SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Microsoft Excel

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The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions.

Concepts: Microsoft Excel, Microsoft, Spreadsheet, Microsoft Office, Lotus 1-2-3, Spreadsheet software, Pivot table, VisiCalc

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SUMMARY: Advances in sequencing technology have greatly reduced the costs incurred in collecting raw sequencing data. Academic laboratories and researchers therefore now have access to very large datasets of genomic alterations but limited time and computational resources to analyze their potential biological importance. Here, we provide a web-based application, Cancer-Related Analysis of VAriants Toolkit (CRAVAT), designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis. CRAVAT provides predictive scores for germline variants, somatic mutations, and relative gene importance, as well as annotations from published literature and databases. Results are emailed to users as MS Excel spreadsheets and/or tab-separated text files. AVAILABILITY: http://www.cravat.us/ CONTACT: karchin@jhu.edu SUPPLEMENTARY INFORMATION: Available at Bioinformatics online.

Concepts: DNA, Gene, Genetics, Bioinformatics, Microsoft Excel, Mutation, Molecular biology, Spreadsheet

29

Interactive modules for Data Exploration and Visualization (imDEV) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data through a user-friendly interface. Individual modules enables interactive and dynamic analyses of large data by interfacing R’s multivariate statistics and highly customizable visualizations with the spreadsheet environment, aiding robust inferences and generating information-rich data visualizations. This tool provides access to multiple comparisons with false discovery correction, hierarchical clustering, principal and independent component analyses, partial least squares regression and discriminant analysis, through an intuitive interface for creating high-quality two- and a three-dimensional visualizations including scatter plot matrices, distribution plots, dendrograms, heat maps, biplots, trellis biplots and correlation networks. Availability and implementation: Freely available for download at http://sourceforge.net/projects/imdev/. Implemented in R and VBA and supported by Microsoft Excel (2003, 2007 and 2010).

Concepts: Regression analysis, Microsoft Excel, Microsoft, Graphical user interface, Spreadsheet, Visual Basic for Applications, Microsoft Office, Lotus 1-2-3

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Enzyme kinetic parameters are usually determined from initial rates nevertheless, laboratory instruments only measure substrate or product concentration versus reaction time (progress curves). To overcome this problem we present a methodology which uses integrated models based on Michaelis-Menten equation. The most severe practical limitation of progress curve analysis occurs when the enzyme shows a loss of activity under the chosen assay conditions. To avoid this problem it is possible to work with the same experimental points utilized for initial rates determination. This methodology is illustrated by the use of integrated kinetic equations with the well-known reaction catalyzed by alkaline phosphatase enzyme. In this work nonlinear regression was performed with the Solver supplement (Microsoft Office Excel). It is easy to work with and track graphically the convergence of SSE (sum of square errors). The diagnosis of enzyme inhibition was performed according to Akaike information criterion.

Concepts: Enzyme kinetics, Microsoft Excel, Enzyme, Microsoft, Spreadsheet, Microsoft Office, Microsoft Office 2007, Microsoft Office 2008 for Mac

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Excel2Genie, a simple and user-friendly Microsoft Excel interface, has been developed to the Genie-2000 Spectroscopic Software of Canberra Industries. This Excel application can directly control Canberra Multichannel Analyzer (MCA), process the acquired data and visualize them. Combination of Genie-2000 with Excel2Genie results in remarkably increased flexibility and a possibility to carry out repetitive data acquisitions even with changing parameters and more sophisticated analysis. The developed software package comprises three worksheets: display parameters and results of data acquisition, data analysis and mathematical operations carried out on the measured gamma spectra. At the same time it also allows control of these processes. Excel2Genie is freely available to assist gamma spectrum measurements and data evaluation by the interested Canberra users. With access to the Visual Basic Application (VBA) source code of this application users are enabled to modify the developed interface according to their intentions.

Concepts: Microsoft Excel, Computer program, Microsoft, Computer software, Spreadsheet, Visual Basic for Applications, Microsoft Office, CP/M

26

Contaminated site remediation is generally difficult, time consuming, and expensive. As a result ranking may aid in efficient allocation of resources. In order to rank the priorities of contaminated sites, input parameters relevant to contaminant fate and transport, and exposure assessment should be as accurate as possible. Yet, in most cases these parameters are vague or not precise. Most of the current remediation priority ranking methodologies overlook the vagueness in parameter values or do not go beyond assigning a contaminated site to a risk class. The main objective of this study is to develop an alternative remedial priority ranking system (RPRS) for contaminated sites in which vagueness in parameter values is considered. RPRS aims to evaluate potential human health risks due to contamination using sufficiently comprehensive and readily available parameters in describing the fate and transport of contaminants in air, soil, and groundwater. Vagueness in parameter values is considered by means of fuzzy set theory. A fuzzy expert system is proposed for the evaluation of contaminated sites and a software (ConSiteRPRS) is developed in Microsoft Office Excel 2007 platform. Rankings are employed for hypothetical and real sites. Results show that RPRS is successful in distinguishing between the higher and lower risk cases.

Concepts: Microsoft Excel, Environmental remediation, Ranking, Parameter, Set, Microsoft, Fuzzy logic, Microsoft Office

25

Graphing is socially significant for behavior analysts; however, graphing can be difficult to learn. Video modeling (VM) may be a useful instructional method but lacks evidence for effective teaching of computer skills. A between-groups design compared the effects of VM, text-based instruction, and no instruction on graphing performance. Participants who used VM constructed graphs significantly faster and with fewer errors than those who used text-based instruction or no instruction. Implications for instruction are discussed.

Concepts: Psychology, Microsoft Excel, Learning, Microsoft, Spreadsheet, Microsoft Office, Lotus 1-2-3, Microsoft Office 2007

7

Despite theoretical evidence that the model commonly referred to as the 3500-kcal rule grossly overestimates actual weight loss, widespread application of the 3500-kcal formula continues to appear in textbooks, on respected government- and health-related websites, and scientific research publications. Here we demonstrate the risk of applying the 3500-kcal rule even as a convenient estimate by comparing predicted against actual weight loss in seven weight loss experiments conducted in confinement under total supervision or objectively measured energy intake. We offer three newly developed, downloadable applications housed in Microsoft Excel and Java, which simulates a rigorously validated, dynamic model of weight change. The first two tools available at http://www.pbrc.edu/sswcp, provide a convenient alternative method for providing patients with projected weight loss/gain estimates in response to changes in dietary intake. The second tool, which can be downloaded from the URL http://www.pbrc.edu/mswcp, projects estimated weight loss simultaneously for multiple subjects. This tool was developed to inform weight change experimental design and analysis. While complex dynamic models may not be directly tractable, the newly developed tools offer the opportunity to deliver dynamic model predictions as a convenient and significantly more accurate alternative to the 3500-kcal rule.

Concepts: Scientific method, Microsoft Excel, Statistics, Mathematics, Prediction, Science, Experiment, Spreadsheet

5

Genomic datasets accompanying scientific publications show a surprisingly high rate of gene name corruption. This error is generated when files and tables are imported into Microsoft Excel and certain gene symbols are automatically converted into dates.

Concepts: Microsoft Excel, Microsoft, Spreadsheet, Microsoft Office, Lotus 1-2-3, CP/M, Microsoft Office 2007, Microsoft Office 2008 for Mac

4

The recent advancement of high-throughput genome sequencing technologies has resulted in a considerable increase in demands for large-scale genome annotation. While annotation is a crucial step for downstream data analyses and experimental studies, this process requires substantial expertise and knowledge of bioinformatics. Here we present MEGANTE, a Web-based annotation system that makes plant genome annotation easy for researchers unfamiliar with bioinformatics. Without any complicated configuration, users can perform genomic sequence annotations simply by uploading a sequence and selecting the species to query. MEGANTE automatically runs several analysis programs and integrates the results to select the appropriate consensus exon-intron structures and to predict open reading frames (ORFs) at each locus. Functional annotation, including a similarity search against known proteins and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with a widely used genome browser, GBrowse. For ease of analysis, the results can be downloaded in Microsoft Excel format. All of the query sequences and annotation results are stored on the server side so that users can access their own data virtually from anywhere on the Web. The current release of MEGANTE targets 24 plant species from the Brassicaceae, Fabaceae, Musaceae, Poaceae, Salicaceae, Solanaceae, Rosaceae, and Vitaceae families, and it allows users to submit a sequence up to 10 Mb in length and to save up to 100 sequences with the annotation information on the server. The MEGANTE Web service is available at https://megante.dna.affrc.go.jp/.

Concepts: DNA, Gene, Microsoft Excel, Series, Genomics, Mathematical analysis, Sequence, World Wide Web