scholarly journals BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence

2021 ◽  
Author(s):  
Benjamin Hepp ◽  
Violette Da Cunha ◽  
Florence Lorieux ◽  
Jacques Oberto
Keyword(s):  
Gene Sequence ◽  
Single Gene ◽  
Daily Basis ◽  
Web Tool ◽  
Web Based ◽  
Internet Explorer ◽  
Prokaryotic Genomes ◽  
Exploration Tool ◽  
Genome Browsers ◽  
Archaeal Gene

Abstract Motivation The retrieval of a single gene sequence and context from completely sequenced bacterial and archaeal genomes constitutes an intimidating task for the wet bench biologist. Existing web-based genome browsers are either too complex for routine use or only provide a subset of the available prokaryotic genomes. Results We have developed BAGET 2.0 (Bacterial and Archaeal Gene Exploration Tool), an updated web service granting access in just three mouse clicks to the sequence and synteny of any gene from completely sequenced bacteria and archaea. User-provided annotated genomes can be processed as well. BAGET 2.0 relies on a local database updated on a daily basis. Availability and implementation BAGET 2.0 befits all current browsers such as Chrome, Firefox, Edge, Opera and Safari. Internet Explorer 11 is supported. BAGET 2.0 is freely accessible at https://archaea.i2bc.paris-saclay.fr/baget/

scholarly journals An Open-Source Web-Based Tool for Resource-Agnostic Interactive Translation Prediction

2014 ◽  
Vol 102 (1) ◽  
pp. 69-80 ◽  
Author(s):  
Torregrosa Daniel ◽  
Forcada Mikel L. ◽  
Pérez-Ortiz Juan Antonio
Keyword(s):  
Open Source ◽  
Machine Translation ◽  
Web Application ◽  
Statistical Machine Translation ◽  
Black Box ◽  
Translation System ◽  
Web Tool ◽  
Web Based ◽  
Strongly Coupled ◽  
Machine Translation System

Abstract We present a web-based open-source tool for interactive translation prediction (ITP) and describe its underlying architecture. ITP systems assist human translators by making context-based computer-generated suggestions as they type. Most of the ITP systems in literature are strongly coupled with a statistical machine translation system that is conveniently adapted to provide the suggestions. Our system, however, follows a resource-agnostic approach and suggestions are obtained from any unmodified black-box bilingual resource. This paper reviews our ITP method and describes the architecture of Forecat, a web tool, partly based on the recent technology of web components, that eases the use of our ITP approach in any web application requiring this kind of translation assistance. We also evaluate the performance of our method when using an unmodified Moses-based statistical machine translation system as the bilingual resource.

Interactive Power Point Lesson

2011 ◽  
pp. 463-468
Author(s):  
Melissa B. Holler
Keyword(s):  
World Wide ◽  
Classroom Teachers ◽  
Technology Coordinators ◽  
Web Based ◽  
Internet Explorer ◽  
The World ◽  
Power Point ◽  
Microsoft Office ◽  
K 12 ◽  
Integrated Software

The foundation for much of the technology being used in today’s classroom is the Microsoft Office suite. It is fast becoming the integrated software package of choice for many schools and school districts. Word, PowerPoint, Excel, and Access are the staples for many students and teachers. Complimenting these capabilities, Internet Explorer and Netscape Communicator are the tools of choice for accessing the World Wide Web. Why not help teachers utilize these same tools to develop text, visual, and Web-based materials for the classroom, and leave the more complex and costly packages to multimedia designers and commercial artists? The success of this philosophy has been borne out by a blistering growth in applications from K-12 classroom teachers, technology coordinators, and corporate trainers.

Matching Clinicians to Operative Cases

2013 ◽  
Vol 04 (03) ◽  
pp. 445-453
Author(s):  
J. Wanderer ◽  
A. Was
Keyword(s):  
Risk Stratification ◽  
Operating Room ◽  
Web Tool ◽  
Physical Status ◽  
Billing Data ◽  
Web Based ◽  
Physical Status Classification ◽  
Status Classification ◽  
One Year ◽  
The Web

Summary Background: Patient and surgical case complexity are important considerations in creating appropriate clinical assignments for trainees in the operating room (OR). The American Society of Anesthesiologists (ASA) Physical Status Classification System is the most commonly used tool to classify patient illness severity, but it requires manual evaluation by a clinician and is highly variable. A Risk Stratification System for surgical patients was recently published which uses administrative billing codes to calculate four Risk Stratification Indices (RSIs) and provides an objective surrogate for patient complexity that does not require clinical evaluation. This risk score could be helpful when assigning operating room cases. Objective: This is a technical feasibility study to evaluate the process and potential utility of incorporating an automatic risk score calculation into a web-based tool for assigning OR cases. Methods: We created a web service implementation of the RSI model for one-year mortality and automatically calculated the RSI values for patients scheduled to undergo an operation the following day. An analysis was conducted on data availability for the RSI model and the correlation between RSI values and ASA physical status. Results: In a retrospective analysis of 46,740 patients who received surgery in the year preceding the web tool implementation, RSI values were generated for 20,638 patients (44%). The Spear-man’s rank correlation coefficient between ASA physical status classification and one-year mortality RSI values was 0.404. Conclusions: We have shown that it is possible to create a web-based tool that uses existing billing data to automatically calculate risk scores for patients scheduled to undergo surgery. Such a risk scoring system could be used to match patient acuity to physician experience, and to provide improved patient and clinician experiences. The web tool could be improved by expanding the input database or utilizing procedure booking codes rather than billing data.

Capturing Volunteered Historical Information

2015 ◽  
Vol 4 (1) ◽  
pp. 19-41 ◽  
Author(s):  
Jennifer Minner ◽  
Michael Holleran ◽  
Andrea Roberts ◽  
Joshua Conrad
Keyword(s):  
Government Agencies ◽  
Historical Survey ◽  
Web Tool ◽  
Web Based ◽  
Potential Barriers ◽  
Planning Processes ◽  
Long Range Planning ◽  
Web Experiment ◽  
Official Data ◽  
The U.S

Government agencies are adopting a variety of web-based strategies to improve information systems, increase civic engagement, and enhance decision-making capabilities and planning processes. Within the U.S., a university research team designed a municipal web tool called the Austin Historical Survey Wiki to fill a pragmatic need for information about historic resources to be used for long range planning and development review purposes. The authors situate this web experiment in relation to an array of models for government interaction with citizens via data collection efforts and the application of GIS and web-based technologies. This experiment offers local government agencies and practitioners a replicable model for tracking official data and citizen contributions to a GIS. In addition, this research offers insights into potential barriers to and requirements for collaboration between government agencies and citizens online.

scholarly journals The training game SALIENCE for the therapy of alcohol use disorder

2019 ◽  
Vol 26 (1) ◽  
pp. 499-512 ◽  
Author(s):  
Sabine Vollstädt-Klein ◽  
Philip Mildner ◽  
Jan Malte Bumb ◽  
Damian Karl ◽  
Christoph Ueberle ◽  
...  
Keyword(s):  
Alcohol Use ◽  
Feasibility Study ◽  
Game Design ◽  
Alcohol Use Disorder ◽  
Standard Treatment ◽  
Real Life ◽  
Daily Basis ◽  
Web Based ◽  
Group 2 ◽  
Group 1

The feasibility study was aimed to develop a web-based gaming tool for the therapy of alcohol use disorder to offer patients a cue-exposure-based extinction and decision training, enhanced with virtual reality. To increase the training effect, patients playfully experience situations that resemble critical real-life situations. For implementing the game, a combination of HTML5 and JavaScript was used. The application comes with an administrator interface, to allow editing the game content. Initially, we included 21 patients (Group 1), 18 suffering from alcohol use disorder and 3 using cannabis (18/3 male/female, mean age 39 ± 13 years). Considering the iterative process of a feasibility study, we developed the game design as suggested by participants of Group 1 and additionally included 11 novel participants (Group 2) (11 suffering from an alcohol use disorder, 7/4 male/female, mean age 46 ± 14 years). Basically, the game was very well received. Usability ratings were generally high, even in patients with little computer experience. Both groups rated the application as realistic, and would generally be willing to play it on a daily basis. Given that SALIENCE is inexpensive, easily available, and engaging, it might be a reasonable add-on intervention to the standard treatment of alcohol use disorder.

scholarly journals The Molecular Phylogeny of the New Zealand Endemic Genus Hadramphus and the Revival of the Genus Karocolens

Diversity ◽  
2018 ◽  
Vol 10 (3) ◽  
pp. 88
Author(s):  
Emily Fountain ◽  
Robert Cruickshank ◽  
Adrian Paterson
Keyword(s):  
New Zealand ◽  
Gene Sequence ◽  
Mitochondrial Gene ◽  
Single Gene ◽  
Morphological Characteristics ◽  
Nuclear Gene ◽  
Similar Species ◽  
Morphological Similarity ◽  
Coalescent Approach ◽  
Systematic Relationships

The delineation of species is important to the fields of evolution, ecology and conservation. The use of only a single line of evidence, e.g., morphology or a single gene sequence, may underestimate or overestimate the level of diversity within a taxon. This problem often occurs when organisms are morphologically similar but genetically different, i.e., for cryptic species. The Hadramphus genus contains four endangered, morphologically similar species of weevils, each endemic to a specific New Zealand region (Hadramphus spinipennis Chatham Islands, H. stilbocarpae Fiordland, H. tuberculatus McKenzie Country, H. pittospori Poor Knights Islands). The systematic relationships among these species are unclear. We used samples from these species and a closely related genus, Lyperobius huttoni, to obtain data from the mitochondrial gene cytochrome c oxidase subunit I and the nuclear gene internal transcribe spacer 2. In addition to the multi-locus coalescent approach, we modelled morphological characteristics combined with the genetic data. We found that H. spinipennis, H. tuberculatus and H. stilbocarpae were a closely related clade. Despite a strong morphological similarity, Hadramphus pittospori was found to be genetically distinct from the other Hadramphus species, which supports the resurrection of the monotypic genus Karocolens for this species.

scholarly journals G4Killer web application: a tool to design G-quadruplex mutations

2020 ◽  
Vol 36 (10) ◽  
pp. 3246-3247
Author(s):  
Vaclav Brazda ◽  
Jan Kolomaznik ◽  
Jean-Louis Mergny ◽  
Jiri Stastny
Keyword(s):  
Dna Sequences ◽  
Web Application ◽  
Rational Design ◽  
Therapeutic Potential ◽  
Supplementary Information ◽  
Web Tool ◽  
Web Based ◽  
Dna Structures ◽  
G Quadruplex ◽  
User Friendly

Abstract Motivation G-quadruplexes (G4) are important regulatory non-B DNA structures with therapeutic potential. A tool for rational design of mutations leading to decreased propensity for G4 formation should be useful in studying G4 functions. Although tools exist for G4 prediction, no easily accessible tool for the rational design of G4 mutations has been available. Results We developed a web-based tool termed G4Killer that is based on the G4Hunter algorithm. This new tool is a platform-independent and user-friendly application to design mutations crippling G4 propensity in a parsimonious way (i.e., keeping the primary sequence as close as possible to the original one). The tool is integrated into our DNA analyzer server and allows for generating mutated DNA sequences having the desired lowered G4Hunter score with minimal mutation steps. Availability and implementation The G4Killer web tool can be accessed at: http://bioinformatics.ibp.cz. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Correlation Between Self-Reported Resident Duty Hours and Time-Stamped Parking Data

2012 ◽  
Vol 4 (2) ◽  
pp. 254-256 ◽  
Author(s):  
Smitha R. Chadaga ◽  
Angela Keniston ◽  
Dan Casey ◽  
Richard K. Albert
Keyword(s):  
Medical Center ◽  
Daily Basis ◽  
Work Hours ◽  
Parking Garage ◽  
Monthly Basis ◽  
Web Based ◽  
Duty Hours ◽  
Resident Work ◽  
Significant Difference ◽  
Reported Data

Abstract Background Failure to comply with Accreditation Council for Graduate Medical Education-mandated resident work hour limitations can result in citations and shortened accreditation cycles. Many programs assess compliance by collecting self-reports of work hours from each resident. Objectives To examine residents' self-reported assessment of work hours recorded on a daily basis using a Web-based product with electronically recorded times collected as residents entered and exited the parking garage. Methods Study participants consisted of 62 University of Colorado Denver internal medicine residents rotating at Denver Health Medical Center on a monthly basis over a 4-month period. Self-reported data submitted by 60 residents were compared with the times these residents entered and exited from the parking garage at Denver Health Medical Center, as assessed by an electronic badge reader. Results A high level of agreement was found between these two data sets. No significant difference was found between the time-stamped parking data and self-reported Web-based data for resident work hours. Conclusions Residents accurately self-reported their work hours, using a daily Web-based duty hours log when compared to an independent, objective and blinded assessment of work hours.

scholarly journals Estimation of prokaryote genomic DNA G+C content by sequencing universally conserved genes

2006 ◽  
Vol 56 (5) ◽  
pp. 1025-1029 ◽  
Author(s):  
Pierre-Edouard Fournier ◽  
Karsten Suhre ◽  
Ghislain Fournous ◽  
Didier Raoult
Keyword(s):  
Strong Correlation ◽  
Genomic Dna ◽  
Gene Sequence ◽  
Single Copy ◽  
Coefficient Of Determination ◽  
Median Size ◽  
Prokaryotic Genomes ◽  
Conserved Genes ◽  
Clusters Of Orthologous Groups

Determination of the DNA G+C content of prokaryotic genomes using traditional methods is time-consuming and results may vary from laboratory to laboratory, depending on the technique used. We explored the possibility of extrapolating the genomic DNA G+C content of prokaryotes from gene sequences. For this, 127 universally conserved genes were studied from 50 prokaryotic genomes in the Clusters of Orthologous Groups database. Of these, 57 genes were present as a single copy in the genomes of 157 different prokaryote species available in GenBank. There was a strong correlation [coefficient of determination (r 2) >95 %] between the DNA G+C contents of 20 genes and their corresponding genomes. For each of the 157 prokaryotic genomes studied, the DNA G+C content of the 20 genes was used to determine a ‘calculated’ genome DNA G+C content (CGC) and this value was compared with the ‘real’ genome DNA G+C content (RGC). In order to select the most suitable gene for the determination of CGC values, we compared the r 2 and median mol% difference between CGC and RGC as well as the sensitivity of each gene to provide CGC values for prokaryotic genomes that differ by less than 5 mol% from their RGC. The highly conserved ftsY gene (median size 1144 nucleotides), a vertically inherited member of the GTPase superfamily, showed the highest r 2 value of 0.98, the smallest median mol% difference between CGC and RGC of 1.06 and a sensitivity of 100 %. Using ftsY DNA G+C content values, the CGC values of 100 genomes not included in the calculation of r 2 differed by less than 5 mol% from their RGC values. These data suggest that the genomic DNA G+C content of prokaryotes may be estimated easily and reliably from the ftsY gene sequence.

scholarly journals GenSensor Suite: A Web-Based Tool for the Analysis of Gene and Protein Interactions, Pathways, and Regulation

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Mark Gosink ◽  
Sawsan Khuri ◽  
Camilo Valdes ◽  
Zhijie Jiang ◽  
Nicholas F. Tsinoremas
Keyword(s):  
Protein Interactions ◽  
Single Gene ◽  
Gene List ◽  
Input List ◽  
Web Based ◽  
Common Gene ◽  
Gene Set ◽  
Web Tools ◽  
Gene Sets

The GenSensor Suite consists of four web tools for elucidating relationships among genes and proteins. GenPath results show which biochemical, regulatory, or other gene set categories are over- or under-represented in an input list compared to a background list. All common gene sets are available for searching in GenPath, plus some specialized sets. Users can add custom background lists. GenInteract builds an interaction gene list from a single gene input and then analyzes this in GenPath. GenPubMed uses a PubMed query to identify a list of PubMed IDs, from which a gene list is extracted and queried in GenPath. GenViewer allows the user to query one gene set against another in GenPath. GenPath results are presented with relevant P- and q-values in an uncluttered, fully linked, and integrated table. Users can easily copy this table and paste it directly into a spreadsheet or document.

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