially in developing countries, to be able to streamline their information processing activities by using modern (and relatively inexpensive) technologies [1]. CDS/ISIS is available for MS-DOS, Windows and Unix operating system platforms. The formatting language of CDS/ISIS is one of its several strengths. It is not only used for formatting records for display but is also used for creating customized indexes. CDS/ISIS by itself does not facilitate in publishing its databases on the Internet nor does it facilitate in publishing on CD-ROMs. However, numbers of open source tools are now available, which enables in publishing CDS/ISIS databases on the Internet and also on CD-ROMs. In this paper, we have discussed the ways and means of integrating CDS/ISIS databases with GSDL, an open source digital library (DL) software.

Landslide Susceptible Locations in Western Ghats: Prediction through openModeller

Many shallow landslides are triggered by heavy rainfall on hill slopes resulting in enormous casualties and huge economic losses in mountainous regions. Hill slope failure usually occurs as soil resistance deteriorates in the presence of the acting stress developed due to a number of reasons such as increased soil moisture content, change in land use causing slope instability, etc. Landslides triggered by rainfall can possibly be foreseen in real time by jointly using rainfall intensity-duration and information related to land surface susceptibility. Terrain analysis applications using spatial data such as aspect, slope, flow direction, compound topographic index, etc. along with information derived from remotely sensed data such as land cover / land use maps permit us to quantify and characterise the physical processes governing the landslide occurrence phenomenon. In this work, the probable landslide prone areas are predicted using two different algorithms – GARP (Genetic Algorithm for Rule-set Prediction) and Support Vector Machine (SVM) in a free and open source software package - openModeller. Several environmental layers such as aspect, digital elevation data, flow accumulation, flow direction, slope, land cover, compound topographic index, and precipitation data were used in modelling. A comparison of the simulated outputs, validated by overlaying the actual landslide occurrence points showed 92% accuracy with GARP and 96% accuracy with SVM in predicting landslide prone areas considering precipitation in the wettest month whereas 91% and 94% accuracy were obtained from GARP and SVM considering precipitation in the wettest quarter of the year.

Scalable Context-Sensitive Points-To Analysis Using Multi-Dimensional Bloom Filters

Context-sensitive points-to analysis is critical for several program optimizations. However, as the number of contexts grows exponentially, storage requirements for the analysis increase tremendously for large programs, making the analysis non-scalable. We propose a scalable flow-insensitive context-sensitive inclusion-based points-to analysis that uses a specially designed multi-dimensional bloom filter to store the points-to information. Two key observations motivate our proposal: (i) points-to information (between pointer-object and between pointer-pointer) is sparse, and (ii) moving from an exact to an approximate representation of points-to information only leads to reduced precision without affecting correctness of the (may-points-to) analysis. By using an approximate representation a multi-dimensional bloom filter can significantly reduce the memory requirements with a probabilistic bound on loss in precision. Experimental evaluation on SPEC 2000 benchmarks and two large open source programs reveals that with an average storage requirement of 4MB, our approach achieves almost the same precision (98.6%) as the exact implementation. By increasing the average memory to 27MB, it achieves precision upto 99.7% for these benchmarks. Using Mod/Ref analysis as the client, we find that the client analysis is not affected that often even when there is some loss of precision in the points-to representation. We find that the NoModRef percentage is within 2% of the exact analysis while requiring 4MB (maximum 15MB) memory and less than 4 minutes on average for the points-to analysis. Another major advantage of our technique is that it allows to trade off precision for memory usage of the analysis.

Demonstrating the Usefulness of CAELinux for Computer Aided Engineering using an Example of the Three Dimensional Reconstruction of a Pig Liver

CAELinux is a Linux distribution which is bundled with free software packages related to Computer Aided Engineering (CAE). The free software packages include software that can build a three dimensional solid model, programs that can mesh a geometry, software for carrying out Finite Element Analysis (FEA), programs that can carry out image processing etc. Present work has two goals: 1) To give a brief description of CAELinux 2) To demonstrate that CAELinux could be useful for Computer Aided Engineering, using an example of the three dimensional reconstruction of a pig liver from a stack of CT-scan images. One can note that instead of using CAELinux, using commercial software for reconstructing the liver would cost a lot of money. One can also note that CAELinux is a free and open source operating system and all software packages that are included in the operating system are also free. Hence one can conclude that CAELinux could be a very useful tool in application areas like surgical simulation which require three dimensional reconstructions of biological organs. Also, one can see that CAELinux could be a very useful tool for Computer Aided Engineering, in general.