Calculating landscape diversity with information-theory based indices: A GRASS GIS solution

The assessment of species diversity in relatively large areas has always been a challenging task for ecologists, mainly because of the intrinsic difficulty to judge the completeness of species lists and to undertake sufficient and appropriate sampling. Since the variability of remotely sensed signal is expected to be related to landscape diversity, it could be used as a good proxy of diversity at species level.It has been demonstrated that the relation between species and landscape diversity measured from remotely sensed data or land use maps varies with scale. However, Free and Open Source tools (allowing an access to the source code) for assessing landscape diversity at different spatial scales are still lacking today. In this paper, we aim at: i) providing a theoretical background of the mostly used diversity indices stemmed from information theory that are commonly applied to quantify landscape diversity from remotely sensed data and ii) proposing a free and robust Open Source tool (r.diversity) with its source code for calculating diversity indices (and allowing an easy potential implementation of new metrics by multiple contributors globally) at different spatial scales from remotely-sensed imagery or land use maps, running under the widely used Open Source program GRASS GIS.r.diversity can be a valuable tool for calculating landscape diversity in an Open Source space given the availability of multiple indices at multiple spatial scales with the possibility to create new indices directly reusing the code.We expect that the subject of this paper will stimulate discussions on the opportunities offered by Free and Open Source Software to calculate landscape diversity indices.     

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included “Data Science;” “Standards and Interoperability;” “Open Science and Reproducibility;” “Translational Bioinformatics;” “Visualization;” and “Bioinformatics Open Source Project Updates”. In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled “Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community,” that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.Open in a separate window     

ArrayQuest: a web resource for the analysis of DNA microarray data

Background  

Numerous microarray analysis programs have been created through the efforts of Open Source software development projects. Providing browser-based interfaces that allow these programs to be executed over the Internet enhances the applicability and utility of these analytic software tools.     

Inequalities in Open Source Software Development: Analysis of Contributor’s Commits in Apache Software Foundation Projects

While researchers are becoming increasingly interested in studying OSS phenomenon, there is still a small number of studies analyzing larger samples of projects investigating the structure of activities among OSS developers. The significant amount of information that has been gathered in the publicly available open-source software repositories and mailing-list archives offers an opportunity to analyze projects structures and participant involvement. In this article, using on commits data from 263 Apache projects repositories (nearly all), we show that although OSS development is often described as collaborative, but it in fact predominantly relies on radically solitary input and individual, non-collaborative contributions. We also show, in the first published study of this magnitude, that the engagement of contributors is based on a power-law distribution.     

Modelling cellular systems with PySCeS

SUMMARY: The Python Simulator for Cellular Systems (PySCeS) is an extendable research tool for the numerical analysis and investigation of cellular systems. AVAILABILITY: PySCeS is distributed as Open Source Software under the GNU General Public Licence and is available for download from http://pysces.sourceforge.net CONTACT: bgoli@sun.ac.za.     

The Bio* toolkits--a brief overview

Bioinformatics research is often difficult to do with commercial software. The Open Source BioPerl, BioPython and Biojava projects provide toolkits with multiple functionality that make it easier to create customised pipelines or analysis. This review briefly compares the quirks of the underlying languages and the functionality, documentation, utility and relative advantages of the Bio counterparts, particularly from the point of view of the beginning biologist programmer.     

Effect of Educational Outreach Timing and Duration on Facility Performance for Infectious Disease Care in Uganda: A Trial with Pre-Post and Cluster Randomized Controlled Components

Background

Classroom-based learning is often insufficient to ensure high quality care and application of health care guidelines. Educational outreach is garnering attention as a supplemental method to enhance health care worker capacity, yet there is little information about the timing and duration required to improve facility performance. We sought to evaluate the effects of an infectious disease training program followed by either immediate or delayed on-site support (OSS), an educational outreach approach, on nine facility performance indicators for emergency triage, assessment, and treatment; malaria; and pneumonia. We also compared the effects of nine monthly OSS visits to extended OSS, with three additional visits over six months.

Methods

This study was conducted at 36 health facilities in Uganda, covering 1,275,960 outpatient visits over 23 months. From April 2010 to December 2010, 36 sites received infectious disease training; 18 randomly selected sites in arm A received nine monthly OSS visits (immediate OSS) and 18 sites in arm B did not. From March 2011 to September 2011, arm A sites received three additional visits every two months (extended OSS), while the arm B sites received eight monthly OSS visits (delayed OSS). We compared the combined effect of training and delayed OSS to training followed by immediate OSS to determine the effect of delaying OSS implementation by nine months. We also compared facility performance in arm A during the extended OSS to immediate OSS to examine the effect of additional, less frequent OSS.

Results

Delayed OSS, when combined with training, was associated with significant pre/post improvements in four indicators: outpatients triaged (44% vs. 87%, aRR = 1.54, 99% CI = 1.11, 2.15); emergency and priority patients admitted, detained, or referred (16% vs. 31%, aRR = 1.74, 99% CI = 1.10, 2.75); patients with a negative malaria test result prescribed an antimalarial (53% vs. 34%, aRR = 0.67, 99% CI = 0.55, 0.82); and pneumonia suspects assessed for pneumonia (6% vs. 27%, aRR = 2.97, 99% CI = 1.44, 6.17). Differences between the delayed OSS and immediate OSS arms were not statistically significant for any of the nine indicators (all adjusted relative RR (aRRR) between 0.76–1.44, all p>0.06). Extended OSS was associated with significant improvement in two indicators (outpatients triaged: aRR = 1.09, 99% CI = 1.01; emergency and priority patients admitted, detained, or referred: aRR = 1.22, 99% CI = 1.01, 1.38) and decline in one (pneumonia suspects assessed for pneumonia: aRR: 0.93; 99% CI = 0.88, 0.98).

Conclusions

Educational outreach held up to nine months after training had similar effects on facility performance as educational outreach started within one month post-training. Six months of bi-monthly educational outreach maintained facility performance gains, but incremental improvements were heterogeneous.     

CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data

In this article we describe a new Bioconductor package 'CALIB' for normalization of two-color microarray data. This approach is based on the measurements of external controls and estimates an absolute target level for each gene and condition pair, as opposed to working with log-ratios as a relative measure of expression. Moreover, this method makes no assumptions regarding the distribution of gene expression divergence. AVAILABILITY: http://bioconductor.org/packages/2.0/bioc Open Source.     

Importing MAGE-ML format microarray data into BioConductor

The microarray gene expression markup language (MAGE-ML) is a widely used XML (eXtensible Markup Language) standard for describing and exchanging information about microarray experiments. It can describe microarray designs, microarray experiment designs, gene expression data and data analysis results. We describe RMAGEML, a new Bioconductor package that provides a link between cDNA microarray data stored in MAGE-ML format and the Bioconductor framework for preprocessing, visualization and analysis of microarray experiments. AVAILABILITY: http://www.bioconductor.org. Open Source.     

The Oxygen-Scavenging System Protecting Nitrogenase from Oxygen in Cells of Blue-Green Algae

There is a heat stable oxygen-scavenging system (OSS) associated with membrane which reduces oxygen endogenously in cells of blue-green algae. Addition of the OSS to cell suspension of heterocystous oxygen sensitive Anabaena mutant and non-heterocystous Pleetonema boryanum led to an increase in their nitrogenase activity by 10–100-fold higher than those under microaerobic condition and also could restore effectively their acetylene reduction activity at higher oxygen concentration since the oxygen presented was reduced effectively. The results suggest that the OSS possesses a function protecting nitrogenase from oxygen in cells. Furthermore, it was found that the efficiency of reducing oxygen of OSS from the Anabaena mutant and Plectonema was lower than those from Anabaena wild and Gloeocapsa in atm. oxygen level. This may be ralated with the susceptibility of nitrogen fixation to oxygen in the cells of Anabaena mutant and Plectonema. The present study firstly indicades the relationship between the heat stable OSS associated with membrane and the mechanism of protecting nitrogenase from oxygen in cells of blue-green algae. Activities of catalase, peroxidase and superoxide dismutase do not show obvious difference in cellfree extract of Anabaena wild and mutant. Methyl viologen can induce nitrogenase activity of Anabaena mutant by subverting a portion of electon flow to accelerate oxygen reduction.     

MathSBML: a package for manipulating SBML-based biological models

MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models. It converts SBML models into Mathematica data structures and provides a platform for manipulating and evaluating these models. Once a model is read by MathSBML, it is fully compatible with standard Mathematica functions such as NDSolve (a differential-algebraic equations solver). MathSBML also provides an application programming interface for viewing, manipulating, running numerical simulations; exporting SBML models; and converting SBML models in to other formats, such as XPP, HTML and FORTRAN. By accessing the full breadth of Mathematica functionality, MathSBML is fully extensible to SBML models of any size or complexity. AVAILABILITY: Open Source (LGPL) at http://www.sbml.org and http://www.sf.net/projects/sbml     

基于土地利用及植被覆盖变化的黄河源区生境质量时空变化特征

位于青藏高原腹地的黄河源地区生态环境脆弱,面临生物多样性锐减、生态系统退化等问题,黄河源区生态系统保护及其高质量发展已成为国家的重点战略之一。土地利用与植被覆盖是影响生境质量的重要因素,定量化土地利用方式、强度及格局和植被覆盖格局对生态质量影响的研究越来越受到关注,但其对黄河源区生态质量的耦合效应尚不明确。基于2000年和2015年黄河源区土地利用类型及生长季归一化植被指数（NDVI）,采用InVEST模型探究了不同时期黄河源区生境质量时空变化,并采用地理加权回归（GWR）模型揭示了生境质量对土地利用和植被覆盖变化的空间响应特征。结果表明,2000年与2015年土地利用类型变化主要为未利用土地向草地的转移。植被覆盖变化方面,源区生长季NDVI整体上升。从生境质量的空间分布来看,黄河源区生境质量总体呈现南高北低的空间格局,高值分布在南部及中部地区,低值分布在北部布青山、东北部高海拔区及黄河乡的黄河沿岸。相较于2000年,2015年黄河源区生境质量平均提高11.47%。草地面积和NDVI与生境质量均呈显著正相关关系,其中NDVI是提高黄河源区生境质量的重要驱动因子。研究结果突出了NDVI对提高黄河源区生境质量的主导作用,可为未来源区生态保护提供借鉴。     

Oxygen-tolerant Strain of Chlorella sorokiniana

An oxygen-tolerant strain (OTS) of Chlorella sorokiniana was isolated by growing and continuously subculturing the oxygen-sensitive strain (OSS) in growth medium bubbled continuously with 95% O(2)-5% CO(2). Under these conditions, 6 to 8 hr were required before the OSS began to grow. The growth rates of the OTS and the OSS were the same when grown in an atmosphere of air-5% CO(2), and the growth rate of the OTS was the same when aerated with 95% O(2)-5% CO(2) and air-5% CO(2). The adaptive process was irreversible since serial transfers of the OTS grown with air-5% CO(2) did not alter the ability of the OTS to grow with 95% O(2)-5% CO(2). Inasmuch as photosynthesis in the OTS and the OSS was inhibited to a similar extent by oxygen and the adaptive process occurred heterotrophically in the absence of photosynthesis, it was concluded that the adaptive process was independent of photosynthesis. Morphological differences between the OTS and the OSS are presented and discussed with respect to the adaptive process.     

Purification and characterization of an ovulation stimulating substance from the male accessory glands of Drosophila suzukii

An ovulation stimulating substance (OSS) was isolated from males of the fruit fly Drosophila suzukii, and purified to a homogeneous state by a 5-step purification procedure: extraction with 80% methanol, chloroform wash, heat treatment, ion-exchange chromatography, and reverse phase high performance liquid chromatography. Approximately 100-fold purification was obtained thereby yielding 39 μg of OSS from 1000 males for an overall yield of 34%. The OSS is a single peptide consisting of at least 35 amino acid residues and having a molecular weight of 3990. The purified OSS not only initiated ovulation in unmated females but also suppressed their receptivity towards males. The peptide of D. suzukii was found to be effective in the females of D. melanogaster, a species that belong to a different subgroup, but was less effective in a more closely related species, D. pulchrella.     

Operant sensation seeking requires metabotropic glutamate receptor 5 (mGluR5)

Pharmacological and genetic studies have suggested that the metabotropic glutamate receptor 5 (mGluR5) is critically involved in mediating the reinforcing effects of drugs of abuse, but not food. The purpose of this study was to use mGluR5 knockout (KO), heterozygous (Het), and wildtype (WT) mice to determine if mGluR5 modulates operant sensation seeking (OSS), an operant task that uses varied sensory stimuli as a reinforcer. We found that mGluR5 KO mice had significantly reduced OSS responding relative to WT mice, while Het mice displayed a paradoxical increase in OSS responding. Neither KO nor Het mice exhibited altered operant responding for food as a reinforcer. Further, we assessed mGluR5 KO, Het and WT mice across a battery of cocaine locomotor, place preference and anxiety related tests. Although KO mice showed expected differences in some locomotor and anxiety measures, Het mice either exhibited no phenotype or an intermediate one. In total, these data demonstrate a key role for mGluR5 in OSS, indicating an important role for this receptor in reinforcement-based behavior.     

Open source tools and toolkits for bioinformatics: significance, and where are we?

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.     

Association between morbidity and skeletal biomarkers of biological aging

The Osseographic Scoring System (OSS) is a synthetic measure of skeletal aging that combines osteoporotic and osteoarthritic changes of the hand. The OSS is used to evaluate biological age in a population. The aim of the present study was to evaluate the association between certain chronic morbidities and the skeletal biomarker of biological aging. We performed a population-based study on a large sample of individuals who were receiving no medications to treat or prevent chronic morbidities [668 male (age 18-89 years) and 608 female (age 18-81 years) Chuvashians]. Morbidity data obtained from the individuals' medical records was sorted into 16 categories. A one-way ANOVA was used to elucidate the association between morbidity and age-adjusted OSS score. Statistically significant differences between means of OSS scores in affected vs. nonaffected individuals were found in the rheumatic diseases group. Ischemic heart disease, pulmonary diseases, traumatic brain injuries, and gynecological diseases also showed differences; however, after correction for multiple testing, the results were statistically nonsignificant. We conclude that individuals who suffer from the mentioned chronic morbidities will show a higher degree of skeletal aging. Further research is needed to clarify the biological mechanisms of association between certain types of morbidities and changes in skeletal aging.     

Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments

SUMMARY: Two Sample Logo is a web-based tool that detects and displays statistically significant differences in position-specific symbol compositions between two sets of multiple sequence alignments. In a typical scenario, two groups of aligned sequences will share a common motif but will differ in their functional annotation. The inclusion of the background alignment provides an appropriate underlying amino acid or nucleotide distribution and addresses intersite symbol correlations. In addition, the difference detection process is sensitive to the sizes of the aligned groups. Two Sample Logo extends WebLogo, a widely-used sequence logo generator. The source code is distributed under the MIT Open Source license agreement and is available for download free of charge.