In-house Projects Research Articles

The LAILAPS Search Engine: A Feature Model for Relevance Ranking in Life Science Databases

AbstractEfficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking. In this paper, we present a feature model for relevance ranking in life science databases and its implementation in the LAILAPS search engine. Motivated by the observation of user behavior during their inspection of search engine result, we condensed a set of 9 relevance discriminating features. These features are intuitively used by scientists, who briefly screen database entries for potential relevance. The features are both sufficient to estimate the potential relevance, and efficiently quantifiable. The derivation of a relevance prediction function that computes the relevance from this features constitutes a regression problem. To solve this problem, we used artificial neural networks that have been trained with a reference set of relevant database entries for 19 protein queries. Supporting a flexible text index and a simple data import format, this concepts are implemented in the LAILAPS search engine. It can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. LAILAPS is publicly available for SWISSPROT data at http://lailaps.ipk-gatersleben.de

The LAILAPS search engine: a feature model for relevance ranking in life science databases.

Efficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking. In this paper, we present a feature model for relevance ranking in life science databases and its implementation in the LAILAPS search engine. Motivated by the observation of user behavior during their inspection of search engine result, we condensed a set of 9 relevance discriminating features. These features are intuitively used by scientists, who briefly screen database entries for potential relevance. The features are both sufficient to estimate the potential relevance, and efficiently quantifiable. The derivation of a relevance prediction function that computes the relevance from this features constitutes a regression problem. To solve this problem, we used artificial neural networks that have been trained with a reference set of relevant database entries for 19 protein queries. Supporting a flexible text index and a simple data import format, this concepts are implemented in the LAILAPS search engine. It can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. LAILAPS is publicly available for SWISSPROT data at http://lailaps.ipk-gatersleben.de.

DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data

BackgroundNew "next generation" DNA sequencing technologies offer individual researchers the ability to rapidly generate large amounts of genome sequence data at dramatically reduced costs. As a result, a need has arisen for new software tools for storage, management and analysis of genome sequence data. Although bioinformatic tools are available for the analysis and management of genome sequences, limitations still remain. For example, restrictions on the submission of data and use of these tools may be imposed, thereby making them unsuitable for sequencing projects that need to remain in-house or proprietary during their initial stages. Furthermore, the availability and use of next generation sequencing in industrial, governmental and academic environments requires biologist to have access to computational support for the curation and analysis of the data generated; however, this type of support is not always immediately available.ResultsTo address these limitations, we have developed DraGnET (Draft Genome Evaluation Tool). DraGnET is an open source web application which allows researchers, with no experience in programming and database management, to setup their own in-house projects for storing, retrieving, organizing and managing annotated draft and complete genome sequence data. The software provides a web interface for the use of BLAST, allowing users to perform preliminary comparative analysis among multiple genomes. We demonstrate the utility of DraGnET for performing comparative genomics on closely related bacterial strains. Furthermore, DraGnET can be further developed to incorporate additional tools for more sophisticated analyses.ConclusionsDraGnET is designed for use either by individual researchers or as a collaborative tool available through Internet (or Intranet) deployment. For genome projects that require genome sequencing data to initially remain proprietary, DraGnET provides the means for researchers to keep their data in-house for analysis using local programs or until it is made publicly available, at which point it may be uploaded to additional analysis software applications. The DraGnET home page is available at http://www.dragnet.cvm.iastate.edu and includes example files for examining the functionalities, a link for downloading the DraGnET setup package and a link to the DraGnET source code hosted with full documentation on SourceForge.

The LAILAPS search engine: relevance ranking in life science databases.

Search engines and retrieval systems are popular tools at a life science desktop. The manual inspection of hundreds of database entries, that reflect a life science concept or fact, is a time intensive daily work. Hereby, not the number of query results matters, but the relevance does. In this paper, we present the LAILAPS search engine for life science databases. The concept is to combine a novel feature model for relevance ranking, a machine learning approach to model user relevance profiles, ranking improvement by user feedback tracking and an intuitive and slim web user interface, that estimates relevance rank by tracking user interactions. Queries are formulated as simple keyword lists and will be expanded by synonyms. Supporting a flexible text index and a simple data import format, LAILAPS can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. With a set of features, extracted from each database hit in combination with user relevance preferences, a neural network predicts user specific relevance scores. Using expert knowledge as training data for a predefined neural network or using users own relevance training sets, a reliable relevance ranking of database hits has been implemented. In this paper, we present the LAILAPS system, the concepts, benchmarks and use cases. LAILAPS is public available for SWISSPROT data at http://lailaps.ipk-gatersleben.de.

CCS project in Recôncavo Basin

Abstract In August 2007, Petrobras and IFP have initiated a common research project on Carbon Capture Storage to determine the feasibility of CO 2 injection and underground storage in an oil field located in Reconcavo Basin, a mature basin of northeastern Brazil. Petrobras has a strong experience of more than 15 years in the management of CO 2 for EOR and aims to develop a long term vision of CO 2 permanent storage. IFP is developing an ambitious R & D program on CCS for knowledge acquisition and technology development on the all chain, both under in-house projects and large collaborative efforts (EU project CASTOR, CO 2 STORE, CO 2 ReMoVe…). The aim of the first phase of the project is to take the opportunity of the existing CO 2 injection for more than 15 years in the Buracica oil field for the development and validation of technology needed for CO 2 storage. The main reservoir unit is predominantly constituted of eolic sandstone facies and is isolated from the other reservoirs by a shaly sand barrier. The cap rock is a thick clay formation. The CO 2 was only injected in the top reservoir of the field. A unique program was design to combine detailed experimental and modeling work to assess the impact of CO 2 injection on the storage. Both petrophysical and mineralogical changes will be assessed along the CO 2 path within the reservoir from the injection to the production wells. One of the main goals is to asses the rock/fluid interactions due to CO 2 injection and the different reactions that took place along the CO 2 migration path within the reservoir and its impact on the cap rock. The aim is to provide a documented data set to enable reaction transport modeling benchmarking. To complement the standard monitoring measurements, geochemical monitoring will be initiated both at reservoir and surface level to ensure storage integrity after CO 2 injection. The paper presents the main features of the project, as well as the results attained so far.

CPM2: A Core Model for Product Data

The initial core product model (CPM), developed at NIST for the support of in-house research projects, has been extended to create CPM2, intended to support a broad range of information relevant to product lifecycle management. CPM2 is a generic, abstract model with generic semantics. CPM2 gives equal status to three aspects of a product or artifact: its function, its form, and its behavior. Thus, CPM2 can support functional reasoning about a product in the conceptual stages of design, the recording and the modeling of its behavior in the postdesign stages as well as the “traditional” design phases. Three levels of CPM2 models, de-noted as the conceptual, intermediate, and implementation models, are described. Extensions of the initial CPM are briefly pre-sented. The facilities in CPM2 for building experimental intermediate systems are demonstrated and a short illustrative example is given. The full practical evaluation of CPM2 will require the development and use of implementation models.

An In Silico 3D Pharmacophore Model of Chalcones Useful in the Design of Novel Antimalarial Agents

Malaria, the most important of the human parasitic diseases, causes about 500 million infections worldwide and over 1 million deaths every year. The search for novel drug candidates against specific parasitic targets is an important goal for antimalarial drug discovery. Recently the antimalarial activity of chalcones has generated great interest. These compounds are small non-chiral molecules with relative high lipophilicity (clogP approximately 5-7), have molecular weights in the range of 300 to 600 g/mol, and possess in vivo efficacy against both P. berghei and P. yeolii. Preliminary data on our on-going chalcone synthesis project indicate that these compounds are active in vitro against P. falciparum, but are rapidly metabolized in liver microsome assays. Structurally-related compounds not including the enone linker are found to be much more metabolically stable and yet have comparable in vitro efficacy. In this study, we have utilized the efficacy data from an in-house on-going chalcone project to develop a 3D pharmacophore for antimalarial activity and used it to conduct virtual screening (in silico search) of a chemical library which resulted in identification of several potent chalcone-like antimalarials. The pharmacophore is found to contain an aromatic and an aliphatic hydrophobic site, one hydrogen bond donor site, and a ring aromatic feature distributed over a 3D space. The identified compounds were not only found to be potent in vitro against several drug resistant and susceptible strains of P. falciparum and have better metabolic stability, but included one with good in vivo efficacy in a mouse model of malaria.

Testing of Inflatable-Structure Shape Control Using Genetic Algorithms and Neural Networks

I NFLATABLE structures have attractedmuch interest in the space community due to their unique advantages in achieving lowmass and high packaging efficiency [1,2]. We are currently working on an in-house research and development project of a membrane synthetic aperture radar antenna and solar array (see Fig. 1). It is expected that the membrane will be subjected to flatness problems during its lifetime in orbit, due to the thermal variation in space. A purely passive control method may not be sufficient to keep the membrane flat. Hence, an active control system is proposed to adjust the tensions according to the thermal variation. Actuators are installed in series with the links, such that the tensions stretching the membrane can be adjusted. A genetic algorithm and neural network (GA–NN) scheme is proposed for modeling and tension optimization. The neural network model of the membrane is established as a mapping from the boundary stretching tensions and space environment to membrane flatness. After the neural network training is completed, the membrane flatness can be estimated by inputting the measured stretching tensions and space environment data to the neural network model. Based on the neural network model, the genetic algorithm is applied to search for the optimal tensions that minimize the membrane wrinkles [3]. Experimental results demonstrate the effectiveness of the proposed scheme.

Problems encountered by owners of design–build projects in Singapore

Even though design–build (DB) arrangements have several advantages, project owners are not using them to a large extent. This may be due to some inherent problems that owners face in their DB projects. This study investigates the problems and difficulties that Singaporean owners face in DB projects and how project managers can help them overcome these problems. Data were collected from public and private sector owners using a structured questionnaire via post and email. The collected data were subjected to statistical analyses. The results show that owners face significant problems in the whole development process of DB projects, especially during tender preparation and evaluation stages. Owners that do not have in-house project management face significantly more problems than those with in-house expertise. Generally, there were no differences on the problems faced by the public and private sector owners. Recommendations are made on how project managers can help owners overcome some of the problems they face in DB projects.

Evidence based research activities, interests and opportunities exist for practitioners in all library sectors in the British Isles

A review of: 
 
 McNicol, Sarah. “Is Research an Untapped Resource in the Library and Information Profession?” Journal of Librarianship and Information Science 36.3 (September 2004):119-26. 
 
 Objective – To scope the range, nature and challenges of present, planned and future research by practitioners within libraries in the British Isles.
 
 Design – A series of survey questionnaires sent by mail. 
 
 Setting – Public, academic, health, special and school libraries of the British Isles.
 
 Subjects – A total of 2384 questionnaires were sent out and 334 responses were received. 62 academic libraries, 83 health libraries, 78 public libraries, 63 school libraries and 48 special libraries participated in the study. 
 
 Methods – This study was undertaken in 2003 by a research team at the University of Central England. Survey questionnaires were sent by mail to library directors in all public library authorities, academic libraries, health libraries and special libraries in England, Wales, Scotland, Northern Ireland and the Republic of Ireland. In addition, questionnaires were sent to the librarians in all state and independent schools within a sample of nine local education authorities.
 
 Each participant was asked to identify past and future research issues of interest and the barriers to research practice within their library. Research was defined to include work on both externally funded and in-house projects and examples of the types of activities that this might include were provided.
 
 Main results – Half the respondents reported that they had been involved in some form of research in the past two years, with the lowest level of involvement from school libraries and the highest in public libraries. Generally, only the library directly involved in conducting the research made use of the findings and a gap in the dissemination of results was identified across sectors. User surveys were the most common form of research undertaken across libraries and slightly fewer respondents intended to carry out research in the coming twelve months than had in the past (the area most commonly mentioned was user surveys). Information and communications technology (ICT) was an area of planned future research in all libraries, as were user needs and user behaviour. The most frequently cited barriers to research activity across all sectors were lack of time and financial resources. Staff skills and the lack of focus on practical problems to solve were indicated as a barrier in health, public and academic libraries.
 
 Libraries reported a range of common uses for the research findings including: informing strategic and service planning; providing benchmarking data and measuring the effectiveness of services; identification of marketing and public relations opportunities; discovery of staff training needs; and use of the results to demonstrate the value of libraries to funding bodies.
 
 Conclusion – This study provides insight into practitioner-focused areas of research interest and possible areas for future investigation. As the author reports in her conclusion, the survey results cannot be considered representative of the wider population. 
 
 Since research interests often overlap, a sector wide or cross-sectoral research approach should be considered to allow library staff to identify and resolve common problems. Wide dissemination of research results within the practitioner community would be of benefit to all. Greater communication between practitioner and information science communities is also encouraged, as these communities’ work is mutually beneficial.

Loose Coalitions: a Memoir of Continuum, 1987–?

Towards the end of 1994 I finished my formal association with Continuum as it passed out of Tom O'Regans editorial hands and moved on to Brian Shoesmith and others at Edith Cowan, eventually to become an international journal published first by Carfax and later (as now) by Taylor & Francis. So most of this memoir of loose coalitions will be about those years, 1987 - 1994 when the journal was very much an in-house project at Murdoch University.

Strategies to Develop and Promote Undergraduate Student Interest and Participation in Research

Undergraduate students are not always exposed to opportunities to participate in research projects and may not even be thoroughly versed in career options in scientific fields other than medicine. Compounding the problem is that a significant number of colleges with strong academic programs do not have the research infrastructure to support a large number of undergraduate student research projects. In our experiences we found students were knowledgeable about career paths for medical doctors, but not for professors. However, students become very interested in going to graduate school to pursuing a Ph.D. after participation in research projects and attending conferences to present their results. To provide research opportunities we formulated a strategy of seeking out and dissemination information about summer undergraduate research programs, as well as applying for grants focusing on student development and strengthening research infrastructure. Additionally, we bring in seminar speakers to talk to students about research topics as well as travel to research institutions and attend conferences as often as possible. Participation at conferences may be the highlight of their undergraduate activities. Approximately 15 – 20 students apply for and are accepted into summer research programs each year, whereas prior to this only 1 or 2 would be interested. We also established in-house research projects on oyster rehabitation, physiology and biochemistry in which about 10 students participate each year. We have grown from a situation where hardly any student attended national conferences to present research reports to now attending 6 – 7 conferences yearly with about 40 – 50 student presentations.

Measuring the Function Points for Migration Project: A Case Study

In this study, we extend the study of Function Point Analysis (FPA) for the measurement of source code based migration project using the migration tooling options. FPA is an objective and structured technique to measure software size by quantifying its functionality provided to the user, based on the requirements and logical design. It is noticed that the procedure for the above measurement is not fully described in FPA method. Hence, the same estimation concept has been applied to an in-house project on an experimental basis at a leading software development organization. The yielded results are compared with FPA for the re-engineering project.

Open-Source Tools for Distributed Device Control within a Service- Oriented Architecture

Within the past few years a new paradigm for software organization and intercommunication has emerged—SOA, or Service-Oriented Architecture. This article explores the relevance of this approach to automation and control of laboratory devices and examines some of the excellent open-source software tools, libraries, and frameworks available to implement software according to SOA principles. Not only can the open-source packages described here serve as the basis for practical laboratory automation systems, they also can serve an educational role to illustrate the principles and advantages of an SOA approach. Open-source software represents a significant opportunity for leveraging the skills and budgets of small automation development groups to produce very sophisticated and reliable software systems that would otherwise be out of reach for such small teams. An added benefit is that because of the standardized protocols involved, opportunities for interoperation with other systems that are following a similar approach becomes a realistic possibility. Although intellectual property and licensing issues may represent a barrier to the open-source approach for commercial developers seeking to market their solutions, it may be the ideal approach for many in-house projects and for standardized elements within commercial packages.

Retrospective Cataloging of Maps in a Small Liberal Arts College

In February 2002, members of Saint Anselm College Geisel Library's Cataloging Unit started a project to retrospectively catalog the Library's small, but diverse, collection of cartographic materials. The Cataloging Unit of Geisel's Technical Services Department is comprised of two full-time catalogers plus one half-time cataloger. The Library's Government Documents Department (Geisel is a selective, 15% depository), where much of these materials are housed, does not have a dedicated cataloging staff. The collection of approximately 950 titles included topographic series maps, topographic/bathymetric maps (367), CIA country study maps (480), remote sensing image maps (20), hanging wall maps (6), globes (3), political ward maps (40), atlases (21), and monographic maps from the late 19th and early 20th centuries (10). This article describes the planning, requirements and challenges faced by a Baccalaureate College Liberal Arts library performing an inhouse retrospective cataloging project of cartographic materials.

A simulation approach to in-house versus contracted out cost comparisons

The purpose of this project was to compare the cost of transportation engineering design services provided by private contractors versus services provided by state transportation agency staff for the Louisiana Department of Transportation and Development (LaDOTD). Due to shrinking budgets, staff cuts, and a trend toward privatization, state transportation agencies now outsource the majority of the services they provide. The merits of doing so, however, have been difficult to discern for lack of “apples-to-apples” comparisons. For engineering design services, this problem is particularly acute due to the uniqueness of many projects (e.g., a bridge over the Mississippi river). A simulation approach was used in this study to make “apples-to-apples” comparisons for 39 design projects, 22 in-house projects and 17 consultant projects. For each in-house design project, the cost was estimated had the work been done by a consulting firm. Similarly, for each consultant design project, the cost was estimated had the work been done by in-house staff. The result of the study was that in-house design costs were cheaper by an average of 17 to 19 percent.

Expressed sequence tags: analysis and annotation.

Expressed sequence tags (ESTs) present a special set of problems for bioinformatic analysis. They are partial and error-prone, and large datasets can have significant internal redundancy. To facilitate analysis of small EST datasets from in-house projects, we present an integrated "pipeline" of tools that take EST data from sequence trace to database submission. These tools also can be used to provide clustering of ESTs into putative genes and to annotate these genes with preliminary sequence similarity searches. The systems are written to use the public-domain LINUX environment and other openly available analytical tools.

Froth modification for reduced fuel oil usage in phosphate flotation

The Florida phosphate industry uses millions of pounds of fuel oil per year for phosphate flotation. It is of significant environmental and economic benefit to reduce the usage of fuel oil. This paper presents laboratory-testing results from both a FIPR in-house research program and a contractual project with University of Utah. In the FIPR in-house project, three different flotation feed samples were obtained for laboratory testing. Initial laboratory rougher flotation tests were performed to compare the response of 10 petroleum-based froth modifiers plus one sample of rosin oil derived from tall oil rosin. Successful flotation tests, in which 1/3 of several selected petroleum-based modifiers was replaced by rosin oil, resulted in a P 2O 5 recovery increase. The Utah project showed that the addition of a nonionic polymer could reduce fuel oil use by up to 50% for flotation of coarse phosphates. The mechanisms by which polymers improve phosphate flotation was studied.

Managing product development collaborations—a process maturity approach

Product development collaborations present additional challenges over purely in-house projects, yet are an increasingly common feature of the new product introduction (NPI) process. This paper introduces the notion of collaborative maturity as a tool to examine the issues confronting firms that outsource a significant amount of design or development activity to a third party, with the aim of providing guidance to managers involved in collaborative projects. Drawing from literature and insights gained from case studies of twelve collaborative development projects involving United Kingdom small- to medium-sized enterprises, a framework is proposed that sets collaboration in the context of task partitioning within the NPI process, on the one hand, and the development and lifecycle of a partnering relationship, on the other. A collaboration maturity grid (CMG) describes each of the following key process areas at four levels of maturity: collaboration strategy, structured development process, system design and task partitioning, partner selection, project initiation, partnership management and partnership development. The grids are incorporated in a workbook (along with a lifecycle scenario tool, checklist and audit questionnaire) that has been tested in six companies.

3108 設計者向け遠隔試作造形システムの提案

The rapid prototyping process in product development is generally done not by the project designers, but by an in-house project leader and a prototyping contractor outside the company. If it were possible for the designers to easily do the prototyping themselves whenever they wished, it would increase te efficiency and shorten the time required for product development. With this in mind, we have developed Smart Prototyping, a system that enables 3D designers to create prototypes using a modeling machine installed in remote location. The system has the following features. ・ The modeling machine can be controlled and monitored by using network technologies. ・ A modeling knowledge supply system based on knowledge creating logic enables the use of expert know-how. As a result, designers who do not have a modeling machine in their department, and who lack specialized modeling knowledge, can easily create prototypes from a remote location, thus helping to short the design time.