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PubMed2005

ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text.

ABNER (A Biomedical Named Entity Recognizer) is an open source software tool for molecular biology text mining. At its core is a machine learning system using conditional random fields with a variety of orthographic and contextual features. The latest version is 1.5, which has an intuitive graphical interface and includes two modules for tagging entities (e.g. protein and cell line) trained on standard corpora, for which performance is roughly state of the art. It also includes a Java application programming interface allowing users to incorporate ABNER into their own systems and train models on new corpora.

Algorithms↗

PubMed2005

Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data.

BACKGROUND: The identification of disease-associated genes using single nucleotide polymorphisms (SNPs) has been increasingly reported. In particular, the Affymetrix Mapping 10 K SNP microarray platform uses one PCR primer to amplify the DNA samples and determine the genotype of more than 10,000 SNPs in the human genome. This provides the opportunity for large scale, rapid and cost-effective genotyping assays for linkage analysis. However, the analysis of such datasets is nontrivial because of the large number of markers, and visualizing the linkage scores in the context of genome maps remains less automated using the current linkage analysis software packages. For example, the haplotyping results are commonly represented in the text format. RESULTS: Here we report the development of a novel software tool called CompareLinkage for automated formatting of the Affymetrix Mapping 10 K genotype data into the "Linkage" format and the subsequent analysis with multi-point linkage software programs such as Merlin and Allegro. The new software has the ability to visualize the results for all these programs in dChip in the context of genome annotations and cytoband information. In addition we implemented a variant of the Lander-Green algorithm in the dChipLinkage module of dChip software (V1.3) to perform parametric linkage analysis and haplotyping of SNP array data. These functions are integrated with the existing modules of dChip to visualize SNP genotype data together with LOD score curves. We have analyzed three families with recessive and dominant diseases using the new software programs and the comparison results are presented and discussed. CONCLUSIONS: The CompareLinkage and dChipLinkage software packages are freely available. They provide the visualization tools for high-density oligonucleotide SNP array data, as well as the automated functions for formatting SNP array data for the linkage analysis programs Merlin and Allegro and calling these programs for linkage analysis. The results can be visualized in dChip in the context of genes and cytobands. In addition, a variant of the Lander-Green algorithm is provided that allows parametric linkage analysis and haplotyping.

Family Health↗

PubMed1998

Tools for immunization guideline knowledge maintenance. II. Automated Web-based generation of user-customized test cases.

IMM/Test is a prototype software tool built to generate test cases that can be used to help test and verify the internal logic of an immunization forecasting program. A forecasting program takes as input a child's immunization history and produces recommendations as to which vaccinations are due and which should be scheduled next. IMM/Test was developed to test a specific immunization forecasting program, IMM/Serve. In addition, IMM/Test has been incorporated into a broader Web-based tool, IMM/Web, which allows the user (e.g., a member of an immunization registry staff) to customize the parameters used for immunization forecasting (e.g., the minimum ages for each dose and the minimum wait intervals between doses) to reflect local practice. IMM/Web then generates a customized set of test cases that may be used to test the user's immunization forecasting program. The user may also request that the test cases be automatically passed to IMM/Serve to analyze using the newly defined parameters. The paper describes the internal design of IMM/Test and IMM/Web and discusses certain lessons learned in the implementation of the two programs.

Adolescent↗

PubMed2006

Statistical analysis of combined dose effects for experiments with two agents.

OBJECTIVE: Classical isobologram analysis offers a way for analysing combined drug effects in dose-response experiments statistically. The aim is to determine as to whether two agents or drugs can be considered synergistic or antagonistic in their effect. METHODS AND MATERIALS: We describe a MATLAB-based software tool for automated isobologram analysis and computation of combination indices. Statistical issues like estimation together with respective confidence intervals are of key interest. Additional predictive values are computed to facilitate a more easy interpretation of obtained results. RESULTS: Analysis of an experimental and a real in vitro data set demonstrates the approach and the way of interpreting results. Results are summarized in two ways: tables and graphical displays containing classical isobolograms. CONCLUSION: Our package supplements the clinical software-equipment and is a tool for automatic evaluation of combined dose-response experiments in experimental oncology in the urologic clinic.

Antineoplastic Agents↗

PubMed2006

The virtual laboratory approach to pharmacokinetics: design principles and concepts.

Modeling and simulation in pharmacokinetics has turned into the focus of pharmaceutical companies, driven by the emerging consensus that in silico predictions, combined with in vitro data, have the potential to significantly increase insight into pharmacokinetic processes. To support in silico methodology adequately, software tools need to be user-friendly and, at the same time, flexible. In brief, the software has to allow the modeling of ideas that go beyond the current knowledge--in the form of a virtual laboratory. In this review, we present and discuss the necessary design principles and concepts required to do this. They have been implemented in the software package MEDICI-PK, demonstrating its feasibility and advantages.

Animals↗

PubMed2000

Proteomic databases and software on the web.

In the wake of sequencing projects, protein function analysis is evolving fast, from the careful design of assays that address specific questions to 'large-scale' proteomics technologies that yield proteome-wide maps of protein expression or interaction. As these new technologies depend heavily on information storage, representation and analysis, existing databases and software tools are being adapted, while new resources are emerging. This paper describes the proteomics databases and software available through the World-Wide Web, focusing on their present use and applicability. As the resource situation is highly transitory, trends and probable evolutions are discussed whenever applicable.

Computational Biology↗

PubMed2003

Statistical and graphical methods for quality control determination of high-throughput screening data.

High-throughput screening (HTS) is used in modern drug discovery to screen hundreds of thousands to millions of compounds on selected protein targets. It is an industrial-scale process relying on sophisticated automation and state-of-the-art detection technologies. Quality control (QC) is an integral part of the process and is used to ensure good quality data and mini mize assay variability while maintaining assay sensitivity. The authors describe new QC methods and show numerous real examples from their biologist-friendly Stat Server HTS application, a custom-developed software tool built from the commercially available S-PLUS and Stat Server statistical analysis and server software. This system remotely processes HTS data using powerful and sophisticated statistical methodology but insulates users from the technical details by outputting results in a variety of readily interpretable graphs and tables. It allows users to visualize HTS data and examine assay performance during the HTS campaign to quickly react to or avoid quality problems.

Computer Graphics↗

PubMed2002

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

Algorithms↗

PubMed2003

Development under extreme conditions: forensic bioinformatics in the wake of the World Trade Center disaster.

The terrorist attacks of September 11, 2001 resulted in death and devastation in three locations, and extraordinary efforts have been exerted to identify the remains of all victims. As mass fatalities go, this one has been unusual at a policy level because the goal has been not merely to identify remains for every decedent, but to identify every bit of remains found so that even small pieces of tissue can be returned to families for burial. While the human impact at the Pentagon and Shanksville, PA was horrific, the World Trade Center site presented a particularly complex challenge for forensic DNA matching and data handling. A complete and definitive list of all those killed is still elusive, and human remains were crushed and co-mingled by the falling towers. Software tools had never been considered for a problem of this scale and scope. New data handling systems had to be created under extreme software development conditions characterized by incomplete requirements specifications, chaotically changing priorities, truly impossible deadlines and rapidly rolling production releases. Partly because of the company's experience with mtDNA tools built for the Armed Forces DNA Identification Lab starting in 1997, the New York City Office of Chief Medical Examiner [OCME] contacted Gene Codes Corporation in late September as existing data-handling tools began to fail. We began work on the project in mid-October, 2001. Our approach to the problem included: Extreme Programming [XP] methodology for functional software development, On-site time and motion analysis at the OCME for user interface design, Evidentiary references between STR, SNP and mtDNA analysis results, and Separate data Quality Control [QC] and software Quality Assurance [QA] initiatives. A substantial software suite was developed called M-FISys, an acronym for Mass-Fatality Identification System.

Computational Biology↗

PubMed2004

Proteomics/genomics and signaling in lymphocytes.

Recent technological advances in genomics, proteomics and bioinformatics have offered new insights into the molecular mechanisms that underlie lymphocyte signaling and function, and the development of new tools in these areas has opened up new avenues for biological investigation. By adding a quantitative dimension to lymphocyte proteome profiling, molecular machines and spatiotemporal regulatory processes can now be analyzed using such discovery-driven approaches. Biologists employing genomic and proteomic tools are gathering data at increasing speed and their struggle to extract maximal biological information is helped by new software tools that enable the detailed comparison of multiple datasets.

Animals↗

PubMed2005

High throughput sequence analysis reveals hitherto unreported recombination in the genus Norovirus.

Viruses of the Norovirus genus (Caliciviridae family) are a major cause of human gastroenteritis. In some viruses, recombination is an important evolutionary process and therefore we should try to discover the quantity and characteristics of such events in Noroviruses. In order to identify recombination events, multiple sequence alignments were assembled from publicly available strains, and were tested using RAT, a recently developed software tool. Strains identified by RAT as putative recombinants were tested further, using a phylogenetic approach, the LARD software, and a Monte Carlo method, to gain additional support for their status. The identification of two previously described recombinants, WUG1 and Snow Mountain, was made. Furthermore, three instances of hitherto unreported recombination implicating Norovirus strains MD 145-12, Gifu'96 and Saitama U4 were found, with good statistical support for the latter two of these cases. Lordsdale-like viruses were highlighted as major contributors to recombination events during Norovirus evolution. Finally, the relevance of recombinants to the worldwide transmission of Norovirus is discussed.

Caliciviridae Infections↗

PubMed2024

A comparison of software for analysis of rare and common short tandem repeat (STR) variation using human genome sequences from clinical and population-based samples.

Short tandem repeat (STR) variation is an often overlooked source of variation between genomes. STRs comprise about 3% of the human genome and are highly polymorphic. Some cause Mendelian disease, and others affect gene expression. Their contribution to common disease is not well-understood, but recent software tools designed to genotype STRs using short read sequencing data will help address this. Here, we compare software that genotypes common STRs and rarer STR expansions genome-wide, with the aim of applying them to population-scale genomes. By using the Genome-In-A-Bottle (GIAB) consortium and 1000 Genomes Project short-read sequencing data, we compare performance in terms of sequence length, depth, computing resources needed, genotyping accuracy and number of STRs genotyped. To ensure broad applicability of our findings, we also measure genotyping performance against a set of genomes from clinical samples with known STR expansions, and a set of STRs commonly used for forensic identification. We find that HipSTR, ExpansionHunter and GangSTR perform well in genotyping common STRs, including the CODIS 13 core STRs used for forensic analysis. GangSTR and ExpansionHunter outperform HipSTR for genotyping call rate and memory usage. ExpansionHunter denovo (EHdn), STRling and GangSTR outperformed STRetch for detecting expanded STRs, and EHdn and STRling used considerably less processor time compared to GangSTR. Analysis on shared genomic sequence data provided by the GIAB consortium allows future performance comparisons of new software approaches on a common set of data, facilitating comparisons and allowing researchers to choose the best software that fulfils their needs.

Humans↗

PubMedDate not supplied

Rigorous, rapid, reliable and qualitative? Computing in qualitative method.

OBJECTIVE: To explore whether qualitative methods are problematic and persuasive in health education research. METHOD: Explored this problem through the 3 goals of rigor, rapidity, and reliability and their special meanings in qualitative analysis. RESULTS: For each, contributions of qualitative computing software are identified and their effects assessed. CONCLUSION: Qualitative researchers are assisted by software tools in pursuit of each of these goals, but in each area there is a need for software design to address the tasks of research where rigor, rapidity, and reliability are paramount requirements.

Australia↗

PubMed2006

Verification of single-peptide protein identifications by the application of complementary database search algorithms.

Data produced from the MudPIT analysis of yeast (S. cerevisiae) and rice (O. sativa) were used to develop a technique to validate single-peptide protein identifications using complementary database search algorithms. This results in a considerable reduction of overall false-positive rates for protein identifications; the overall false discovery rates in yeast are reduced from near 25% to less than 1%, and the false discovery rate of yeast single-peptide protein identifications becomes negligible. This technique can be employed by laboratories utilizing a SEQUEST-based proteomic analysis platform, incorporating the XTandem algorithm as a complementary tool for verification of single-peptide protein identifications. We have achieved this using open-source software, including several data-manipulation software tools developed in our laboratory, which are freely available to download.

Algorithms↗

PubMed2005

ErmineJ: tool for functional analysis of gene expression data sets.

BACKGROUND: It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis uses the hypergeometric distribution (or a related technique) to look for "over-representation" of groups among genes selected as being differentially expressed or otherwise of interest based on a gene-by-gene analysis. However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported. RESULTS: We introduce ErmineJ, a multiplatform user-friendly stand-alone software tool for the analysis of functionally-relevant sets of genes in the context of microarray gene expression data. ErmineJ implements multiple algorithms for gene set analysis, including over-representation and resampling-based methods that focus on gene scores or correlation of gene expression profiles. In addition to a graphical user interface, ErmineJ has a command line interface and an application programming interface that can be used to automate analyses. The graphical user interface includes tools for creating and modifying gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene expression data. ErmineJ comes with a complete user manual, and is open-source software licensed under the Gnu Public License. CONCLUSION: The availability of multiple analysis algorithms, together with a rich feature set and simple graphical interface, should make ErmineJ a useful addition to the biologist's informatics toolbox. ErmineJ is available from http://microarray.cu.genome.org.

Animals↗

PubMed1996

ALBERT: a real-time visual feedback computer tool for professional vocal development.

This paper considers the nature of real-time visual feedback for vocal analysis and development and presents a new software tool, called ALBERT (acoustic and laryngeal biofeedback enhancement in real time), designed for use with those developing their voices professionally. This tool embodies several important issues in the provision of real-time visual feedback, including: (a) support for user-configurable visual displays, (b) the ability to use colour as a complementary or sole medium for the presentation of information, (c) the ability to combine algorithmically any number of vocal parameters to create a new single parameter representative of some aspect of vocal measurement which may be displayed and updated in real time, and (d) a rate of information update which may be altered by the user at any point for the most appropriate use according to the context of the feedback task. Several examples of system use are given, including the real-time display of fundamental frequency, jitter, and larynx closed quotient (CQ) parameters in a variety of visual configurations. Several examples are given relating to developing professional voice users, including the derivation of a new parameter which reflects the measure of progress of subjects along a linear correlation line between CQ and the level of energy in the singer's formant region.

Computers↗

PubMed1999

Technical validation of low-cost videoconferencing systems applied in orthopaedic teleconsulting services.

Investigation on the applicability of low-cost videoconferencing (VC) for health care services is becoming a real need. Reduced resources drive the administrators to evaluate inexpensive solutions for telemedicine. Considering this scenario, this work is a preliminary step to validate, from a technical point of view, if low-cost VC systems could be suitable for orthopaedic teleconsulting services. For this purpose, four different videoconferencing systems were tested. Each VC system was composed of a computer and a VC device installed in. VC devices were chosen among the most popular and distributed products (made by Intel, PictureTel and Aethra). The Telemedicine Benchmark, a specific tool defined by the authors, was applied to measure the overall systems performances in terms of time delays during basic rate ISDN connections (128 Kbit/s). Results showed that it is possible to apply low-cost videoconferencing systems for orthopaedic teleconsulting services. Most of the systems provided acceptable performance for medical image visualization and real time joint working. Further developments are recommendable to enhance the VC software tools capabilities and to improve software-user interface. reserved.

Costs and Cost Analysis↗

PubMed2003

Identification of children with special health care needs within a managed care setting.

OBJECTIVE: To assess 2 established methods of identifying children with special health care needs (CSHCN) within a health plan population for intensified service coordination. METHODS: The tools tested were the Questionnaire for Identifying Children With Chronic Conditions (QuICCC) and the Clinical Risk Grouper (CRG) software. The QuICCC was administered by telephone to the parents of 517 children. The CRG software tool was then applied to the health plan database. The accuracy of identifying the target population was assessed by a single trained reviewer by comparison with the comprehensive medical record. RESULTS: According to the QuICCC, 37.1% of the parents surveyed had CSHCN. According to the CRG, 11% of the health plan's pediatric population was categorized as CSHCN. The medical record review agreed with overall QuICCC findings in 53% to 61% of cases and overall CRG findings in 66% to 73% of cases. CONCLUSIONS: Administering the QuICCC was a time- and labor-intensive endeavor with a relatively low overall level of sensitivity. The CRG was less labor intensive with slightly higher sensitivity. Identifying the target population in an effective and efficient manner remains a challenge for health plans.

Child↗