Computing chemistry on the web.
The development of on-line software tools is changing the way we traditionally perform our analysis in drug design, but will chemoinformatics be forever behind bioinformatics in this development?
Computer Simulation↗
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Results for “software tools”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
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REPuter: fast computation of maximal repeats in complete genomes.
SUMMARY: A software tool was implemented that computes exact repeats and palindromes in entire genomes very efficiently. AVAILABILITY: Via the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rep uter/).
DNA↗
FUSE-PhyloTree: linking functions and sequence conservation modules of a protein family through phylogenomic analysis.
SUMMARY: FUSE-PhyloTree is a phylogenomic analysis software for identifying local sequence conservation associated with the different functions of a multi-functional (e.g. paralogous or multi-domain) protein family. FUSE-PhyloTree introduces an original approach that combines advanced sequence analysis with phylogenetic methods. First, local sequence conservation modules within the family are identified using partial local multiple sequence alignment. Next, the evolution of the detected modules and known protein functions is inferred within the family's phylogenetic tree using three-level phylogenetic reconciliation and ancestral state reconstruction. As a result, FUSE-PhyloTree provides a gene tree annotated with both predicted sequence modules and ancestral gene functions, enabling the association of functions with specific sequence regions based on their co-emergence. AVAILABILITY AND IMPLEMENTATION: FUSE-PhyloTree is provided as Docker and Singularity images including all the required software tools. Images, source code, test data, and documentation are available at https://github.com/OcMalde/fuse-phylotree and https://zenodo.org/records/15855068.
Phylogeny↗
MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers.
BACKGROUND: Various software tools are available for the display of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website. However, these approaches are limited in their use of data from multiallelic markers and provide limited information in a graphical form. RESULTS: We have developed a software package (MIDAS - Multiallelic Interallelic Disequilibrium Analysis Software) for the estimation and graphical display of interallelic linkage disequilibrium. Linkage disequilibrium is analysed for each allelic combination (of one allele from each of two loci), between all pairwise combinations of any type of multiallelic loci in a contig (or any set) of many loci (including single nucleotide polymorphisms, microsatellites, minisatellites and haplotypes). Data are presented graphically in a novel and informative way, and can also be exported in tabular form for other analyses. This approach facilitates visualisation of patterns of linkage disequilibrium across genomic regions, analysis of the relationships between different alleles of multiallelic markers and inferences about patterns of evolution and selection. CONCLUSION: MIDAS is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers.
Algorithms↗
Informatics and quantitative analysis in biological imaging.
Biological imaging is now a quantitative technique for probing cellular structure and dynamics and is increasingly used for cell-based screens. However, the bioinformatics tools required for hypothesis-driven analysis of digital images are still immature. We are developing the Open Microscopy Environment (OME) as an informatics solution for the storage and analysis of optical microscope image data. OME aims to automate image analysis, modeling, and mining of large sets of images and specifies a flexible data model, a relational database, and an XML-encoded file standard that is usable by potentially any software tool. With this design, OME provides a first step toward biological image informatics.
Algorithms↗
Improved quality data systems through the use of standard electronic data deliverables (EDDs) and environmental data assessment software.
One of the challenges facing professionals in the environmental arena today is the collection and assessment of large amounts of environmental analytical data. The assessment of the quality of that data is essential as multi-million dollar decisions for environmental site cleanups and/or long term monitoring efforts are made based on the analytical results. Also critical to environmental programs is the sharing and access of data across multiple data users. The ability to share data allows for better use of the limited resources available to clean up and monitor contaminated environmental sites. Standardization of electronic deliverables allows for collection of data from multiple data collectors into a single database for use by numerous data users and stakeholders on a project. This paper discusses the benefits of using a standard EDD deliverable format and use of environmental data assessment software tools to do project planning and data assessment throughout the duration of the environmental project.
Database Management Systems↗
Computer-based approaches for maxillofacial interventions.
Computers used as supporting tools for diagnostics, operation planning and therapy are of increasing relevance in surgery. Rapid progress in imaging techniques such as computed tomography (CT), magnetic resonance imaging (MRT) and ultrasound already allows to represent anatomical and physiological conditions with maximal authenticity. In order to simulate complex surgeries we must develop ergonomic and intuitively useable software tools, thus enabling a precise and fast virtual execution of the planned surgical intervention preoperatively. Intraoperative support will consist of passive navigation tools, available already today, supporting the intraoperative orientation and, in the future, robots performing specific steps autonomously. Methods of augmented reality for the interaction of virtual objects and the real surgical scene are also suitable for the visualization of planning data and other medically relevant information in the operation situs . In maxillofacial and craniofacial surgery the techniques mentioned have been applied in all fields from dental implantology up to the correction of craniofacial malformations and the resection of skull base tumors. Many applications are still being developed or are still in the form of a prototype. However, it is already clear that developments in this area will have a considerable effect on a surgeon's routine work.
Journal Article↗
Complete genome sequence and genomic characterization of the probiotic Limosilactobacillus reuteri PSC102.
BACKGROUND: Gut microbiota are potential sources of probiotics and play an essential role in maintaining intestinal health. Limosilactobacillus reuteri PSC102 (L. reuteri PSC102), which was isolated from the feces of healthy pigs, exhibited health-beneficial properties. AIM: We aimed to conduct a whole-genome sequencing analysis of L. reuteri PSC102 to determine its molecular characteristics as a probiotic strain. METHODS: Limosilactobacillus reuteri PSC102 cells were cultured in De Man-Rogosa-Sharpe medium, followed by DNA extraction for genomic analysis using the PacBio-Illumina sequencing platform. The EzBioCloud software was used to perform gene assembly, and the genes were interpreted by the National Center for Biotechnology Information (NCBI) and the Glimmer program. Core and pan-genomic analyses were performed to assess the extent of functional conservation in the genomic sequence. Moreover, the NCBI database and the Basic Local Alignment Search Tool software were used to identify antimicrobial resistance genes and virulence factors. RESULTS: Limosilactobacillus reuteri PSC102 consists of a single circular chromosome with 2,048,626 bp, a guanine- cytosine of 38.9%, 18 rRNA genes, and 69 tRNA genes. Among the 1,846 protein-coding sequences, genes associated with probiotic characteristics were identified, including genes involved in host-microbe interactions, stress tolerance, biogenesis, and defense mechanisms. Furthermore, the genome of L. reuteri PSC102 comprises 2,446 pan-genome and 1,222 core-genome orthologous gene clusters. A total of 74 unique genes were identified in L. reuteri PSC102 genome. These genes mostly encode proteins potentially involved in the transport and metabolism of amino acids and carbohydrates. Moreover, antibacterial resistance genes and virulence factors were absent in L. reuteri PSC102. CONCLUSION: The results of the molecular insight into L. reuteri PSC102 corroborates its use as a probiotic in humans and other animals.
Limosilactobacillus reuteri↗
Data mining for regulatory elements in yeast genome.
We have examined methods and developed a general software tool for finding and analyzing combinations of transcription factor binding sites that occur relatively often in gene upstream regions (putative promoter regions) in the yeast genome. Such frequently occurring combinations may be essential parts of possible promoter classes. The regions upstream to all genes were first isolated from the yeast genome database MIPS using the information in the annotation files of the database. The ones that do not overlap with coding regions were chosen for further studies. Next, all occurrences of the yeast transcription factor binding sites, as given in the IMD database, were located in the genome and in the selected regions in particular. Finally, by using a general purpose data mining software in combination with our own software, which parametrizes the search, we can find the combinations of binding sites that occur in the upstream regions more frequently than would be expected on the basis of the frequency of individual sites. The procedure also finds so-called association rules present in such combinations. The developed tool is available for use through the WWW.
Binding Sites↗
Multidimensional analysis: a management tool for monitoring HIPAA compliance and departmental performance.
Most RIS and PACS systems include extensive auditing capabilities as part of their security model, but inspecting those audit logs to obtain useful information can be a daunting task. Manual analysis of audit trails, though cumbersome, is often resorted to because of the difficulty to construct queries to extract complex information from the audit logs. The approach proposed by the authors uses standard off-the-shelf multidimensional analysis software tools to assist the PACS/RIS administrator and/or security officer in analyzing those audit logs to identify and scrutinize suspicious events. Large amounts of data can be quickly reviewed and graphical analysis tools help explore system utilization. While additional efforts are required to fully satisfy the demands of the ever-increasing security and confidentiality pressures, multidimensional analysis tools are a practical step toward actually using the information that is already being captured in the systems' audit logs. In addition, once the work is performed to capture and manipulate the audit logs into a viable format for the multidimensional analysis tool, it is relatively easy to extend the system to incorporate other pertinent data, thereby enabling the ongoing analysis of other aspects of the department's workflow.
Computer Security↗
W3MCSim: an online and reconfigurable Monte Carlo simulator for interactive probabilistic/statistical modeling.
We have implemented a Monte Carlo simulator (W3MCSim) as an Internet software tool, primarily for interactive use by students, educators, life and other physical scientists, as well as other practitioners of probabilistic and statistical modeling. Interested users download, install and run W3MCSim by visiting the application website. This application incorporates three freely available Microsoft web technologies, namely the Internet Explorer web browser, the Component Object Model software framework and the JScript web page script interpreter. We define the software architecture here, as a web application model, and show how incorporation of these technologies provides an efficient solution to W3MCSim software deployment. We demonstrate the usability and versatility of this simulator with three distinct tutorial examples: simulating the sum of six-sided dice, estimating intersection frequency in "Buffon's needle problem", and testing an animal experiment design model a priori. We also show how the program components can be reconfigured into other programs.
Computer Simulation↗
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs.
MOTIVATION: Variant call format (VCF) files are the standard output format for various software tools that identify genetic variation from DNA sequencing experiments. Downstream analyses require the ability to query, filter, and modify them simply and efficiently. Several tools are available to perform these operations from the command line, including BCFTools, vembrane, slivar, and others. RESULTS: Here, we introduce vcfexpress, a new, high-performance toolset for the analysis of VCF files, written in the Rust programming language. It is nearly as fast as BCFTools, but adds functionality to execute user expressions in the lua programming language for precise filtering and reporting of variants from a VCF or BCF file. We demonstrate performance and flexibility by comparing vcfexpress to other tools using the vembrane benchmark. AVAILABILITY AND IMPLEMENTATION: vcfexpress is available under the MIT license at https://github.com/brentp/vcfexpress with code used for the manuscript deposited in https://doi.org/10.5281/zenodo.14756838.
Software↗
Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis.
MOTIVATION: Metabolic flux analysis of biochemical reaction networks using isotope tracers requires software tools that can analyze the dynamics of isotopic isomer (isotopomer) accumulation in metabolites and reveal the underlying kinetic mechanisms of metabolism regulation. Since existing tools are restricted by the isotopic steady state and remain disconnected from the underlying kinetic mechanisms, we have recently developed a novel approach for the analysis of tracer-based metabolomic data that meets these requirements. The present contribution describes the last step of this development: implementation of (i) the algorithms for the determination of the kinetic parameters and respective metabolic fluxes consistent with the experimental data and (ii) statistical analysis of both fluxes and parameters, thereby lending it a practical application. RESULTS: The C++ applications package for dynamic isotopomer distribution data analysis was supplemented by (i) five distinct methods for resolving a large system of differential equations; (ii) the 'simulated annealing' algorithm adopted to estimate the set of parameters and metabolic fluxes, which corresponds to the global minimum of the difference between the computed and measured isotopomer distributions; and (iii) the algorithms for statistical analysis of the estimated parameters and fluxes, which use the covariance matrix evaluation, as well as Monte Carlo simulations. An example of using this tool for the analysis of (13)C distribution in the metabolites of glucose degradation pathways has demonstrated the evaluation of optimal set of parameters and fluxes consistent with the experimental pattern, their range and statistical significance, and also the advantages of using dynamic rather than the usual steady-state method of analysis. AVAILABILITY: Software is available free from http://www.bq.ub.es/bioqint/selivanov.htm
Algorithms↗
WebaCGH: an interactive online tool for the analysis and display of array comparative genomic hybridisation data.
UNLABELLED: Gene copy number variations occur both in normal cells and in numerous pathologies including cancer and developmental diseases. Array comparative genomic hybridisation (aCGH) is an emerging technology that allows detection of chromosomal gains and losses in a high-resolution format. When aCGH is performed on cDNA and oligonucleotide microarrays, the impact of DNA copy number on gene transcription profiles may be directly compared. We have created an online software tool, WebaCGH, that functions to (i) upload aCGH and gene transcription results from multiple experiments; (ii) identify significant aberrant regions using a local Z-score threshold in user-selected chromosomal segments subjected to smoothing with moving averages; and (iii) display results in a graphical format with full genome and individual chromosome views. In the individual chromosome display, data can be zoomed in/out in both dimensions (i.e. ratio and physical location) and plotted features can have 'mouse over' linking to outside databases to identify loci of interest. Uploaded data can be stored indefinitely for subsequent retrieval and analysis. WebaCGH was created as a Java-based web application using the open-source database MySQL. AVAILABILITY: WebaCGH is freely accessible at http://129.43.22.27/WebaCGH/welcome.htm CONTACT: Xiaolin Wu (forestwu@mail.nih.gov) or Ulises Urzúa (uurzua@med.uchile.cl).
Animals↗
1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis.
Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for disease-gene discovery in cancer and developmental disorders as well as numerous other applications. However, widespread utilization of a CGH has been limited by the lack of well characterized, high-resolution clone sets optimized for consistent performance in aCGH assays and specifically designed analytic software. We have assembled a set of approximately 4100 publicly available human bacterial artificial chromosome (BAC) clones evenly spaced at approximately 1-Mb resolution across the genome, which includes direct coverage of approximately 400 known cancer genes. This aCGH-optimized clone set was compiled from five existing sets, experimentally refined, and supplemented for higher resolution and enhancing mapping capabilities. This clone set is associated with a public online resource containing detailed clone mapping data, protocols for the construction and use of arrays, and a suite of analytical software tools designed specifically for aCGH analysis. These resources should greatly facilitate the use of aCGH in gene discovery.
Cell Line, Tumor↗
A Step-by-Step Guide to Sequencing and Assembly of Complete Bacterial Genomes Using the Oxford Nanopore MinION.
The Oxford Nanopore (ONT) MinION enables sequencing of longer DNA/RNA fragments compared to other sequencers, such as Illumina, etc. This nanopore method provides distinct advantages for generating complete genome assemblies from microorganisms. Specifically, the R9.4 flow cells used for MinION sequencing have much lower error rates compared with earlier versions of the ONT platform. Coupled with base calling using Dorado software, higher-quality long reads can now be generated for complete bacterial genome assembly. In this chapter, we describe a detailed MinION method to assemble a complete genome from a microorganism, polish the final assembly, and evaluate the genome quality using various software tools. Because of the low cost for MinION sequencing, this platform could be an asset for virtually any laboratory interested in generating complete genomes from microorganisms.
Genome, Bacterial↗
A primer of ophthalmic computer graphics.
Computer graphics offers an unprecedented opportunity to probe new and old ideas in vision testing, without going to the expense of building dedicated equipment. However, the large variety of computer hardware is bewildering and only occasionally can commercial software tools be used. This mini review of the basic principles of computer graphics on personal computers is intended to help the newcomer to the field.
Computer Graphics↗
Rapid prototyping of interactive software for automated instrumentation in rehabilitative therapy.
Rapid prototyping is a quick, efficient way to evaluate new electrical instruments. A hardware interface between a computer and an instrument can be simulated in software. The authors demonstrate the technique of rapid prototyping by developing interfaces for two therapeutic strength-testing devices and an electromagnetic tracker/digitizer. The LabVIEW rapid prototyping software tool was used to create "virtual instruments," which combine to form interfaces. The functions and connections of each virtual instrument are described.
Equipment Design↗