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At least 847 records · Page 47Linked to original sources
PubMed1994

BUILD: a program generator for modelling experimental biological data.

BUILD is a program generator acting at source code level. The generated code corresponds to a whole application in order to model a biological process of interest using an iterative adjustment of experimental data. The program is designed to be executed in command line mode for processing of multiple data files with an individual execution control for each file. The results are completed by modular statistical and graphical functions. This approach has been shown to reduce the time and the amount of work needed for program development, debugging and maintenance. To date, BUILD has been successfully used in mathematical analysis of phenomenological approaches, but other fields of activity, such as educational software, are also conceivable.

Algorithms↗
PubMed2000

Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions.

UNLABELLED: This paper examines a new technique for the visualization of and the interaction with trees, objects frequently used to convey hierarchical relationships in biological data. Motivated by the quality of 2D tree interaction, we adapt the planar tree-of-life metaphor to a virtual, semi-immersive 3D environment. A 3D environment extends the utility of this metaphor by allowing the user to view an entire data set in a single screen. Interrogation of the tree is implemented using 3D input devices. This real-time interrogation of the tree itself provides a quick means by which to qualitatively analyse the hierarchical data. In this paper, we describe the techniques underlying the implementation of such an environment. We conclude by considering the utility of tree metaphors as a basis for the representation of highly dimensional data sets. AVAILABILITY: Arbor3D (source code, a binary executable for SGI IRIX 6.4, Perl parsers, and sample Newick data files) are available via the Internet (http://xian.tamu.edu/Arbor3D/). Arbor3D can be displayed in "CAVE simulator" mode on an SGI workstation screen, or as an interactive virtual environment on a projection workbench. CONTACT: druths@rice.edu; echen@cs.rice.edu; leland@xian.tamu.edu

Classification↗
PubMed2001

MRBAYES: Bayesian inference of phylogenetic trees.

SUMMARY: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. AVAILABILITY: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.

Algorithms↗
PubMed1986

IBM microcomputer programs that analyze DNA sequences for tRNA genes.

A set of four computer programs that search DNA sequence data files for transfer RNA genes have been written in IBM (Microsoft) BASIC for the IBM personal computer. These programs locate and plot predicted secondary structures of tRNA genes in the cloverleaf conformation. The set of programs are applicable to eukaryotic tRNA genes, including those containing intervening sequences, and to prokaryotic and mitochondrial tRNA genes. In addition, two of the programs search up to 150 residues downstream of tRNA gene sequences for possible eukaryotic RNA polymerase III termination sites comprised of at least four consecutive T residues. Molecular biologists studying a variety of gene sequence and flanking regions can use these programs to search for the additional presence of tRNA genes. Furthermore, investigators studying tRNA gene structure-to-function relationships would not need to do extensive restriction mapping to locate tRNA gene sequences within their cloned DNA fragments.

Algorithms↗
PubMed1986

SEQGEL: a versatile and comfortable DNA editor which supports a special keyboard and a speech synthesizer.

A DNA editor for an Apple II is described which contains many additional functions apart from just editing sequences. The data files are normal ASCII text or binary files and can thus be used easily by other programs. The program supports a special keyboard which greatly facilitates typing of DNA sequences. Furthermore a speech synthesizer is supported by the editor. The speech feedback, together with the special keyboard, reduces typing errors to a minimum.

Base Sequence↗
PubMed1989

SDSE: a software package to simulate the evolution of a pair of DNA sequences.

An algorithm to simulate DNA sequence evolution under a general stochastic model, including as particular cases all the previously used schemes of nucleotide substitution, is described. The stimulation is carried out on finite, variable length, DNA sequences through a strict stochastic process, according to the particular substitution rates imposed by each scheme. Five FORTRAN programs, running on an IBM PC and compatibles, carry out all the tasks needed for the simulation. They are menu driven and interfaced to the system through a principal menu. All sequence data files used and generated by the SDSE package conform to the standard GenBank database format, thus allowing the use of any sequence retrieved from this databank, as well as the application of other packages to analyse, manipulate or retrieve stimulated sequences.

Algorithms↗
PubMed1993

GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems.

GEPASI is a software system for modelling chemical and biochemical reaction networks on computers running Microsoft Windows. For any system of up to 45 metabolites and 45 reactions, each with any user-defined or one of 35 predefined rate equations, one can produce trajectories of the metabolite concentrations and obtain a steady state (if it does exist). When steady-state solutions are produced, elasticity and control coefficients, as defined in metabolic control analysis, are calculated. GEPASI also allows the automatic generation of a sequence of simulations with different combinations of parameter values, effectively scanning a hyper-solid in parameter space. Together with the ability to produce user-defined columnar data files, these features allow for both very quick and systematic study of biochemical pathway models. The source code (in C) is available on request from the author, and while the user interface is dependent on having MS-Windows as the operating system, the numerical part is portable to other operating systems. GEPASI is suitable both for research and educational purposes. Although GEPASI was written with biochemical pathways in mind, it can equally be used to stimulate other dynamical systems.

Algorithms↗
PubMed2026

igv-reports: embedding interactive genomic visualizations in HTML reports to aid variant review.

SUMMARY: We present igv-reports, a command-line tool to create standalone HTML pages embedding interactive genomic visualizations of read alignments and associated annotations to support variant inspection workflows. The reports contain all data and code required for visualization of the variant sites, with no dependencies on the input data files. AVAILABILITY AND IMPLEMENTATION: igv-reports is a command-line application written in Python. It is freely available at https://github.com/igvteam/igv-reports under an MIT license.

Software↗
PubMed2026

Using cancer profiles to identify synthetic lethal therapeutic targets and predictive biomarkers in cancer gene dependency data.

MOTIVATION: Large scale loss-of-function screens utilising CRISPR or siRNA can provide profound insights into the importance of individual genes for the survival of a cancer cell and can drive the identification of therapeutic targets and biomarkers, and the development of targeted drugs. However, the analysis of these data and the substantial bodies of metadata that relate to them, is technically challenging and typically requires substantial expertise in data science and computer coding. RESULTS: To facilitate the analysis of cancer gene dependency data by cancer biologists and clinical scientists, we have developed DepMine-a computational toolkit providing a powerful system for framing complex queries relating cancer gene dependency to the underlying genetic changes that occur in cancer cells. DepMine identifies synthetic lethal relationships between putative target genes and complex 'cancer profiles' built from user-specified combinations of mutations, copy-number variation, and expression levels, and can refine these to optimal biomarker definitions for target dependency. AVAILABILITY: The Python implementation of DepMine and associated data files can be obtained at https://github.com/UOSbioinformaticslab/depmine and is free to academics and Not-For-Profit organisations. The DepMine release referenced in this paper is archived as DOI: 10.5281/zenodo.19570601.

Humans↗
PubMed2003

Talisman--rapid application development for the grid.

In order to make use of the emerging grid and network services offered by various institutes and mandated by many current research projects, some kind of user accessible client is required. In contrast with attempts to build generic workbenches, Talisman is designed to allow a bioinformatics expert to rapidly build custom applications, immediately visible using standard web technology, for users who wish to concentrate on the biology of their problem rather than the informatics aspects. As a component of the MyGrid project, it is intended to allow access to arbitrary resources, including but not limited to relational, object and flat file data sources, analysis programs and grid based storage, tracking and distributed annotation systems.

Computational Biology↗
PubMed2003

TSGDB: a database system for tumor suppressor genes.

UNLABELLED: A Web-based database system was constructed and implemented that contains 174 tumor suppressor genes. The database homepage was created to accommodate these genes in a pull-down window so that each gene can be viewed individually in a separate Web page. Information displayed on each page includes gene name, aliases, source organism, chromosome location, expression cells/tissues, gene structure, protein size, gene functions and major reference sources. Queries to the database can be conducted through a user-friendly interface, and query results are returned in the HTML format on dynamically generated web pages. AVAILABILITY: The database is available at http://www.cise.ufl.edu/~yy1/HTML-TSGDB/Homepage.html (data files also at http://www.patcar.org/Databases/Tumor_Suppressor_Genes)

Abstracting and Indexing↗
PubMed2004

HMMGEP: clustering gene expression data using hidden Markov models.

SUMMARY: The package HMMGEP performs cluster analysis on gene expression data using hidden Markov models. AVAILABILITY: HMMGEP, including the source code, documentation and sample data files, is available at http://www.bioinfo.tsinghua.edu.cn:8080/~rich/hmmgep_download/index.html.

Algorithms↗
PubMed2005

Mtreemix: a software package for learning and using mixture models of mutagenetic trees.

SUMMARY: Mixture models of mutagenetic trees constitute a class of probabilistic models for describing evolutionary processes that are characterized by the accumulation of permanent genetic changes. They have been applied to model the accumulation of chromosomal gains and losses in tumor development and the development of drug resistance-associated mutations in the HIV genome.Mtreemix is a software package for estimating mutagenetic trees mixture models from observed cross-sectional data and for using these models for predictions. We provide programs for model fitting, model selection, simulation, likelihood computation and waiting time estimation. AVAILABILITY: Mtreemix, including source code, documentation, sample data files and precompiled Solaris and Linux binaries, is freely available for non-commercial users at http://mtreemix.bioinf.mpi-sb.mpg.de/

Algorithms↗
PubMed2005

CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays.

SUMMARY: To increase compatibility between different generations of Affymetrix GeneChip arrays, we propose a method of filtering probes based on their sequences. Our method is implemented as a web-based service for downloading necessary materials for converting the raw data files (*.CEL) for comparative analysis. The user can specify the appropriate level of filtering by setting the criteria for the minimum overlap length between probe sequences and the minimum number of usable probe pairs per probe set. Our website supports a within-species comparison for human and mouse GeneChip arrays. AVAILABILITY: http://www.crosschip.org

Algorithms↗
PubMed2005

Nexplorer: phylogeny-based exploration of sequence family data.

SUMMARY: Nexplorer is a web-based program for interactive browsing and manipulation of character data in NEXUS format, well suited for use with alignments and trees representing families of homologous genes or proteins. Users may upload a sequence family dataset, or choose from one of several thousand already available. Nexplorer provides a flexible means to develop customized views that combine a tree and a data matrix or alignment, to create subsets of data, and to output data files or publication-quality graphics. AVAILABILITY: Web access is from http://www.molevol.org/nexplorer

Animals↗
PubMed2006

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach.

MOTIVATION: New developments in post-genomic technology now provide researchers with the data necessary to study regulatory processes in a holistic fashion at multiple levels of biological organization. One of the major challenges for the biologist is to integrate and interpret these vast data resources to gain a greater understanding of the structure and function of the molecular processes that mediate adaptive and cell cycle driven changes in gene expression. In order to achieve this biologists require new tools and techniques to allow pathway related data to be modelled and analysed as network structures, providing valuable insights which can then be validated and investigated in the laboratory. RESULTS: We propose a new technique for constructing and analysing qualitative models of genetic regulatory networks based on the Petri net formalism. We take as our starting point the Boolean network approach of treating genes as binary switches and develop a new Petri net model which uses logic minimization to automate the construction of compact qualitative models. Our approach addresses the shortcomings of Boolean networks by providing access to the wide range of existing Petri net analysis techniques and by using non-determinism to cope with incomplete and inconsistent data. The ideas we present are illustrated by a case study in which the genetic regulatory network controlling sporulation in the bacterium Bacillus subtilis is modelled and analysed. AVAILABILITY: The Petri net model construction tool and the data files for the B. subtilis sporulation case study are available at http://bioinf.ncl.ac.uk/gnapn.

Algorithms↗
PubMed1984

Effects of coronary artery disease on the aging heart: observations from cardiac catheterization.

We evaluated catheterization laboratory data from 691 individuals (219 normals and 472 coronary patients) using a computerized data file that provided several measures of cardiovascular performance in 10-year age increments. The expected increase in arterial pressure with age was noted in normals and coronary patients. Left ventricular end diastolic pressure, end diastolic volume, and end systolic volume remained constant with age but were higher in all age groups in the coronary patients. Ejection fraction showed no change with age but was lower in all age groups in patients with coronary disease. Left ventricular mass increased with age in normals and coronary patients. Cardiac index declined with age, whereas arteriovenous oxygen difference and oxygen consumption were unchanged. Age-related changes in the circulation were for the most part unaffected by the presence of coronary disease. Resting left ventricular function was not altered by age but coronary disease produced a decline in left ventricular function in all ages.

Adolescent↗
PubMed1988

Completeness of cancer registration in Denmark 1943-1966 and efficacy of record linkage procedures.

The completeness of registration in the national, population based cancer registry in Denmark was evaluated for the first 23 years (1943-1966) of operation. The registry was linked to a complementary data file on 5674 Danish invasive cervical cancer patients enrolled in an international, clinical follow-up study on the basis of identifying information including name, month and year of birth and date of cervical cancer diagnosis. The cancer register had a deficit of 2.2% (95% confidence interval, 1.8-2.6) cervical cancer patients; this figure is low compared to those of other cancer registers. Some 80% of the identified cases were retrieved by computerized matching alone, and an additional 15% were identified by combining computerized and visual matching procedures. Scrutiny of non-retrieved case records revealed that major errors in the identifiers of the cohort used for linkage were responsible for inability to identify an additional 1.7%. The presents study underlines the importance of meticulously recorded, high quality key identifiers in registers, and linkage of cohorts to establish the presence or absence of disease.

Denmark↗