scholarly journals Complete recovery of values in Diophantine systems (CORVIDS)

2018 ◽  
Author(s):  
Sean Wilner ◽  
Katherine Wood ◽  
Daniel J. Simons
Keyword(s):  
Standard Deviation ◽  
Open Source ◽  
Diophantine Equations ◽  
Source Code ◽  
Complete Recovery ◽  
Summary Statistics ◽  
Data Set ◽  
Raw Data ◽  
Source Program ◽  
User Friendly

Raw data are often unavailable, and all that may remain of a data set are its summary statistics. When these data are integers on a fixed scale, such as Likert-style ratings, and their mean, standard deviation, and sample size are known, it is possible to reconstruct every raw distribution that gives rise to those summary statistics using a system of Diophantine equations. We have developed the open-source program CORVIDS (COmplete Reconstruction of Values In Diophantine Systems) to deterministically reconstruct raw data from summary statistics using this technique. The solutions generated by the program are provably complete. Here we describe the implementation, provide examples and use cases, and prove the correctness of the underlying mathematics. CORVIDS is open-source and available as source code or as stand-alone, user-friendly applications for macOS and Windows.

scholarly journals MOSGA: Modular Open-Source Genome Annotator

2020 ◽  
Author(s):  
Roman Martin ◽  
Thomas Hackl ◽  
Georges Hattab ◽  
Matthias G Fischer ◽  
Dominik Heider
Keyword(s):  
Open Source ◽  
Source Code ◽  
Supplementary Information ◽  
Web Interface ◽  
Fully Integrated ◽  
Sequencing Technologies ◽  
A Genome ◽  
Wide Range ◽  
User Friendly ◽  
Eukaryotic Genomes

Abstract Motivation The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies. However, the annotation of these assemblies—a crucial step toward unlocking the biology of the organism of interest—has remained a complex challenge that often requires advanced bioinformatics expertise. Results Here, we present MOSGA (Modular Open-Source Genome Annotator), a genome annotation framework for eukaryotic genomes with a user-friendly web-interface that generates and integrates annotations from various tools. The aggregated results can be analyzed with a fully integrated genome browser and are provided in a format ready for submission to NCBI. MOSGA is built on a portable, customizable and easily extendible Snakemake backend, and thus, can be tailored to a wide range of users and projects. Availability and implementation We provide MOSGA as a web service at https://mosga.mathematik.uni-marburg.de and as a docker container at registry.gitlab.com/mosga/mosga: latest. Source code can be found at https://gitlab.com/mosga/mosga Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Effects of Secular Changes in Frequency of Observations and Observational Errors on Monthly Mean MSLP Summary Statistics Derived from ICOADS

2005 ◽  
Vol 18 (17) ◽  
pp. 3623-3633 ◽  
Author(s):  
Edmund K. M. Chang
Keyword(s):  
Standard Deviation ◽  
Reanalysis Data ◽  
Summary Statistics ◽  
Observational Error ◽  
Error Statistics ◽  
Cyclone Activity ◽  
Data Set ◽  
Sea Level Pressure ◽  
Increasing Trend ◽  
Order Of Magnitude

Abstract A Monte Carlo technique has been employed to assess how sextile mean sea level pressure (MSLP) statistics derived from ship observations can be affected by changes in the frequency of observations. The results show that when the number of observations is small (less than 20 per month), the estimates of the first sextile as well as the intersextile range, which is considered to be a resistant estimate of the standard deviation, can contain large biases. The results also suggest that, while changes in the frequency of observations do not have strong impacts on the standard way of estimating the standard deviation, such statistics are strongly affected by secular trends in observational error statistics. The results are applied to examine the increasing trend in cool season (December–March) Pacific cyclone activity during the second half of the twentieth century. The results show that the trends in sextile statistics derived from the NCEP–NCAR reanalysis data are only consistent with those derived from the International Comprehensive Ocean–Atmosphere Data Set (ICOADS) summary statistics if biases due to changes in the frequency of observation are not taken into account. When such biases are accounted for, the trends derived from the observations are significantly smaller than those derived from the reanalysis data. As for the increasing trend in MSLP variance, the trends derived from the ICOADS statistics are smaller than those derived from the reanalysis regardless of whether corrections are made to account for the secular trend in MSLP error statistics. In either case, the corrections that have to be applied have the same order of magnitude as the observed trends. The two main conclusions are that 1) climate statistics can be strongly affected by changes in frequency of observations as well as changes in observational error statistics and 2) the trends in North Pacific winter cyclone activity, as derived from NCEP–NCAR reanalysis data, appear to be significantly larger than similar trends computed from ICOADS sextile and variance statistics, when biases due to changes in frequency of observations and observational error statistics have been taken into account.

scholarly journals RhythmicAlly: Your R and Shiny–Based Open-Source Ally for the Analysis of Biological Rhythms

2019 ◽  
Vol 34 (5) ◽  
pp. 551-561 ◽  
Author(s):  
Lakshman Abhilash ◽  
Vasu Sheeba
Keyword(s):  
Time Series ◽  
Open Source ◽  
Time Series Data ◽  
Biological Rhythms ◽  
Series Data ◽  
Biological Time ◽  
Source Program ◽  
Wide Range ◽  
Infradian Rhythms ◽  
User Friendly

Research on circadian rhythms often requires researchers to estimate period, robustness/power, and phase of the rhythm. These are important to estimate, owing to the fact that they act as readouts of different features of the underlying clock. The commonly used tools, to this end, suffer from being very expensive, having very limited interactivity, being very cumbersome to use, or a combination of these. As a step toward remedying the inaccessibility to users who may not be able to afford them and to ease the analysis of biological time-series data, we have written RhythmicAlly, an open-source program using R and Shiny that has the following advantages: (1) it is free, (2) it allows subjective marking of phases on actograms, (3) it provides high interactivity with graphs, (4) it allows visualization and storing of data for a batch of individuals simultaneously, and (5) it does what other free programs do but with fewer mouse clicks, thereby being more efficient and user-friendly. Moreover, our program can be used for a wide range of ultradian, circadian, and infradian rhythms from a variety of organisms, some examples of which are described here. The first version of RhythmicAlly is available on Github, and we aim to maintain the program with subsequent versions having updated methods of visualizing and analyzing time-series data.

DiffractWD: an open-source program for powder pattern comparison and visualization

2010 ◽  
Vol 44 (1) ◽  
pp. 219-220 ◽  
Author(s):  
Volodimir Vreshch
Keyword(s):  
Single Crystal ◽  
Open Source ◽  
Phase Analysis ◽  
Powder Pattern ◽  
Crystal Data ◽  
Open Source Program ◽  
Source Program ◽  
Pattern Comparison ◽  
User Friendly ◽  
Qualitative Phase

A new program for basic powder pattern manipulations and visualization is described. It provides a user-friendly interface for comparison of spectra with each other and with simulated patterns based on single-crystal data. The program contains all necessary tools for the preparation of routine images for qualitative phase analysis and can be downloaded free of charge from http://diffractwd.com.

scholarly journals Development of graphical user interface for open source VLSI digital synthesis tool Qflow

2018 ◽  
Vol 7 (2) ◽  
pp. 710
Author(s):  
K. Sripath Roy ◽  
K. Abhiram ◽  
M. Arun Sumanth ◽  
Jaishree Jaishankar ◽  
P. Abhishek ◽  
...  
Keyword(s):  
User Interface ◽  
Open Source ◽  
Graphical User Interface ◽  
Source Code ◽  
Command Line ◽  
Simulation Process ◽  
Vlsi Technology ◽  
Synthesis Tool ◽  
Digital Synthesis ◽  
User Friendly

There are many tools that are used for simulation in the domain of VLSI technology but none of them are easily accessible. There is a need for Free and open source tools in this stream so as to make them accessible to everyone. There are efficient tools that already exist in open source in VLSI stream but are not used widely because of their command line user interface. Hence, creating a user friendly interface will help many developers and users to work easily. This paper deals with the idea to solve the above issue by creating a Graphical User Interface for the open source VLSI tool called QFlow. Qflow is a tool used in synthesizing a VLSI circuit from the Verilog source code. There are multiple tools integrated with this tool to assure the simulation process. It is a combination of many dependencies that are used for synthesis, placement, layout viewing and routing in a fabrication process. All the independent tools used for the Verilog code simulation are integrated onto a single platform. Qt is used for creating the cross-stage application.

Technology Tips: Visual Representations of Mean and Standard Deviation

1996 ◽  
Vol 89 (8) ◽  
pp. 688-692
Author(s):  
Charles Vonder Embse ◽  
Arne Engebretsen
Keyword(s):  
Standard Deviation ◽  
Visual Representations ◽  
Visual Display ◽  
Graphing Calculators ◽  
Statistical Information ◽  
Summary Statistics ◽  
Data Set ◽  
The Mean ◽  
Nonparametric Statistical ◽  
Bar Graphs

Summary statistics used to describe a data set are some of the most commonly taught statistical concepts in the secondary curriculum. Mean, median, mode, range, and standard deviation are topics that can be found in nearly every program. Technology empowers us to access these concepts and easily to create visual displays that interpret and describe the data in ways that enhance students' understanding. Many graphing calculators allow students to display nonparametric statistical information using a box-and-whiskers plot or a modified box plot showing a visual representation of the median, upper and lower quartiles, and the range of the data. But how can students visually display the mean of the data or show what it means to be within one standard deviation of the mean? One way to create this type of visual display is with a bar graph and constant functions. Unfortunately, graphing calculators, and some computer programs, only display histograms and not bar graphs. The tips in this issue focus on using graphing calculators to draw bar graphs that can help students visualize and interpret the mean and standard deviation of a data set.

scholarly journals RegioSQM20: improved prediction of the regioselectivity of electrophilic aromatic substitutions

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Nicolai Ree ◽  
Andreas H. Göller ◽  
Jan H. Jensen
Keyword(s):  
Open Source ◽  
Tight Binding ◽  
Electrophilic Aromatic Substitution ◽  
Data Sets ◽  
Aromatic Substitution ◽  
Success Rates ◽  
Proton Affinities ◽  
Data Set ◽  
Tautomeric Forms ◽  
Source Program

AbstractWe present RegioSQM20, a new version of RegioSQM (Chem Sci 9:660, 2018), which predicts the regioselectivities of electrophilic aromatic substitution (EAS) reactions from the calculation of proton affinities. The following improvements have been made: The open source semiempirical tight binding program is used instead of the closed source program. Any low energy tautomeric forms of the input molecule are identified and regioselectivity predictions are made for each form. Finally, RegioSQM20 offers a qualitative prediction of the reactivity of each tautomer (low, medium, or high) based on the reaction center with the highest proton affinity. The inclusion of tautomers increases the success rate from 90.7 to 92.7%. RegioSQM20 is compared to two machine learning based models: one developed by Struble et al. (React Chem Eng 5:896, 2020) specifically for regioselectivity predictions of EAS reactions (WLN) and a more generally applicable reactivity predictor (IBM RXN) developed by Schwaller et al. (ACS Cent Sci 5:1572, 2019). RegioSQM20 and WLN offers roughly the same success rates for the entire data sets (without considering tautomers), while WLN is many orders of magnitude faster. The accuracy of the more general IBM RXN approach is somewhat lower: 76.3–85.0%, depending on the data set. The code is freely available under the MIT open source license and will be made available as a webservice (regiosqm.org) in the near future.

Impact of Clone Refactoring on External Quality Attributes of Open Source Softwares

2018 ◽  
pp. 86-94
Author(s):  
Himanshi Vashisht ◽  
Sanjay Bharadwaj ◽  
Sushma Sharma
Keyword(s):  
Open Source ◽  
Internal Structure ◽  
Software Quality ◽  
Source Code ◽  
Quality Attributes ◽  
Software Component ◽  
External Quality ◽  
Code Refactoring ◽  
Observable Behaviour

Code refactoring is a “Process of restructuring an existing source code.”. It also helps in improving the internal structure of the code without really affecting its external behaviour”. It changes a source code in such a way that it does not alter the external behaviour yet still it improves its internal structure. It is a way to clean up code that minimizes the chances of introducing bugs. Refactoring is a change made to the internal structure of a software component to make it easier to understand and cheaper to modify, without changing the observable behaviour of that software component. Bad smells indicate that there is something wrong in the code that have to refactor. There are different tools that are available to identify and emove these bad smells. A software has two types of quality attributes- Internal and external. In this paper we will study the effect of clone refactoring on software quality attributes.

MackDroid - An Android based Application to monitor devices

2016 ◽  
Vol 9 ◽  
pp. 1
Author(s):  
Maaz Sirkhot ◽  
Ekta Sirwani ◽  
Aishwarya Kourani ◽  
Akshit Batheja ◽  
Kajal Jethanand Jewani
Keyword(s):  
Operating System ◽  
Open Source ◽  
Vital Role ◽  
Mobile Users ◽  
Android Application ◽  
Web Page ◽  
Technological World ◽  
Monitoring Service ◽  
User Friendly

In this technological world, smartphones can be considered as one of the most far-reaching inventions. It plays a vital role in connecting people socially. The number of mobile users using an Android based smartphone has increased rapidly since last few years resulting in organizations, cyber cell departments, government authorities feeling the need to monitor the activities on certain targeted devices in order to maintain proper functionality of their respective jobs. Also with the advent of smartphones, Android became one of the most popular and widely used Operating System. Its highlighting features are that it is user friendly, smartly designed, flexible, highly customizable and supports latest technologies like IoT. One of the features that makes it exclusive is that it is based on Linux and is Open Source for all the developers. This is the reason why our project Mackdroid is an Android based application that collects data from the remote device, stores it and displays on a PHP based web page. It is primarily a monitoring service that analyzes the contents and distributes it in various categories like Call Logs, Chats, Key logs, etc. Our project aims at developing an Android application that can be used to track, monitor, store and grab data from the device and store it on a server which can be accessed by the handler of the application.

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