MacStylet, software to analyse electrical penetration graph data on the Macintosh

Conclusion Since the EPG method is increasingly utilized in the investigation of plant-Homoptera interactions, this software has been developed to enable fast processing of abundant data. The objective seems to have been achieved and, with a little practice, a 2-hour experiment may be analysed in about 10–15 minutes. Mac-Stylet is stand-alone shareware, freely distributed to all persons interested (request to G. Febvay, email: febvay@jouy.inra.fr).     

RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials

A new software package, RASPA, for simulating adsorption and diffusion of molecules in flexible nanoporous materials is presented. The code implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo (MC) in various ensembles including symplectic/measure-preserving integrators, Ewald summation, configurational-bias MC, continuous fractional component MC, reactive MC and Baker's minimisation. We show example applications of RASPA in computing coexistence properties, adsorption isotherms for single and multiple components, self- and collective diffusivities, reaction systems and visualisation. The software is released under the GNU General Public License.     

burnr: Fire history analysis and graphics in R

We developed a new software package, burnr, for fire history analysis and plotting in the R statistical programming environment. It was developed for tree-ring fire-scar analysis, but is broadly applicable to other event analyses (e.g., avalanches, frost rings, or culturally modified trees). Our new package can read, write, and manipulate standard tree-ring fire history FHX files, produce fire—demography charts, calculate fire frequency and seasonality statistics, and run superposed epoch analysis (SEA). A key benefit of burnr is that it enables automation of analyses and plotting, especially for large data sets. The package also facilitates creative plotting, mapping, and analyses when combined with the thousands of packages available in R. In this paper, we describe the basic functionality of burnr and introduce users to fire history analyses in R.     

FIM Imaging and FIMtrack: Two New Tools Allowing High-throughput and Cost Effective Locomotion Analysis

The analysis of neuronal network function requires a reliable measurement of behavioral traits. Since the behavior of freely moving animals is variable to a certain degree, many animals have to be analyzed, to obtain statistically significant data. This in turn requires a computer assisted automated quantification of locomotion patterns. To obtain high contrast images of almost translucent and small moving objects, a novel imaging technique based on frustrated total internal reflection called FIM was developed. In this setup, animals are only illuminated with infrared light at the very specific position of contact with the underlying crawling surface. This methodology results in very high contrast images. Subsequently, these high contrast images are processed using established contour tracking algorithms. Based on this, we developed the FIMTrack software, which serves to extract a number of features needed to quantitatively describe a large variety of locomotion characteristics. During the development of this software package, we focused our efforts on an open source architecture allowing the easy addition of further modules. The program operates platform independent and is accompanied by an intuitive GUI guiding the user through data analysis. All locomotion parameter values are given in form of csv files allowing further data analyses. In addition, a Results Viewer integrated into the tracking software provides the opportunity to interactively review and adjust the output, as might be needed during stimulus integration. The power of FIM and FIMTrack is demonstrated by studying the locomotion of Drosophila larvae.     

ImShot: An Open-Source Software for Probabilistic Identification of Proteins In Situ and Visualization of Proteomics Data

Imaging mass spectrometry (IMS) has developed into a powerful tool allowing label-free detection of numerous biomolecules in situ. In contrast to shotgun proteomics, proteins/peptides can be detected directly from biological tissues and correlated to its morphology leading to a gain of crucial clinical information. However, direct identification of the detected molecules is currently challenging for MALDI–IMS, thereby compelling researchers to use complementary techniques and resource intensive experimental setups. Despite these strategies, sufficient information could not be extracted because of lack of an optimum data combination strategy/software. Here, we introduce a new open-source software ImShot that aims at identifying peptides obtained in MALDI–IMS. This is achieved by combining information from IMS and shotgun proteomics (LC–MS) measurements of serial sections of the same tissue. The software takes advantage of a two-group comparison to determine the search space of IMS masses after deisotoping the corresponding spectra. Ambiguity in annotations of IMS peptides is eliminated by introduction of a novel scoring system that identifies the most likely parent protein of a detected peptide in the corresponding IMS dataset. Thanks to its modular structure, the software can also handle LC–MS data separately and display interactive enrichment plots and enriched Gene Ontology terms or cellular pathways. The software has been built as a desktop application with a conveniently designed graphic user interface to provide users with a seamless experience in data analysis. ImShot can run on all the three major desktop operating systems and is freely available under Massachusetts Institute of Technology license.     

Information and Communication Technology‐Enabled Low Carbon Technologies

This article outlines the subsector of the information and communication technology (ICT) industry concerned with reducing the economy's environmental impact, dubbed ICT‐enabled low carbon technologies (ICTeLCTs). The article is based on a study funded by United Kingdom (UK) Trade and Investment, a division of the UK Department for Business, Innovation and Skills. ICTeLCTs can be segmented into specialist and generalist operators. Specialists focus on one or two ICT applications to monitor or reduce environmental issues, while generalists supply products and services enabling a firm or a private household to reduce the environmental impact of its activities. The subsector can be further segmented into green ICT, energy management, building management, carbon accounting, waste management, intelligent transport systems (ITSs), and water management. The main factors driving ICTeLCTs include legislation, voluntary environmental standards, corporate social responsibility (CSR) activities, customer demand, and competitive market factors. Policy makers should continue to drive the growth of ICTeLCTs with the introduction and refinement of environmental legislation regulating energy use and markets.     

hw‐quickcheck: an easy‐to‐use computer program for checking genotypes for agreement with Hardy–Weinberg expectations

Deviations from Hardy–Weinberg expectations are frequently a sign of genotyping error. hw‐quickcheck is an easy‐to‐use computer program for detecting departures from Hardy–Weinberg equilibrium. hw‐quickcheck uses exact tests for all of its calculations. These tests include a global test for heterozygote excess/deficiency and genotype‐specific tests.     

Screening the Main Factors Affecting Extraction of the Antimicrobial Substance from Bacillus sp. fmbJ using the Plackett–Burman Method

Summary The Plackett–Burman screening method was utilized as a tool to evaluate the importance of the selected six factors, including methanol, ethanol, propanol, butanol, pH and time, which are relevant to the extraction of the antimicrobial substance produced by Bacillus sp. fmbJ. The main factors that affected the extraction of the antimicrobial substance were determined as methanol (P < 0.0001), ethanol (P < 0.0001), pH (P = 0.0032), and time (P < 0.0001) by using the JMP software. Within the test ranges, methanol, ethanol, and time showed a significant positive relativity to the total extracted amounts respectively; while pH had a significant negative effect. The maximum prediction profile indicated that the total extracted amounts for the antimicrobial substance would reach 50.21 mg/100 ml with 99.64% probability.     

Hematopoietic chimerism monitoring based on STRs: quantitative platform performance on sequential samples.

Hematopoietic stem cell transplantation (HSCT) creates a donor-recipient cellular chimerism in the patient, which is quantitatively assayed from peripheral blood based on STR-DNA. Since chimerism values often vary across a patient's samples, it is important to determine to what extent this variability reflects technical aspects of platform performance. This issue is systematically assessed in the current study for the first time. Using the SGM Plus multiplex PCR kit and ABI platform, the longitudinal performance of STR markers was quantitatively evaluated in two chimeric models with true values, and in patient samples (n >500 marker loci). Computation of percent chimerism for each marker, and mean (sample) percent chimerism, standard deviation, and coefficient of variance was performed by our ChimerTrack utility. In chimeric models with known values, individual markers exhibited an accuracy (observed/true) of 88-98%; replication precision was 92-100% true, with a mean error of 2%. Fragment size calling was greater than 99% accurate and precise. Patient results were comparable for markers, relaive to sample means. One source of technical variability in chimerism estimation was allelic differential amplification efficiency. The latter was influenced by signal amplitude, dye label, marker size, and allelic size interval. It can be concluded that long-term chimeric tracking is routinely feasible using this platform in conjunction with ChimerTrack software. Importantly, mean percent chimerism, for any sample, should closely approximate the true chimeric status, with a technical accuracy of 98%. Guidelines are presented for selecting an optimized marker profile.