Mac Operating Systems Research Articles

An Efficient Workflow for Collecting, Entering, and Proofing Field Data: Harnessing Voice Recording and Dictation Software

An Efficient Workflow for Collecting, Entering, and Proofing Field Data: Harnessing Voice Recording and Dictation Software

ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences.

Identification of viral integration sites has been important in understanding the pathogenesis and progression of diseases associated with particular viral infections. The advent of next-generation sequencing (NGS) has enabled researchers to understand the impact that viral integration has on the host, such as tumorigenesis. Current computational methods to analyze NGS data of virus-host junction sites have been limited in terms of their accessibility to a broad user base. In this study, we developed a software application (named ChimericSeq), that is the first program of its kind to offer a graphical user interface, compatibility with both Windows and Mac operating systems, and optimized for effectively identifying and annotating virus-host chimeric reads within NGS data. In addition, ChimericSeq’s pipeline implements custom filtering to remove artifacts and detect reads with quantitative analytical reporting to provide functional significance to discovered integration sites. The improved accessibility of ChimericSeq through a GUI interface in both Windows and Mac has potential to expand NGS analytical support to a broader spectrum of the scientific community.

Abstract 2584: The UCSC Xena system for cancer genomics data visualization and interpretation

Abstract The UCSC Xena platform (http://xena.ucsc.edu/) allows biologists and bioinformaticians to securely analyze and visualize their private functional genomics data in the context of public genomic and clinical data sets. The Xena platform consists of a set of federated data hubs and the Xena browser, which integrates across hubs, providing one location to analyze and visualize all data. Our expanding public Xena Data Hubs currently hosts 1400+ data sets from more than 35 cancer types, as well as Pan-Cancer data sets. Our public data hubs serve seminal cancer genomics and functional genomics data set to the scientific community, including the latest TCGA, TARGET, ICGC, and GTEx data sets. We support most data types including somatic and germline SNPs, INDELs, large structural variants, CNV, gene-, transcript-, exon- protein-, miRNA-expression, DNA methylation, phenotypes, clinical data, subtype classifications and genomic biomarkers. Additionally, investigators’ own functional genomics data can be hosted on private hubs running on their laptop or behind the firewall. Data is integrated on the UCSC Xena Browser, allowing biologists to view and interpretation of their genomic data in the context of a large collection of cancer genomics data sets such as TCGA. The lightweight Xena data hubs are straightforward to install on Windows, Mac and Linux operating systems and loading data is easy using either our application or command line interface. This system of the browser and hubs helps researchers combine new or preliminary results from their laptops or internal servers, or even data from a new paper, securely with vetted data from the public sphere. Visualizations and analyses include dynamic Kaplan-Meier survival analysis to assess survival stratification by any information in addition to our visual spreadsheet, scatter plots and bar graphs. We seek feedback at our poster on new visualizations and functionalities. Citation Format: Mary Goldman, Brian Craft, Jingchun Zhu, David Haussler. The UCSC Xena system for cancer genomics data visualization and interpretation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2584. doi:10.1158/1538-7445.AM2017-2584

Cybersecurity: Time Series Predictive Modeling of Vulnerabilities of Desktop Operating System Using Linear and Non-Linear Approach

Vulnerability forecasting models help us to predict the number of vulnerabilities that may occur in the future for a given Operating System (OS). There exist few models that focus on quantifying future vulnerabilities without consideration of trend, level, seasonality and non linear components of vulnerabilities. Unlike traditional ones, we propose a vulnerability analytic prediction model based on linear and non-linear approaches via time series analysis. We have developed the models based on Auto Regressive Moving Average (ARIMA), Artificial Neural Network (ANN), and Support Vector Machine (SVM) settings. The best model which provides the minimum error rate is selected for prediction of future vulnerabilities. Utilizing time series approach, this study has developed a predictive analytic model for three popular Desktop Operating Systems, namely, Windows 7, Mac OS X, and Linux Kernel by using their reported vulnerabilities on the National Vulnerability Database (NVD). Based on these reported vulnerabilities, we predict ahead their behavior so that the OS companies can make strategic and operational decisions like secure deployment of OS, facilitate backup provisioning, disaster recovery, diversity planning, maintenance scheduling, etc. Similarly, it also helps in assessing current security risks along with estimation of resources needed for handling potential security breaches and to foresee the future releases of security patches. The proposed non-linear analytic models produce very good prediction results in comparison to linear time series models.

SarConfoCal: simultaneous sarcomere length and cytoplasmic calcium measurements for laser scanning confocal microscopy images.

Simultaneous recordings of myocytes contractility and their cytoplasmic calcium concentration allow powerful studies, particularly on heart failure and other cardiac dysfunctions. Such studies require dedicated and expensive experimental devices that are difficult to use. Thus we propose SarConfoCal, the first and only software to simultaneously analyse both cytoplasmic calcium variations (from fluorescence signal) and myocytes contractility (from sarcomere length measurement) on laser scanning confocal microscopy images. SarConfoCal is easy to set up and use, especially by people without programming skills. The software is freely distributed under the GNU General Public License. Download and setup instructions are available at http://pccv.univ-tours.fr/ImageJ/SarConfoCal . It is provided as a toolset for ImageJ (the open-source program for image analysis provided by the National Institutes of Health). SarConfoCal has been tested under Windows, Mac and Linux operating systems. come.pasqualin@univ-tours.fr. Supplementary data are available at Bioinformatics online.

Abstract 5270: The UCSC Xena system for integrating and visualizing functional genomics

Abstract UCSC Xena (http://xena.ucsc.edu/) is a bioinformatics tool to visualize functional genomics data from multiple sources simultaneously, including both public and private data. The Xena system consists of a set of federated data hubs and the Xena browser, which integrates across hubs, providing one location to analyze and visualize all data. The lightweight Xena data hubs are straightforward to install on Windows, Mac and Linux operating systems and easily allow hub administrators to authenticate users, ensuring that only authorized users have access to secure data. Loading data into a Xena hub is easy using either our application or command line interface. Hosting public data from major projects, such as TCGA, on public Xena hubs gives users access without having to download these large datasets. The Xena system makes it easy to aggregate across many hubs, allowing users to integrate public datasets and private secure data together or view them separately. This system of the browser and hubs helps researchers combine new or preliminary results from their laptops or internal servers, or even data from a new paper, securely with vetted data from the public sphere. The largest public Xena hub, based at UCSC, currently hosts an expanding set of searchable data, including 806 public datasets from several large consortiums including TCGA (The Cancer Genome Atlas), ICGC (International Cancer Genome Consortium), Treehouse Childhood Cancer Project, CCLE (Cancer Cell Line Encyclopedia), and more. Xena hubs are flexible enough to handle most data types, including gene, exon, miRNA and protein expression, copy number, DNA methylation and somatic mutation data along with phenotypes, subtype classifications and genomic biomarkers. Dynamic Kaplan-Meier survival analysis helps investigators to assess survival stratification by any information while scatter plots and bar graphs offer new insights into the data. Integration with Galaxy gives users access to a myriad of bioinformatics tools for further analysis and hypothesis testing. Citation Format: Mary Goldman, Brian Craft, Jingchun Zhu, Teresa Swatloski, Melissa Cline, David Haussler. The UCSC Xena system for integrating and visualizing functional genomics. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5270.

SarcOptiM for ImageJ: high-frequency online sarcomere length computing on stimulated cardiomyocytes.

Accurate measurement of cardiomyocyte contraction is a critical issue for scientists working on cardiac physiology and physiopathology of diseases implying contraction impairment. Cardiomyocytes contraction can be quantified by measuring sarcomere length, but few tools are available for this, and none is freely distributed. We developed a plug-in (SarcOptiM) for the ImageJ/Fiji image analysis platform developed by the National Institutes of Health. SarcOptiM computes sarcomere length via fast Fourier transform analysis of video frames captured or displayed in ImageJ and thus is not tied to a dedicated video camera. It can work in real time or offline, the latter overcoming rotating motion or displacement-related artifacts. SarcOptiM includes a simulator and video generator of cardiomyocyte contraction. Acquisition parameters, such as pixel size and camera frame rate, were tested with both experimental recordings of rat ventricular cardiomyocytes and synthetic videos. It is freely distributed, and its source code is available. It works under Windows, Mac, or Linux operating systems. The camera speed is the limiting factor, since the algorithm can compute online sarcomere shortening at frame rates >10 kHz. In conclusion, SarcOptiM is a free and validated user-friendly tool for studying cardiomyocyte contraction in all species, including human.

PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems.

PASMet (Prediction, Analysis and Simulation of Metabolic networks) is a web-based platform for proposing and verifying mathematical models to understand the dynamics of metabolism. The advantages of PASMet include user-friendliness and accessibility, which enable biologists and biochemists to easily perform mathematical modelling. PASMet offers a series of user-functions to handle the time-series data of metabolite concentrations. The functions are organised into four steps: (i) Prediction of a probable metabolic pathway and its regulation; (ii) Construction of mathematical models; (iii) Simulation of metabolic behaviours; and (iv) Analysis of metabolic system characteristics. Each function contains various statistical and mathematical methods that can be used independently. Users who may not have enough knowledge of computing or programming can easily and quickly analyse their local data without software downloads, updates or installations. Users only need to upload their files in comma-separated values (CSV) format or enter their model equations directly into the website. Once the time-series data or mathematical equations are uploaded, PASMet automatically performs computation on server-side. Then, users can interactively view their results and directly download them to their local computers. PASMet is freely available with no login requirement at http://pasmet.riken.jp/ from major web browsers on Windows, Mac and Linux operating systems.

Microsoft Windows vs. Apple Mac OS X: Resilience against ARP cache poisoning attack in a local area network

ABSTRACTRobust security measures are integrated into new release versions of operating systems (OSs) to ensure that users have a more secure and reliable environment in which to run their daily tasks. In this article, through extensive practical experiments, we evaluate and compare the resilience of popular versions of Microsoft Windows OSs and Apple Mac OS X against Address Resolution Protocol (ARP) cache poisoning attack in a local area network (LAN). The experimental results demonstrate clearly that all tested versions of Windows OSs and Apple Mac OS X are vulnerable to the ARP cache poisoning attack, and do not deploy built-in efficient security features to prevent success of this attack. In addition, the experimental results directly contradict the common belief that Windows OSs are always less secure than Apple OSs. On the other hand, the article analyzes the efforts that have been made and the different methods that have been applied to detect and prevent ARP cache poisoning attacks. The article shows that none of these efforts and methods has been able to give satisfactory results.

0426 : SarcOptiM, an ImageJ plug-in for cardiomyocyte contractility recording

Accurate measurement of cardiomyocyte contractility is a critical issue for scientists working on cardiac physiology and physiopathology of diseases implying contraction impairment such as heart failure. The most reliable method for the evaluation of the cardiomyocyte contraction amplitude and kinetics consists in the measurement of sarcomere shortening. The few tools available for this are always tied to dedicated video cameras and none is freely distributed. Here, we describe SarcOptiM, a free open-source plug-in developed in Java for ImageJ/Fiji image analysis platform of the NIH, running under Windows, Mac and Linux operating systems. It computes sarcomere length via Fourier transform analysis of video frames captured or displayed in ImageJ and thereby allows real-time or offline sarcomere measurements. This plug-in has been validated with experimental recordings of rat ventricular cardiomyocyte in several conditions including beta adrenergic stimulation, and with synthetic videos of contracting cardiomyocyte with known features. SarcOptiM is not tied to a specific hardware contrary to marketed software, and works with all digital and analogical video cameras interfaced with ImageJ. Thus, the video camera can be chosen according to the experimental needs. The sampling frequency of the sarcomere length recording is set by the video camera frame rate; a sampling frequency of 1000 Hz is easily reachable with a mid-range costless video camera. Moreover, SarcOptiM overcomes some common problems such as displacements related artifacts and orientation of the cardiomyocyte in the visual field. In conclusion, SarcOptiM is a free, powerful and user-friendly tool for researchers studying cardiomyocyte contractility in all species including human. The author hereby declares no conflict of interest

An Analysis on Host Vulnerability Evaluation of Modern Operating Systems

Security is a major concern in all computing environments. One way to achieve security is to deploy a secure operating system (OS). A trusted OS can actually secure all the resources and can resist the vulnerabilities and attacks effectively. In this paper, our contribution is twofold. Firstly, we critically analyze the host vulnerabilities in modern desktop OSs. We group existing approaches and provide an easy and concise view of different security models adapted by most widely used OSs. The comparison of several OSs regarding structure, architecture, mode of working, and security models also form part of the paper. Secondly, we use the current usage statistics for Windows, Linux, and MAC OSs and predict their future. Our forecast will help the designers, developers and users of the different OSs to prepare for the upcoming years accordingly.

DeID - a data sharing tool for neuroimaging studies.

Funding institutions and researchers increasingly expect that data will be shared to increase scientific integrity and provide other scientists with the opportunity to use the data with novel methods that may advance understanding in a particular field of study. In practice, sharing human subject data can be complicated because data must be de-identified prior to sharing. Moreover, integrating varied data types collected in a study can be challenging and time consuming. For example, sharing data from structural imaging studies of a complex disorder requires the integration of imaging, demographic and/or behavioral data in a way that no subject identifiers are included in the de-identified dataset and with new subject labels or identification values that cannot be tracked back to the original ones. We have developed a Java program that users can use to remove identifying information in neuroimaging datasets, while still maintaining the association among different data types from the same subject for further studies. This software provides a series of user interaction wizards to allow users to select data variables to be de-identified, implements functions for auditing and validation of de-identified data, and enables the user to share the de-identified data in a single compressed package through various communication protocols, such as FTPS and SFTP. DeID runs with Windows, Linux, and Mac operating systems and its open architecture allows it to be easily adapted to support a broader array of data types, with the goal of facilitating data sharing. DeID can be obtained at http://www.nitrc.org/projects/deid.

Automatically Assessing Lexical Sophistication: Indices, Tools, Findings, and Application

This study explores the construct of lexical sophistication and its applications for measuring second language lexical and speaking proficiency. In doing so, the study introduces the Tool for the Automatic Analysis of LExical Sophistication (TAALES), which calculates text scores for 135 classic and newly developed lexical indices related to word frequency, range, bigram and trigram frequency, academic language, and psycholinguistic word information. TAALES is freely available; runs on Windows, Mac, and Linux operating systems; and has a simple graphic user interface that allows for batch processing of .txt files. The tool is fast, reliable, and outputs results to a comma‐separated value file that can be accessed using spreadsheet software. The study examines the ability of TAALES indices to explain the variance in human judgments of lexical proficiency and speaking proficiency for second language (L2) learners. Overall, these indices were able to explain 47.5% of the variance in holistic scores of lexical proficiency and 48.7% of the variance in holistic scores of speaking proficiency. This study has important implications for second language acquisition, for assessing L2 learners' productive skills (writing and speaking), and for L2 pedagogy. Limitations and future directions are also discussed.

PYFLOW: A computer code for the calculation of the impact parameters of Dilute Pyroclastic Density Currents (DPDC) based on field data

PYFLOW is a computer code designed for quantifying the hazard related to Dilute Pyroclastic Density Currents (DPDC). DPDCs are multiphase flows that form during explosive volcanic eruptions. They are the major source of hazard related to volcanic eruptions, as they exert a significant stress over buildings and transport significant amounts of volcanic ash, which is hot and unbreathable. The program calculates the DPDC׳s impact parameters (e.g. dynamic pressure and particle volumetric concentration) and is founded on the turbulent boundary layer theory adapted to a multiphase framework. Fluid-dynamic variables are searched with a probabilistic approach, meaning that for each variable the average, maximum and minimum solutions are calculated. From these values, PYFLOW creates probability functions that allow to calculate the parameter at a given percentile. The code is written in Fortran 90 and can be compiled and installed on Windows, Mac OS X, Linux operating systems (OS). A User׳s manual is provided, explaining the details of the theoretical background, the setup and running procedure and the input data. The model inputs are DPDC deposits data, e.g. particle grainsize, layer thickness, particles shape factor and density. PYFLOW reads input data from a specifically designed input file or from the user׳s direct typing by command lines. Guidelines for writing input data are also contained in the package. PYFLOW guides the user at each step of execution, asking for additional data and inputs. The program is a tool for DPDC hazard assessment and, as an example, an application to the DPDC deposits of the Agnano–Monte Spina eruption (4.1ky BP) at Campi Flegrei (Italy) is presented.

MicrOMEGAs_3: A program for calculating dark matter observables

micrOMEGAs is a code to compute dark matter observables in generic extensions of the standard model. This new version of micrOMEGAs is a major update which includes a generalization of the Boltzmann equations to accommodate models with asymmetric dark matter or with semi-annihilation and a first approach to a generalization of the thermodynamics of the Universe in the relic density computation. Furthermore a switch to include virtual vector bosons in the final states in the annihilation cross sections or relic density computations is added. Effective operators to describe loop-induced couplings of Higgses to two-photons or two-gluons are introduced and reduced couplings of the Higgs are provided allowing for a direct comparison with recent LHC results. A module that computes the signature of DM captured in celestial bodies in neutrino telescopes is also provided. Moreover the direct detection module has been improved as concerns the implementation of the strange “content” of the nucleon. New extensions of the standard model are included in the distribution. Program summaryTitle of program: micrOMEGAs3.Program obtainable from:http://lapth.cnrs.fr/micromegasComputers for which the program is designed and others on which it has been tested: PC, MacOperating systems under which the program has been tested : UNIX (Linux, Darwin)Programming language used: C and FortranMemory required to execute with typical data: 50 MB depending on the number of processes required.No. of processors used: 1Has the code been vectorized or parallelized: noNo. of bytes in distributed program, including test data: 70736 kBExternal routines/libraries used: noCPC Program Library subprograms used: CalcHEP, SuSpect, NMSSMTools, CPSuperH, LoopTools, HiggsBoundsCatalogue identifier of previous version: ADQR_v1_3Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 842Does the new version supersede the previous version: yesNature of physical problem: Calculation of the relic density and direct and indirect detection rates of the lightest stable particle in a generic new model of particle physics.Method of solution: In numerically solving the evolution equation for the density of dark matter, relativistic formulae for the thermal average are used. All tree-level processes for annihilation and coannihilation of new particles in the model are included as well as some 3-body final states. The cross-sections for all processes are calculated exactly with CalcHEP after definition of a model file. The propagation of the charged cosmic rays is solved within a semi-analytical two-zone model.Reasons for the new version: There are many experiments that are currently searching for the remnants of dark matter annihilation and the relic density is determined precisely from cosmological measurements. In this version we add the computation of dark matter signals in neutrino telescopes, we generalize the Boltzmann equations so as to take into account a larger class of dark matter models and improve the precision in the prediction of the relic density for DM masses that are below the W mass. We compute the signal strength for Higgs production in different channels to compare with the results of the LHC.Summary of revisions:•Generalization of the Boltzmann equations to include asymmetric dark matter and semi-annihilations: the DM asymmetry is taken into account when computing direct/indirect detection rates.•Incorporating loop-induced decays of Higgs particles to two-photons and two-gluons, and computing the signal strength for Higgs production in various channels that can be compared to results from LHC searches.•New module for neutrino signature from DM capture in the Sun and the Earth•Annihilation cross sections for some selected 3-body processes in addition to the 2-body tree-level processes. The 3-body option can be included in the computation of the relic density and/or for annihilation of dark matter in the galaxy.•Possibility of using different tables for the effective degrees of freedom in the early Universe•Annihilation cross sections for the loop induced processes γγ and γZ0 in the NMSSM and the CPVMSSM•New function for incorporating DM clumps•New function to define the strange quark content of the nucleon•The LanHEP source code for new models is included•New models with scalar DM are included (Inert doublet model and model with Z3 symmetry)•New implementation of the NMSSM which uses the Higgs self-couplings and the particle spectrum calculated in NMSSMTools_4.1•New versions of spectrum generators used in the MSSM (Suspect_2.4.1) and in the CPVMSSM (CPsuperH2.3)•Extended routines for flavor physics in the MSSM•New facilities to compute DM observables independently of the model•Update in interface tools to read files produced by other codes, this allows easy interface to other codesTypical running time: 4 sUnusual features of the program: Depending on the parameters of the model, the program generates additional new code, compiles it and loads it dynamically.

Developing a conceptual and practical framework for outcomes measurement to support a quality improvement project in Rwanda: an observational study

BackgroundA landmark study in 2009 demonstrated that a WHO surgical safety checklist decreased mortality and complications in surgical patients. Attempts to replicate this in the developing world have been mixed. We piloted the implementation of a surgical safety checklist with outcomes measurement in one district hospital in Rwanda, with the goal of creating a scalable model to use in all public hospitals in the country. MethodsWe sought to develop a conceptual and practical framework for ongoing outcomes measurement that can be applied to quality improvement projects in resource-poor settings. We accomplished this through interviews with global checklist implementation teams and Rwandan hospital staff, as well as observation. FindingsWe developed the following framework with specific examples from our experience. (1) Define the elements of data collection and who will perform each. In particular, the data audit function must be carefully outlined. (2) Understand the potential motivators for each participant in data collection and align incentives; these may be financial or non-financial. (3) Choose a data collection training method including initiation, maintenance, and troubleshooting. (4) Select a database software considering the following: availability of consistent or intermittent internet access, user interface complexity, flexibility of software for Mac and PC operating systems, need for mobile access, initial and ongoing costs, and technical support. Based on these criteria, we chose to pilot a new offline version of REDCap, which may have important implications for global health projects in settings without consistent internet access. (5) Be flexible. The framework provides a best first guess at the methods that will work for high-quality data collection, but a willingness to change course is critical. InterpretationMonitoring outcomes in quality improvement projects in resource-poor settings is difficult, but a framework makes it possible to effectively plan, initiate, and sustain data collection. FundingLifebox Foundation, London, UK.

Corrected ISICSoo class version

The Coster–Kronig enhancement factor calculation for M3 shell x-ray production cross sections was found to be incorrect in both ISICSoo class (Batič et al. (2012) [1]) and isics program (Cipolla (2013) [2]). The affected functions of ISICSoo class have been corrected. The resulting X-ray production cross sections are modified by less than 15%, while ionization cross sections are unchanged. NEW VERSION PROGRAM SUMMARYProgram Title: ISICSooJournal Reference:Catalogue identifier: AEKN_v1_1Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKN_v1_1.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc: 26417No. of bytes in distributed program, including test data, etc: 440762Distribution format: tar.gzProgramming language: C++Computer: 80486 or higher-level PC or MacOperating system: any OS with gcc compiler version 4.1 (or newer)Classification: 16.7Catalogue identifier of previous version: AEKN_v1_0Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 398–404Does the new version supersede the previous version?: yesNature of problem: Ionization and X-ray production cross section calculations for ion–atom collisions.Solution method: Numerical integration of form factor using a logarithmic transform and Gaussian quadrature, plus exact integration limits.Reasons for the new version: The Coster–Kronig enhancement factor calculation for M3 shell x-ray production cross sections was found to be incorrect in ISICSoo. The affected function has been corrected.Summary of revisions: The corresponding function members of ISICSoo class have been corrected. Fig. 1 shows the relative differences between plain PWBA x-ray production cross sections between old and new ISICSoo versions. The relative differences are largest at small energies and heavy targets, but in our calculations never surpassing 15%. Ionization cross sections were not affected by implemented correction.Running time: Same as in previous version. [Display omitted] References[1] M. Batič, M. G. Pia, S. J. Cipolla, Comp. Phys. Comm. 183 (2012), pp. 398–404.[2] S. J. Cipolla, Comp. Phys. Comm., 2013 (http://dx.doi.org/10.1016/j.cpc.2013.02.017).

JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison

BackgroundCross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species. Existing tools to investigate genomic contexts, however, lack features for dynamically comparing and exploring genomic regions from multiple species. As DNA sequencing technologies improve and the number of whole sequenced microbial genomes increases, a user-friendly genome context comparison platform designed for use by a broad range of users promises to satisfy a growing need in the biological community.ResultsHere we present JContextExplorer: a tool that organizes genomic contexts into branching diagrams. We implement several alternative context-comparison and tree rendering algorithms, and allow for easy transitioning between different clustering algorithms. To facilitate genomic context analysis, our tool implements GUI features, such as text search filtering, point-and-click interrogation of individual contexts, and genomic visualization via a multi-genome browser. We demonstrate a use case of our tool by attempting to resolve annotation ambiguities between two highly homologous yet functionally distinct genes in a set of 22 alpha and gamma proteobacteria.ConclusionsJContextExplorer should enable a broad range of users to analyze and explore genomic contexts. The program has been tested on Windows, Mac, and Linux operating systems, and is implemented both as an executable JAR file and java WebStart. Program executables, source code, and documentation is available at http://www.bme.ucdavis.edu/facciotti/resources_data/software/.

New Learning Spaces? M-learning's, in Particular the iPadâ??s Potentials in Education

The iPad is a very popular touchscreen tablet computer, which was introduced approximately two, two and a half years ago. It runs the MAC operating system making it suitable for different general and special uses. The paper focuses on the fact how the use of iPads can help education, make teaching and learning more efficient. In addition to the technical, infrastructural parameters, which are essential as much as the userâ??s experience and it usability are concerned, the paper provides a few concrete applications as well. Today, the use of iPads is general either in everyday life, or in public education or tertiary education. The author analysis his experiences from the viewpoint of students, but also mentions applications useful for teachers. Students can use iPads with the appropriate applications in any stage of the learning process, e.g. using notes, course materials, schedules and assignments, cooperation, group assignments by collaboration. The paper also describes such solutions or respectively suggestions by means of which the monitoring of shared content and data can be realized by the teacher. A few professional applications (e.g. used by students of medicine, engineering and natural sciences) are also listed.

Setting Up an Integrated Development Environment for Python (Mac)

This lesson will help you set up an integrated development environment for Python on a computer running a Mac operating system.