scholarly journals Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases

2019 ◽  
Vol 36 (12) ◽  
pp. 2922-2924 ◽  
Author(s):  
Anurag Priyam ◽  
Ben J Woodcroft ◽  
Vivek Rai ◽  
Ismail Moghul ◽  
Alekhya Munagala ◽  
...  
Keyword(s):  
User Interface ◽  
Amino Acid ◽  
Graphical User Interface ◽  
Amino Acid Sequences ◽  
Biological Research ◽  
Data Sets ◽  
Potential Analysis ◽  
Biological Interpretation ◽  
User Centric ◽  
Analysis Errors

Abstract Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers.

scholarly journals Sequenceserver: a modern graphical user interface for custom BLAST databases

2015 ◽  
Author(s):  
Anurag Priyam ◽  
Ben J Woodcroft ◽  
Vivek Rai ◽  
Alekhya Munagala ◽  
Ismail Moghul ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Sequence Data ◽  
Biological Research ◽  
Work Patterns ◽  
User Input ◽  
Blast Analysis ◽  
Graphical Interfaces ◽  
User Centric ◽  
Computational Processes

The dramatic drop in DNA sequencing costs has created many opportunities for novel biological research. These opportunities largely rest upon the ability to effectively compare newly obtained and previously known sequences. This is commonly done with BLAST, yet using BLAST directly on new datasets requires substantial technical skills or helpful colleagues. Furthermore, graphical interfaces for BLAST are challenging to install and largely mimic underlying computational processes rather than work patterns of researchers. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver (http://sequenceserver.com), a modern graphical user interface for BLAST. Sequenceserver substantially increases the efficiency of researchers working with sequence data. This is due first to innovations at three levels. First, our software can be installed and used on custom datasets extremely rapidly for personal and shared applications. Second, based on analysis of user input and simple algorithms, Sequenceserver reduces the amount of decisions the user must make, provides interactive visual feedback, and prevents common potential errors that would otherwise cause erroneous results. Finally, Sequenceserver provides multiple highly visual and text-based output options that mirror the requirements and work patterns of researchers. Together, these features greatly facilitate BLAST analysis and interpretation and thus substantially enhance researcher productivity.

scholarly journals ProteoCat: a tool for planning of proteomic experiments

2015 ◽  
Vol 61 (6) ◽  
pp. 770-776 ◽  
Author(s):  
V.S. Skvortsov ◽  
N.N. Alekseychuk ◽  
D.V. Khudyakov ◽  
A.V. Mikurova ◽  
A.V. Rybina ◽  
...  
Keyword(s):  
User Interface ◽  
Amino Acid ◽  
Graphical User Interface ◽  
Retention Time ◽  
Large Scale ◽  
Data File ◽  
Mass Spectrometric ◽  
Amino Acid Sequences ◽  
Peptide Fragments ◽  
Peptide Detection

ProteoCat is a computer program has been designed to help researchers in the planning of large-scale proteomic experiments. The central part of this program is the subprogram of hydrolysis simulation that supports 4 proteases (trypsin, lysine C, endoproteinases AspN and GluC). For the peptides obtained after virtual hydrolysis or loaded from data file a number of properties important in mass-spectrometric experiments can be calculated or predicted. The data can be analyzed or filtered to reduce a set of peptides. The program is using new and improved modification of our methods developed to predict pI and probability of peptide detection; pI can also be predicted for a number of popular pKa's scales, proposed by other investigators. The algorithm for prediction of peptide retention time was realized similar to the algorithm used in the program SSRCalc. ProteoCat can estimate the coverage of amino acid sequences of proteins under defined limitation on peptides detection, as well as the possibility of assembly of peptide fragments with user-defined size of “sticky” ends. The program has a graphical user interface, written on JAVA and available at http://www.ibmc.msk.ru/LPCIT/ProteoCat.

HOW TO USE CROP GROWTH MODEL WOFOST FOR FORECASTING GROWTH AND YIELD OF A CROP

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
LAL SINGH ◽  
PARMEET SINGH ◽  
RAIHANA HABIB KANTH ◽  
PURUSHOTAM SINGH ◽  
SABIA AKHTER ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Input Data ◽  
Growth And Yield ◽  
Weather Data ◽  
Data Sets ◽  
Crop Growth Model ◽  
Control Center ◽  
Field Crops ◽  
Crop Calendar

WOFOST version 7.1.3 is a computer model that simulates the growth and production of annual field crops. All the run options are operational through a graphical user interface named WOFOST Control Center version 1.8 (WCC). WCC facilitates selecting the production level, and input data sets on crop, soil, weather, crop calendar, hydrological field conditions, soil fertility parameters and the output options. The files with crop, soil and weather data are explained, as well as the run files and the output files. A general overview is given of the development and the applications of the model. Its underlying concepts are discussed briefly.

scholarly journals Phylogenetic relationships of the nematode subfamily Phascolostrongylinae from macropodid and vombatid marsupials inferred using mitochondrial protein sequence data

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Tanapan Sukee ◽  
Ian Beveridge ◽  
Anson V. Koehler ◽  
Ross Hall ◽  
Robin B. Gasser ◽  
...  
Keyword(s):  
Amino Acid ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Mitochondrial Protein ◽  
Amino Acid Sequences ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
Data Sets ◽  
Sister Relationship

Abstract Background The subfamily Phascolostrongylinae (Superfamily Strongyloidea) comprises nematodes that are parasitic in the gastrointestinal tracts of macropodid (Family Macropodidae) and vombatid (Family Vombatidae) marsupials. Currently, nine genera and 20 species have been attributed to the subfamily Phascolostrongylinae. Previous studies using sequence data sets for the internal transcribed spacers (ITS) of nuclear ribosomal DNA showed conflicting topologies between the Phascolostrongylinae and related subfamilies. Therefore, the aim of this study was to validate the phylogenetic relationships within the Phascolostrongylinae and its relationship with the families Chabertiidae and Strongylidae using mitochondrial amino acid sequences. Methods The sequences of all 12 mitochondrial protein-coding genes were obtained by next-generation sequencing of individual adult nematodes (n = 8) representing members of the Phascolostrongylinae. These sequences were conceptually translated and the phylogenetic relationships within the Phascolostrongylinae and its relationship with the families Chabertiidae and Strongylidae were inferred from aligned, concatenated amino acid sequence data sets. Results Within the Phascolostrongylinae, the wombat-specific genera grouped separately from the genera occurring in macropods. Two of the phascolostrongyline tribes were monophyletic, including Phascolostrongylinea and Hypodontinea, whereas the tribe Macropostrongyloidinea was paraphyletic. The tribe Phascolostrongylinea occurring in wombats was closely related to Oesophagostomum spp., also from the family Chabertiidae, which formed a sister relationship with the Phascolostrongylinae. Conclusion The current phylogenetic relationship within the subfamily Phascolostrongylinae supports findings from a previous study based on ITS sequence data. This study contributes also to the understanding of the phylogenetic position of the subfamily Phascolostrongylinae within the Chabertiidae. Future studies investigating the relationships between the Phascolostrongylinae and Cloacininae from macropodid marsupials may advance our knowledge of the phylogeny of strongyloid nematodes in marsupials. Graphical Abstract

scholarly journals The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes

2016 ◽  
Author(s):  
Luis M Rodriguez-R ◽  
Konstantinos T Konstantinidis
Keyword(s):  
User Interface ◽  
Case Studies ◽  
Graphical User Interface ◽  
Biological Research ◽  
Microbial Genomics ◽  
Online Analysis ◽  
Microbial Genomes ◽  
Novel Method ◽  
Over Dispersion ◽  
New Algorithms

Genomic and metagenomic analyses are increasingly becoming commonplace in several areas of biological research, but recurrent specialized analyses are frequently reported as in-house scripts rarely available after publication. We describe the enveomics collection, a growing set of actively maintained scripts for several recurrent and specialized tasks in microbial genomics and metagenomics, and present a graphical user interface and several case studies. Our resource includes previously described as well as new algorithms such as Transformed-space Resampling In Biased Sets (TRIBS), a novel method to evaluate phylogenetic under- or over-dispersion in reference sets with strong phylogenetic bias. The enveomics collection is freely available under the terms of the Artistic License 2.0 at https://github.com/lmrodriguezr/enveomics and for online analysis at http://enve-omics.ce.gatech.edu

scholarly journals DatView: a graphical user interface for visualizing and querying large data sets in serial femtosecond crystallography

2019 ◽  
Vol 52 (6) ◽  
pp. 1440-1448
Author(s):  
Natasha Stander ◽  
Petra Fromme ◽  
Nadia Zatsepin
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Large Data ◽  
Large Data Sets ◽  
Data Sets ◽  
Mode Iii ◽  
Multiple Parameters ◽  
Serial Crystallography ◽  
Serial Femtosecond Crystallography ◽  
Tabulated Data

DatView is a new graphical user interface (GUI) for plotting parameters to explore correlations, identify outliers and export subsets of data. It was designed to simplify and expedite analysis of very large unmerged serial femtosecond crystallography (SFX) data sets composed of indexing results from hundreds of thousands of microcrystal diffraction patterns. However, DatView works with any tabulated data, offering its functionality to many applications outside serial crystallography. In DatView's user-friendly GUI, selections are drawn onto plots and synchronized across all other plots, so correlations between multiple parameters in large multi-parameter data sets can be rapidly identified. It also includes an item viewer for displaying images in the current selection alongside the associated metadata. For serial crystallography data processed by indexamajig from CrystFEL [White, Kirian, Martin, Aquila, Nass, Barty & Chapman (2012). J. Appl. Cryst. 45, 335–341], DatView generates a table of parameters and metadata from stream files and, optionally, the associated HDF5 files. By combining the functionality of several commonly needed tools for SFX in a single GUI that operates on tabulated data, the time needed to load and calculate statistics from large data sets is reduced. This paper describes how DatView facilitates (i) efficient feedback during data collection by examining trends in time, sample position or any parameter, (ii) determination of optimal indexing and integration parameters via the comparison mode, (iii) identification of systematic errors in unmerged SFX data sets, and (iv) sorting and highly flexible data filtering (plot selections, Boolean filters and more), including direct export of subset CrystFEL stream files for further processing.

XDSAPP: a graphical user interface for the convenient processing of diffraction data usingXDS

2012 ◽  
Vol 45 (3) ◽  
pp. 568-572 ◽  
Author(s):  
Michael Krug ◽  
Manfred S. Weiss ◽  
Udo Heinemann ◽  
Uwe Mueller
Keyword(s):  
User Interface ◽  
Data Collection ◽  
Data Processing ◽  
Graphical User Interface ◽  
Diffraction Data ◽  
Easy Access ◽  
Translational Symmetry ◽  
Data Sets ◽  
Data Set ◽  
Radiation Decay

XDSAPPis a Tcl/Tk-based graphical user interface for the easy and convenient processing of diffraction data sets usingXDS. It provides easy access to allXDSfunctionalities, automates the data processing and generates graphical plots of various data set statistics provided byXDS. By incorporating additional software, further information on certain features of the data set, such as radiation decay during data collection or the presence of pseudo-translational symmetry and/or twinning, can be obtained. Intensity files suitable forCCP4,CNSandSHELXare generated.

Groundwater-surface water exchange: A New Graphical User Interface for temperature time-series analysis

2021 ◽  
Author(s):  
Andrea Bertagnoli ◽  
Matthijs van Berkel ◽  
Uwe Schneidewind ◽  
Ricky van Kampen ◽  
Stefan Krause ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Hyporheic Zone ◽  
Low Cost ◽  
Extraction Process ◽  
Data Sets ◽  
Analysis Process ◽  
Improve Result ◽  
Signal Processing Methods ◽  
Dynamic Exchange

<p>Riverine systems have a dynamic exchange of water with the hyporheic zone and groundwater. Exchange fluxes can be challenging to estimate because they vary spatially and temporally and depend on many geological and hydrological properties. Temperature as a tracer has become a low-cost and robust method to monitor such fluxes both at local and reach (several channel widths) scales. Here, we present the capabilities and functionality of a new graphical user interface (GUI) developed in Python which is operating system independent. The GUI integrates standard and state-of-the-art signal processing methods with data visualization and analysis techniques. The signal analysis library allows the user to select the important frequencies to improve result confidence while the advanced LPMLEn and window function in FFT to reduce leakage in the extraction process of the amplitude and phase of the signals. The GUI streamlines the entire analysis process, from evaluating the raw temperature data to obtaining end-user specified parameters such as flux and streambed thermal properties. It allows for the analysis of single-probe and multi-probe data from short to long-term data sets.</p>

An Automated Approach to Recording and Analyzing Design Activities Using a Graphical User Interface

2019 ◽  
Author(s):  
Fares M. Adly Taha ◽  
Ramez M. Adly Taha ◽  
Keegan West ◽  
Mohammad Fazelpour ◽  
Jeffrey W. Herrmann ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Human Error ◽  
Quantitative Methods ◽  
Study Data ◽  
Data Sets ◽  
Qualitative And Quantitative Methods ◽  
Automated Method ◽  
Final Design ◽  
Design Activities

Abstract Design researchers use protocol studies to understand the cognition of designers and how they think. Although different qualitative and quantitative methods have been employed, analyzing protocol data often requires manual coding, which is tedious, time-consuming, and susceptible to human error. To address these challenges, this paper presents an automated method to record and analyze the designer’s actions. To demonstrate the proposed method, we designed and conducted an experimental study that used a graphical user interface to record design actions while the designer solves a factory layout problem. Then, we used spectral clustering to analyze the data and identify the subproblems that the designer considered. The final design layouts were evaluated using two metrics: travel distance and adjacency score. Our automated method to record and analyze designers’ actions provides a framework to analyze protocol study data sets objectively and quickly.

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