scholarly journals CapiPy: python-based GUI-application to assist in protein immobilization

2021 ◽  
Author(s):  
David Roura Padrosa ◽  
Valentina Marchini ◽  
Francesca Paradisi
Keyword(s):  
Protein Immobilization ◽  
Protein Characterization ◽  
Ease Of Use ◽  
Random Sets ◽  
Supplementary Information ◽  
Special Focus ◽  
Supplementary Data ◽  
Data Set ◽  
Protein Model ◽  
User Friendly

Abstract Summary Protein immobilization, while widespread to unlock enzyme potential in biocatalysis, remains tied to a trial an error approach. Nonetheless, several databases and computational methods have been developed for protein characterization and their study. CapiPy is a user-friendly application for protein model creation and subsequent analysis with a special focus on the ease of use and interpretation of the results to help the users to make an informed decision on the immobilization approach which should be ideal for a protein of interest. The package has been tested with three separate random sets of 150 protein sequences from Uniprot with more than a 70% overall success rate (see Supplementary information and Supplementary Data set). Availability and implementation The package is free to use under the GNU General Public License v3.0. All necessary files can be downloaded from https://github.com/drou0302/CapiPy or https://pypi.org/project/CapiPy/. All external requirements are also freely available, with some restrictions for non-academic users. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CapiPy: Python Based GUI-Application to Assist in Protein Immobilization

2020 ◽  
Author(s):  
David Roura Padrosa ◽  
Valentina Marchini ◽  
Francesca Paradisi
Keyword(s):  
Protein Immobilization ◽  
Ease Of Use ◽  
Special Focus ◽  
Protein Model ◽  
User Friendly ◽  
Result Interpretation

CapiPy is a user-friendly application for protein model creation and subsequent analysis with special focus on its ease of use and result interpretation to help in protein immobilization. More information can be found in https://github.com/drou0302/CapiPy. <br>

scholarly journals CapiPy: Python Based GUI-Application to Assist in Protein Immobilization

2020 ◽  
Author(s):  
David Roura Padrosa ◽  
Valentina Marchini ◽  
Francesca Paradisi
Keyword(s):  
Protein Immobilization ◽  
Ease Of Use ◽  
Special Focus ◽  
Protein Model ◽  
User Friendly ◽  
Result Interpretation

CapiPy is a user-friendly application for protein model creation and subsequent analysis with special focus on its ease of use and result interpretation to help in protein immobilization. More information can be found in https://github.com/drou0302/CapiPy. <br>

scholarly journals dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit

2020 ◽  
Author(s):  
Daniel G Bunis ◽  
Jared Andrews ◽  
Gabriela K Fragiadakis ◽  
Trevor D Burt ◽  
Marina Sirota
Keyword(s):  
Single Cell ◽  
R Package ◽  
Color Blindness ◽  
Ease Of Use ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Rnaseq Data ◽  
Visualization Toolkit ◽  
User Friendly ◽  
Publication Quality

Abstract Summary A visualization suite for major forms of bulk and single-cell RNAseq data in R. dittoSeq is color blindness-friendly by default, robustly documented to power ease-of-use and allows highly customizable generation of both daily-use and publication-quality figures. Availability and implementation dittoSeq is an R package available through Bioconductor via an open source MIT license. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells

2019 ◽  
Vol 35 (21) ◽  
pp. 4525-4527 ◽  
Author(s):  
Alex X Lu ◽  
Taraneh Zarin ◽  
Ian S Hsu ◽  
Alan M Moses
Keyword(s):  
Image Analysis ◽  
Web Application ◽  
Single Cells ◽  
Yeast Cells ◽  
Supplementary Information ◽  
Supplementary Data ◽  
User Friendly ◽  
Microscopy Images

Abstract Summary We introduce YeastSpotter, a web application for the segmentation of yeast microscopy images into single cells. YeastSpotter is user-friendly and generalizable, reducing the computational expertise required for this critical preprocessing step in many image analysis pipelines. Availability and implementation YeastSpotter is available at http://yeastspotter.csb.utoronto.ca/. Code is available at https://github.com/alexxijielu/yeast_segmentation. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos

2019 ◽  
Author(s):  
A Trullo ◽  
J Dufourt ◽  
M Lagha
Keyword(s):  
Graphical User Interface ◽  
Transcriptional Activation ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Automatic Image Analysis ◽  
Lineage Tree ◽  
Automatic Software ◽  
Integrated Software ◽  
Lineage Tracking ◽  
User Friendly

Abstract Motivation During development, progenitor cells undergo multiple rounds of cellular divisions during which transcriptional programs must be faithfully propagated. Investigating the timing of transcriptional activation, which is a highly stochastic phenomenon, requires the analysis of large amounts of data. In order to perform automatic image analysis of transcriptional activation, we developed a software that segments and tracks both small and large objects, leading the user from raw data up to the results in their final form. Results MitoTrack is a user-friendly open-access integrated software that performs the specific dual task of reporting the precise timing of transcriptional activation while keeping lineage tree history for each nucleus of a living developing embryo. The software works automatically but provides the possibility to easily supervise, correct and validate each step. Availability and implementation MitoTrack is an open source Python software, embedded within a graphical user interface (download here). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MetumpX—a metabolomics support package for untargeted mass spectrometry

2019 ◽  
Vol 36 (5) ◽  
pp. 1647-1648 ◽  
Author(s):  
Bilal Wajid ◽  
Hasan Iqbal ◽  
Momina Jamil ◽  
Hafsa Rafique ◽  
Faria Anwar
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Small Molecules ◽  
Software Package ◽  
Life Sciences ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Software Packages ◽  
Develop Software ◽  
User Friendly

Abstract Motivation Metabolomics is a data analysis and interpretation field aiming to study functions of small molecules within the organism. Consequently Metabolomics requires researchers in life sciences to be comfortable in downloading, installing and scripting of software that are mostly not user friendly and lack basic GUIs. As the researchers struggle with these skills, there is a dire need to develop software packages that can automatically install software pipelines truly speeding up the learning curve to build software workstations. Therefore, this paper aims to provide MetumpX, a software package that eases in the installation of 103 software by automatically resolving their individual dependencies and also allowing the users to choose which software works best for them. Results MetumpX is a Ubuntu-based software package that facilitate easy download and installation of 103 tools spread across the standard metabolomics pipeline. As far as the authors know MetumpX is the only solution of its kind where the focus lies on automating development of software workstations. Availability and implementation https://github.com/hasaniqbal777/MetumpX-bin. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Temporal network alignment via GoT-WAVE

2019 ◽  
Vol 35 (18) ◽  
pp. 3527-3529 ◽  
Author(s):  
David Aparício ◽  
Pedro Ribeiro ◽  
Tijana Milenković ◽  
Fernando Silva
Keyword(s):  
User Interface ◽  
State Of The Art ◽  
Source Code ◽  
Network Alignment ◽  
Supplementary Information ◽  
Temporal Network ◽  
Temporal Networks ◽  
Supplementary Data ◽  
Node Similarity ◽  
User Friendly

Abstract Motivation Network alignment (NA) finds conserved regions between two networks. NA methods optimize node conservation (NC) and edge conservation. Dynamic graphlet degree vectors are a state-of-the-art dynamic NC measure, used within the fastest and most accurate NA method for temporal networks: DynaWAVE. Here, we use graphlet-orbit transitions (GoTs), a different graphlet-based measure of temporal node similarity, as a new dynamic NC measure within DynaWAVE, resulting in GoT-WAVE. Results On synthetic networks, GoT-WAVE improves DynaWAVE’s accuracy by 30% and speed by 64%. On real networks, when optimizing only dynamic NC, the methods are complementary. Furthermore, only GoT-WAVE supports directed edges. Hence, GoT-WAVE is a promising new temporal NA algorithm, which efficiently optimizes dynamic NC. We provide a user-friendly user interface and source code for GoT-WAVE. Availability and implementation http://www.dcc.fc.up.pt/got-wave/ Supplementary information Supplementary data are available at Bioinformatics online.

Uncovering multiloci-ordering by algebraic property of Laplacian matrix and its Fiedler vector

2015 ◽  
Vol 32 (6) ◽  
pp. 801-807 ◽  
Author(s):  
Mookyung Cheon ◽  
Choongrak Kim ◽  
Iksoo Chang
Keyword(s):  
Source Code ◽  
Algebraic Property ◽  
Laplacian Matrix ◽  
Recombination Fraction ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Data Set ◽  
Variable Threshold ◽  
Fiedler Vector ◽  
Complex Graph

AbstractMotivation: The loci-ordering, based on two-point recombination fractions for a pair of loci, is the most important step in constructing a reliable and fine genetic map.Results: Using the concept from complex graph theory, here we propose a Laplacian ordering approach which uncovers the loci-ordering of multiloci simultaneously. The algebraic property for a Fiedler vector of a Laplacian matrix, constructed from the recombination fraction of the loci-ordering for 26 loci of barley chromosome IV, 846 loci of Arabidopsisthaliana and 1903 loci of Malus domestica, together with the variable threshold uncovers their loci-orders. It offers an alternative yet robust approach for ordering multiloci.Availability and implementation : Source code program with data set is available as supplementary data and also in a software category of the website (http://biophysics.dgist.ac.kr)Contact: [email protected] or [email protected] information: Supplementary data are available at Bioinformatics online.

scholarly journals mixtureS: a novel tool for bacterial strain genome reconstruction from reads

2020 ◽  
Author(s):  
Xin Li ◽  
Haiyan Hu ◽  
Xiaoman Li
Keyword(s):  
Environmental Samples ◽  
De Novo ◽  
Source Code ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Bacterial Strains ◽  
Metagenomic Sample ◽  
Almost All ◽  
User Friendly ◽  
Strain Genome

Abstract Motivation It is essential to study bacterial strains in environmental samples. Existing methods and tools often depend on known strains or known variations, cannot work on individual samples, not reliable, or not easy to use, etc. It is thus important to develop more user-friendly tools that can identify bacterial strains more accurately. Results We developed a new tool called mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS reliably identified the strains, their numbers and their abundance. Compared with three tools, mixtureS showed better performance in almost all simulated datasets and the vast majority of experimental datasets. Availability and implementation The source code and tool mixtureS is available at http://www.cs.ucf.edu/˜xiaoman/mixtureS/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals SEABED: Small molEcule activity scanner weB servicE baseD

2014 ◽  
Vol 31 (5) ◽  
pp. 773-775 ◽  
Author(s):  
Carlos Fenollosa ◽  
Marcel Otón ◽  
Pau Andrio ◽  
Jorge Cortés ◽  
Modesto Orozco ◽  
...  
Keyword(s):  
Web Service ◽  
Web Server ◽  
Software As A Service ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Ensemble Docking ◽  
Web Tools ◽  
Protein Mutants ◽  
User Friendly ◽  
Hybrid Docking

Abstract Motivation: The SEABED web server integrates a variety of docking and QSAR techniques in a user-friendly environment. SEABED goes beyond the basic docking and QSAR web tools and implements extended functionalities like receptor preparation, library editing, flexible ensemble docking, hybrid docking/QSAR experiments or virtual screening on protein mutants. SEABED is not a monolithic workflow tool but Software as a Service platform. Availability and implementation: SEABED is a free web server available athttp://www.bsc.es/SEABED. No registration is required. Contact: [email protected] Supplementary information: Supplementary data are available atBioinformatics online.

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