BioBOSS: a bioprocessing software tool.
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Fermentation↗
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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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Generator program for computer-assisted instruction: MACGEN. A software tool for generating computer-assisted instructional texts.
This publication describes MACGEN, an interactive development tool to assist teachers to create, modify and extend case simulations, tutorial exercises and multiple-choice question tests designed for computer-aided instruction. The menu-driven software provides full authoring facilities for text files in MACAID format by means of interactive editing. Authors are prompted for items which they might want to change whereas all user-independent items are provided automatically. Optional default values and explanatory messages are available with every prompt. Errors are corrected automatically or commented upon. Thus the program eliminates the need to familiarize with a new language or details of the text file structure. The options for modification of existing text files include display, renumbering of frames and a line-oriented editor. The resulting text files can be interpreted by the MACAID driver without further changes. The text file is held as ASCII records and as such is also accessible with many standard word-processing systems if desired.
Computer-Assisted Instruction↗
Computational sequence analysis revisited: new databases, software tools, and the research opportunities they engender.
The increasing quantity and complexity of sequences and structural data for proteins and nucleic acids create both problems and opportunities for biomedical researchers. Fortunately, a new generation of practical computer tools for data analysis and integrated information retrieval is emerging. Recent developments in fast database searching, multiple sequence alignment, and molecular modeling are discussed and windows-based, mouse-driven software for CD-ROM and network information retrieval are described. Each method is illustrated with a practical example pertinent to lipid research. In particular, the connection among cholesteryl ester transfer protein, bactericidal permeability-increasing protein, and lipopolysaccharide-binding proteins is determined; novel repetitive sequence motifs in mammalian farnesyltransferase subunits and related yeast prenyltransferases are derived; biochemical insights from a three-dimensional model of human apolipoprotein D based on two insect lipocalins are discussed; the relationship between apolipoprotein D and gross cystic disease fluid protein from human breast is reviewed; and prospects for modeling apolipoprotein E-related proteins are described. In addition, information on a number of general and special-purpose sequence, motif, and structural databases is included.
Amino Acid Sequence↗
A software tool for the analysis of mass spectrometric disulfide mapping experiments.
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Amino Acid Sequence↗
Multicompartmental modeling of hippocampal pyramidal cells and interneurons with the GENESIS software tool.
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Animals↗
A software tool for fetal blood flow analysis.
Doppler ultrasonography is a widely used technique for determination of the fetal blood flow pattern. Determination of the waveform qualities was done manually, with considerable inter- and intraobserver variations. In order to limit the variations and the time-consuming data entry, a Fetal Blood Flow Analysis software program was developed to facilitate ease of determination of Doppler signals. This article describes the development and unique features of the software program, made specifically to meet the obstetric and gynecology department's needs.
Arteries↗
The effects of text-based and graphics-based software tools on planning and organizing of stories.
This article describes a research study comparing the effects of two computer-based writing tools on the story-writing skills of fourth-through eighth-grade students with language-related learning disabilities. The first tool, the prompted writing feature of FrEdWriter (Rogers, 1985), allowed students to answer story grammar questions, then type stories using those responses as the plan; the second tool, Once Upon a Time (Urban, Rushing, & Star, 1990), allowed students to create graphic scenes, then type stories about those scenes. Nine students attended a series of after-school writing labs twice weekly for 11 weeks, using each tool for half of the writing sessions. Group results did not clearly favor either tool; however, individual differences suggested that use of planning features should be linked to student needs. Students who had less internal organizational ability benefited from the computer-presented story grammar prompts and wrote less mature stories when using the graphics-based tool. Students with relatively strong organizational skills wrote more mature stories with the graphics-based tool.
Achievement↗
Software tools for analysis and visualization of fMRI data.
The tools needed for analysis and visualization of three-dimensional human brain functional magnetic resonance image results are outlined, covering the processing categories of data storage, interactive vs batch mode operations, visualization, spatial normalization (Talairach coordinates, etc.), analysis of functional activation, integration of multiple datasets, and interface standards. One freely available software package is described in some detail. The features and scope that a generally useful and extensible fMRI toolset should have are contrasted with what is available today. The article ends with a discussion of how the fMRI research community can cooperate to create standards and develop software that meets the community's needs.
Brain↗
1999 Joseph E. Whitley, MD, Award. Facilitating the production of digital radiology teaching files with the radiology annotation and publishing system: a software tool for radiology educators.
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Awards and Prizes↗
MTT: a software tool for quality control in sequence assembly.
A large-scale sequencing project requires a tool to control the quality of the input data because a sizable number of trace data may be of low quality. If these data are allowed to enter the sequence assembly pipeline, harm will be done. Hence, it is important to detect such data as soon as possible. MTT (Move-Track-Trim) is a software package analyzing the quality of the lanes. It subjects each lane to a series of tests, and if a lane does not pass all tests, it is flagged as a "bad" lane. The use has a chance to examine both the "good" and the "bad" lanes and reclassify a "bad" lane as "good," or vice versa. Alternatively, the user may decide to retrack the gel or get rid of some lanes altogether. As a by-product of the analysis, MTT performs other useful functions. It trims the lanes and compresses the lane files and moves them to the directories where assembly is carried out. It also generates some useful statistics describing the quality of the gel.
Base Sequence↗
Gamma knife radiosurgery as a primary treatment for prolactinomas.
OBJECT: The purpose of this study was to estimate the efficacy of gamma knife radiosurgery (GKS) in controlling tumor growth and endocrinopathy associated with prolactinomas. METHODS: Between 1993 and 1997, 164 of 469 patients with pituitary adenomas treated by GKS harbored prolactinomas. The dose to the tumor margin ranged from 9 to 35 Gy (mean 31.2 Gy), and the visual pathways were exposed to a dose of less than 10 Gy. The mean tumor diameter was 13.4 mm. The mean follow-up time for 128 cases was 33.2 months (range 6-72 months). Tumor control was observed in all but two patients who underwent surgery 18 and 36 months, respectively, after GKS. Clinical cure was achieved in 67 cases. Clinical improvement was noted with a decrease in the hyperprolactinemia after GKS. Nonetheless, in 31 (29%) of 108 patients who were followed for more than 2 years no improvement in serum prolactin levels was demonstrated, although this could be normalized by bromocriptine administration after treatment. Nine infertile women became pregnant 2 to 13 months after GKS and all gave birth to normal children. There was no visual deterioration related to GKS. Five women experienced premature menopause. In these patients there was subtotal disappearance of the tumor and an empty sella developed. CONCLUSIONS: Gamma knife radiosurgery as a primary treatment for prolactinomas can be safe and effective both for controlling tumor growth and for normalization of prolactin hypersecretion. A higher margin dose (> or = 30 Gy) seemed to be associated with a better clinical outcome. Gamma knife radiosurgery may make prolactinomas more sensitive to the bromocriptine.
Humans↗
A protocol building software tool for medical device quality control tests.
Q-Pro is an application for Quality Control and Inspection of Medical Devices. General system requirements include friendly and comprehensive graphical environment and proper, quick, easy and intuitive user interface. Functions such as, a tool library for protocol design widely used multimedia, as well as, a support of a local database for protocol and inventory data archiving are provided by the system. In order to serve the different categories of users, involved in Quality Control procedures, the system has been split into three modules of different functionality and complexity, each of which can work as a stand-alone application. The implementation of protocols and use of the software functions, as well as, the user interface itself have been proved by the evaluators to be clear and intuitive. The software seems to adapt easily to different kinds of Quality Control procedures and objectives. Q-Pro effectively supports and enhances the processes to attain a highly tuned, professional, responsive and effective quality control and preventive maintenance procedures for biomedical equipment management.
Data Collection↗
A collision prevention software tool for complex three-dimensional isocentric set-ups.
During treatment planning it can be difficult to check whether a particular plan is workable, that is it avoids obstructing treatment beams with parts of the patient couch and it avoids collisions between the treatment machine head and the patient couch. To overcome this problem, the trigonometric relationships between the placement of treatment beams and the patient couch are examined. From these relationships a set of useful equations that can be generally applied is derived. The application of these equations practically as a simple (non-graphical) planning tool is described. The resulting tool enables the feasibility of a plan to be checked during treatment planning, and gives guidance as to how a patient could be repositioned to allow the use of a plan when potential beam obstructions are detected, prior to verification of the treatment on a simulator.
Algorithms↗
GRable Version 1.0: A Software Tool for Site-Specific Glycoform Analysis With Improved MS1-Based Glycopeptide Detection With Parallel Clustering and Confidence Evaluation With MS2 Information.
High-throughput intact glycopeptide analysis is crucial for elucidating the physiological and pathological status of the glycans attached to each glycoprotein. Mass spectrometry-based glycoproteomic methods are challenging because of the diversity and heterogeneity of glycan structures. Therefore, we developed an MS1-based site-specific glycoform analysis method named "Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile (Glyco-RIDGE)" for a more comprehensive analysis. This method detects glycopeptide signals as a cluster based on the mass and chromatographic properties of glycopeptides and then searches for each combination of core peptides and glycan compositions by matching their mass and retention time differences. Here, we developed a novel browser-based software named GRable for semi-automated Glyco-RIDGE analysis with significant improvements in glycopeptide detection algorithms, including "parallel clustering." This unique function improved the comprehensiveness of glycopeptide detection and allowed the analysis to focus on specific glycan structures, such as pauci-mannose. The other notable improvement is evaluating the "confidence level" of the GRable results, especially using MS2 information. This function facilitated reduced misassignment of the core peptide and glycan composition and improved the interpretation of the results. Additional improved points of the algorithms are "correction function" for accurate monoisotopic peak picking; one-to-one correspondence of clusters and core peptides even for multiply sialylated glycopeptides; and "inter-cluster analysis" function for understanding the reason for detected but unmatched clusters. The significance of these improvements was demonstrated using purified and crude glycoprotein samples, showing that GRable allowed site-specific glycoform analysis of intact sialylated glycoproteins on a large-scale and in-depth. Therefore, this software will help us analyze the status and changes in glycans to obtain biological and clinical insights into protein glycosylation by complementing the comprehensiveness of MS2-based glycoproteomics. GRable can be freely run online using a web browser via the GlyCosmos Portal (https://glycosmos.org/grable).
Glycopeptides↗
Development of software tools at BioInformatics Centre (BIC) at the National University of Singapore (NUS).
There is burgeoning volume of information and data arising from the rapid research and unprecedented progress in molecular biology. This has been particularly affected by the Human Genome Project which is trying to completely sequence three billion nucleotides of the human genome (1),(1a). Other genome sequencing projects are also contributing substantially to this exponential growth in the number of DNA nucleotides and proteins sequenced. The number of journals, reports and research papers and tools required for the analysis of these sequences has also increased. For this the life sciences today needs tools in information technology and computation to prevent degeneration of this data into an inchoate accretion of unconnected facts and figures. The recently formed BioInformatics Centre (BIC) at the National University of Singapore (NUS) provides access to various commonly used computational tools available over the World Wide Web (WWW)--using a uniform interface and easy access. We have also come up with a new database tool. BioKleisli, which allows you to interact with various geographically scattered, heterogeneous, structurally complex and constantly evolving data sources. This paper summarises the importance of network access and database integration to biomedical research and gives a glimpse of current research conducted at BIC.
Animals↗
0j.py: a software tool for low complexity proteins and protein domains.
Low complexity proteins and protein domains have sequences which appear highly non-random. Over the years, these sequences have been routinely filtered out during sequence similarity searches because interest has been focused on globular proteins, and inclusion of these domains can severely skew search results. However, early work on these proteins and more recent studies of the related area of repeated protein sequences suggests that low complexity protein domains have function and therefore are in need of further investigation. 0j.py is a new tool for demarcating low complexity protein domains more accurately than has been possible to date. The paper describes 0j.py and its use in revealing proteins with repeated and poly-amino-acid peptides. Statistical methods are then employed to to examine the distribution of these proteins across species, while keyword clustering is used to suggest roles performed by proteins through the use of low complexity domains.
Algorithms↗
New software tools ease move to electronic medical records.
Converting a hospital to electronic medical records can save big bucks, but it's easier said than done. Huge savings await hospitals that eliminate the cost of storing, filing and retrieving charts. But making that move is more complex than simply converting written notes to an automated format. Learn how one California hospital is embarking on its journey to a paperless environment with the help of some innovative information systems technology that will take some of the pain out of the transformation.
Abstracting and Indexing↗
Software tools for motif and pattern scanning: program descriptions including a universal sequence reading algorithm.
Two programs, MOTIF and PATTERN, that scan sequences for matches to user-defined motifs and patterns of motifs based on identity and set membership are described. The programs use a simple and logical notation to define motifs, and may be used either interactively or by using command line parameters (suitable for batch processing). The two programs described also incorporate a simple, yet reliable, algorithm that automatically detects in which of six possible formats the sequence entry is written.
Algorithms↗