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 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

The Design of Embedded Systems GUI Message Based on Mobile and Intelligent Materials

2012 ◽  
Vol 460 ◽  
pp. 210-213
Author(s):  
Shu Zhou
Keyword(s):  
Information Technology ◽  
User Interface ◽  
Embedded Systems ◽  
Graphical User Interface ◽  
Application Framework ◽  
The Novel ◽  
Interaction Interface ◽  
Novel Method ◽  
Personal Assistant ◽  
Embedded Gui

Research and development of embedded systems is the hot information technology and the graphical user interface (GUI) is the most important part of human-computer interaction interface. These embedded GUI system has been widely used because of its strong and powerful functionality. But many times , it is necessary to sacrifice performance for its versatility. In this paper, the embedded GUI systems based on the message mechanism is study considering the short of current embedded GUI systems. The novel method of a message-driven application framework is suggested to solve the problem of the current message mechanisms for the implementation. Meanwhile, a circular queue algorithm is given in order to achieve messaging unit. Then, the message has been classified considering of efficiency. In the end, the design example of personal assistant is given.

scholarly journals The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes

2020 ◽  
Vol 49 (D1) ◽  
pp. D639-D643 ◽  
Author(s):  
Kai Blin ◽  
Simon Shaw ◽  
Satria A Kautsar ◽  
Marnix H Medema ◽  
Tilmann Weber
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Genome Mining ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
High Quality ◽  
Microbial Genomes ◽  
Fungal Genomes ◽  
Interactive Graphical User Interface

Abstract Microorganisms produce natural products that are frequently used in the development of antibacterial, antiviral, and anticancer drugs, pesticides, herbicides, or fungicides. In recent years, genome mining has evolved into a prominent method to access this potential. antiSMASH is one of the most popular tools for this task. Here, we present version 3 of the antiSMASH database, providing a means to access and query precomputed antiSMASH-5.2-detected biosynthetic gene clusters from representative, publicly available, high-quality microbial genomes via an interactive graphical user interface. In version 3, the database contains 147 517 high quality BGC regions from 388 archaeal, 25 236 bacterial and 177 fungal genomes and is available at https://antismash-db.secondarymetabolites.org/.

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 Mediation of Lazy Update Propagation in a Replicated Database over a Decentralized P2P Architecture

2019 ◽  
pp. 1-31
Author(s):  
Katembo Kituta Ezéchiel ◽  
Shri Kant ◽  
Ruchi Agarwal
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Execution Time ◽  
Prediction Models ◽  
Data Migration ◽  
P2p Network ◽  
Update Propagation ◽  
Methodological Approaches ◽  
Network Overload ◽  
New Algorithms

While replicating data over a decentralized Peer-to- Peer (P2P) network, transactions broadcasting updates arising from different peers run simultaneously so that a destination peer replica can be updated concurrently, that always causes transaction and data conflicts. Moreover, during data migration, connectivity interruption and network overload corrupt running transactions so that destination peers can experience duplicated data or improper data or missing data, hence replicas remain inconsistent. Different methodological approaches have been combined to solve these problems: the audit log technique to capture the changes made to data; the algorithmic method to design and analyse algorithms and the statistical method to analyse the performance of new algorithms and to design prediction models of the execution time based on other parameters. A Graphical User Interface software as prototype, have been designed with C #, to implement these new algorithms to obtain a database synchronizer-mediator. A stream of experiments, showed that the new algorithms were effective. So, the hypothesis according to which “The execution time of replication and reconciliation transactions totally depends on independent factors.” has been confirmed.

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.

Meta-analysis of non-statistically significant unreported effects

2018 ◽  
Vol 28 (12) ◽  
pp. 3741-3754 ◽  
Author(s):  
Anton Albajes-Eizagirre ◽  
Aleix Solanes ◽  
Joaquim Radua
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Effect Size ◽  
Meta Analysis ◽  
Statistical Significance ◽  
R Package ◽  
Effect Sizes ◽  
Multiple Imputations ◽  
Null Effect ◽  
Novel Method

Published studies in Medicine (and virtually any other discipline) sometimes report that a difference or correlation did not reach statistical significance but do not report its effect size or any statistic from which the latter may be derived. Unfortunately, meta-analysts should not exclude these studies because their exclusion would bias the meta-analytic outcome, but also they cannot be included as null effect sizes because this strategy is also associated to bias. To overcome this problem, we have developed MetaNSUE, a novel method based on multiple imputations of the censored information. We also provide an R package and an easy-to-use Graphical User Interface for non-R meta-analysts.

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