Biomechanical stresses in computer-aided design and in data entry.
(9/48)
A study of the risk factors of musculoskeletal disorders (MSDs) of the upper limbs was carried out on 2 populations, 1 performing a computer-aided design (CAD) task and the other performing a data entry task. A questionnaire on MSD complaints and working life was completed by a sample of each population. Biomechanical measurements of the forces, the angles, and the repetitiveness of movements of the upper limbs were carried out on some operators in each sample. It emerged that complaints of the upper limbs seem to be linked to the use of input devices. The grip forces exerted when using the keyboard and mouse were higher in CAD than in data entry. (+info)
Finishing, i.e. gap closure and editing, is the most time-consuming part of genome sequencing. Repeated sequences together with sequencing errors complicate the assembly and often result in misassemblies that are difficult to correct. Repeat Discrepancy Tagger (ReDiT) is a tool designed to aid in the finishing step. This software processes assembly results produced by any fragment assembly program that outputs ace files. The input sequences are analyzed to determine possible differences between repeated sequences. The output is written as tags in an ace file that can be viewed by, e.g. the Consed sequence editor. AVAILABILITY: The ReDiT program is freely available at http://web.cgb.ki.se/redit (+info)
CAAT-Box, Contigs-Assembly and Annotation Tool-Box for genome sequencing projects.
(11/48)
MOTIVATION: Contigs-Assembly and Annotation Tool-Box (CAAT-Box) is a software package developed for the computational part of a genome project where the sequence is obtained by a shotgun strategy. CAAT-Box contains new tools to predict links between contigs by using similarity searches with other whole genome sequences. Most importantly, it allows annotation of a genome to commence during the finishing phase using a gene-oriented strategy. For this purpose, CAAT-Box creates an Individual Protein file (IPF) for each ORF of an assembly. The nucleotide sequence reported in an IPF corresponds to the sequence of the ORF with 500 additional bases before the ORF and 200 bases after. For annotation, additional information like Blast results can be added or linked to the IPFs as well as automatic and/or manual annotations. When a new assembly is performed, CAAT-Box creates new IPFs according to the old IPF panel. CAAT-Box recognizes the modified IPFs which are the only ones used for a new automatic analysis after each assembly. Using this strategy, the user works with a group of IPFs independently of the closure phase progression. The IPFs are accessible by a web server and can therefore be modified and commented by different groups. RESULT: CAAT-Box was used to obtain and to annotate several complete genomes like Listeria monocytogenes or Streptococcus agalactiae. AVAILABILITY: The program may be obtained from the authors and is freely available to non-profit organisations. (+info)
A frequency-based technique to improve the spelling suggestion rank in medical queries.
(12/48)
OBJECTIVE: There is an abundance of health-related information online, and millions of consumers search for such information. Spell checking is of crucial importance in returning pertinent results, so the authors propose a technique for increasing the effectiveness of spell-checking tools used for health-related information retrieval. DESIGN: A sample of incorrectly spelled medical terms was submitted to two different spell-checking tools, and the resulting suggestions, derived under two different dictionary configurations, were re-sorted according to how frequently each term appeared in log data from a medical search engine. MEASUREMENTS: Univariable analysis was carried out to assess the effect of each factor (spell-checking tool, dictionary type, re-sort, or no re-sort) on the probability of success. The factors that were statistically significant in the univariable analysis were then used in multivariable analysis to evaluate the independent effect of each of the factors. RESULTS: The re-sorted suggestions proved to be significantly more accurate than the original list returned by the spell-checking tool. The odds of finding the correct suggestion in the number one rank were increased by 63% after re-sorting using the authors' method. This effect was independent of both the dictionary and the spell-checking tools that were used. CONCLUSION: Using knowledge about the frequency of a given word's occurrence in the medical domain can significantly improve spelling correction for medical queries. (+info)
Improving the quality of emergency department documentation using the voice-activated word processor: interim results.
(13/48)
We examined whether voice-activated word processors provide an acceptable means for emergency physicians to create medical records. Our study addressed three areas of inquiry: whether physicians can be induced to try this new technology, whether they will continue to use it after outside technical support is withdrawn, and the factors contributing to adoption and substantial use of voice-activated computers by practicing emergency physicians. This paper presents findings from the first half of the study, reflecting physicians' reported experiences while receiving onsite training followed by technical support for three months after system installation. Based on preliminary assessments, the keys to successful use appear to include physician and group commitment, acceptance of a steep learning curve, and flexibility in adapting the computer software and/or practice habits. (+info)
The Jalview Java alignment editor.
(14/48)
Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple sequence alignments can often be improved by manual editing. Therefore, tools are needed to view and edit multiple sequence alignments. Due to growth in the sequence databases, multiple sequence alignments can often be large and difficult to view efficiently. The Jalview Java alignment editor is presented here, which enables fast viewing and editing of large multiple sequence alignments. (+info)
Drawing phylogenetic trees in LATEX and Microsoft Word.
(15/48)
newicktree is a PSTricks-based LATEX package which enables phylogenetic trees described in the Newick format to be drawn directly into LATEX documents. mswordtree is a macro for producing phylogenetic trees using the drawing elements available in Microsoft Word. AVAILABILITY: Both programs are available free from the John Innes Centre's Bioinformatics Research Group website at http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html. SUPPLEMENTARY INFORMATION: A full user-guide for newicktree and installation and usage instructions for mswordtree and available at http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html (+info)
RALEE--RNA ALignment editor in Emacs.
(16/48)
Production of high quality multiple sequence alignments of structured RNAs relies on an iterative combination of manual editing and structure prediction. An essential feature of an RNA alignment editor is the facility to mark-up the alignment based on how it matches a given secondary structure prediction, but few available alignment editors offer such a feature. The RALEE (RNA ALignment Editor in Emacs) tool provides a simple environment for RNA multiple sequence alignment editing, including structure-specific colour schemes, utilizing helper applications for structure prediction and many more conventional editing functions. This is accomplished by extending the commonly used text editor, Emacs, which is available for Linux, most UNIX systems, Windows and Mac OS. AVAILABILITY: The ELISP source code for RALEE is freely available from http://www.sanger.ac.uk/Users/sgj/ralee/ along with documentation and examples. CONTACT: [email protected] (+info)