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Do academic social networks share academics’ interests?

Do academic social networks share academics’ interests? | The science toolbox | Scoop.it
David Matthews examines the approach of ResearchGate, Academia.edu and Mendeley to profit, user data and open access publishing
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Rescooped by Niklaus Grunwald from Fungal|Oomycete Biology
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FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild | The science toolbox | Scoop.it
Fungi typically live in highly diverse communities composed of multiple ecological guilds. Although high-throughput sequencing has greatly increased the ability to quantify the diversity of fungi in environmental samples, researchers currently lack a simple and consistent way to sort large sequence pools into ecologically meaningful categories. We address this issue by introducing FUNGuild, a tool that can be used to taxonomically parse fungal OTUs by ecological guild independent of sequencing platform or analysis pipeline. Using a database and an accompanying bioinformatics script, we demonstrate the application of FUNGuild to three high-throughput sequencing datasets from different habitats: forest soils, grassland soils, and decomposing wood. We found that guilds characteristic of each habitat (i.e., saprotrophic and ectomycorrhizal fungi in forest soils, saprotrophic and arbuscular mycorrhizal fungi in grassland soils, saprotrophic, wood decomposer, and plant pathogenic fungi in decomposing wood) were each well represented. The example datasets demonstrate that while we could quickly and efficiently assign a large portion of the data to guilds, another large portion could not be assigned, reflecting the need to expand and improve the database as well as to gain a better understanding of natural history for many described and undescribed fungal species. As a community resource, FUNGuild is dependent on third-party annotation, so we invite researchers to populate it with new categories and records as well as refine those already in existence.

Via Alejandro Rojas
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Rescooped by Niklaus Grunwald from Genomics and metagenomics of microbes
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Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus

Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus | The science toolbox | Scoop.it
Abstract Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by> 3000 collections. Sources of error...

Via Bradford Condon
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VcfR: an R package to manipulate and visualize VCF format data

VcfR: an R package to manipulate and visualize VCF format data | The science toolbox | Scoop.it

Software to call single nucleotide polymorphisms or related genetic variants has converged on the variant call format (VCF) as the output format of choice. This has created a need for tools to work with VCF files. While an increasing number of software exists to read VCF data, many only extract the genotypes without including the data associated with each genotype that describes its quality. We created the R package vcfR to address this issue. We developed a VCF file exploration tool implemented in the R language because R provides an interactive experience and an environment that is commonly used for genetic data analysis. Functions to read and write VCF files into R as well as functions to extract portions of the data and to plot summary statistics of the data are implemented. VcfR further provides the ability to visualize how various parameterizations of the data affect the results. Additional tools are included to integrate sequence (FASTA) and annotation data (GFF) for visualization of genomic regions such as chromosomes. Conversion functions translate data from the vcfR data structure to formats used by other R genetics packages. Computationally intensive functions are implemented in C++ to improve performance. Use of these tools is intended to facilitate VCF data exploration, including intuitive methods for data quality control and easy export to other R packages for further analysis. VcfR thus provides essential, novel tools currently not available in R.

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Biologists urged to hug a preprint

Biologists urged to hug a preprint | The science toolbox | Scoop.it
ASAPbio meeting discusses the ins and outs of posting work online before peer review.
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Rescooped by Niklaus Grunwald from Genomics and metagenomics of microbes
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On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-binary Gene Trees

On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-binary Gene Trees | The science toolbox | Scoop.it

Duplication-Transfer-Loss (DTL) reconciliation has emerged as a powerful technique for studying gene family evolution in the presence of horizontal gene transfer. DTL reconciliation takes as input a gene family phylogeny and the corresponding species phylogeny, and reconciles the two by postulating speciation, gene duplication, horizontal gene transfer, and gene loss events. Efficient algorithms exist for finding optimal DTL reconciliations when the gene tree is binary. However, gene trees are frequently non-binary. With such non-binary gene trees, the reconciliation problem seeks to find a binary resolution of the gene tree that minimizes the reconciliation cost. Given the prevalence of non-binary gene trees, many efficient algorithms have been developed for this problem in the context of the simpler Duplication-Loss (DL) reconciliation model. Yet, no efficient algorithms exist for DTL reconciliation with non-binary gene trees and the complexity of the problem remains unknown. In this work, we resolve this open question by showing that the problem is, in fact, NP-hard. Our reduction applies to both the dated and undated formulations of DTL reconciliation. By resolving this long-standing open problem, this work will spur the development of both exact and heuristic algorithms for this important problem.


Via Bradford Condon
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Q&A: The academic satirist Jorge Cham on The PhD Movie 2: Still in Grad School | Nature

Q&A: The academic satirist Jorge Cham on The PhD Movie 2: Still in Grad School | Nature | The science toolbox | Scoop.it
Cartoonist and former robotics researcher Jorge Cham wowed graduate students with The PhD Movie in 2011. With the follow-up The PhD Movie 2: Still in Grad School [mdash] an astute, funny look at more academic tribulations [mdash] set to screen at campuses worldwide from the end of September, Cham talks about crowdfunding, the grim scrabble for grants, the under-representation of women in science and coaxing a cameo from a Nobel laureate.
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Science Isn’t Broken

Science Isn’t Broken | The science toolbox | Scoop.it
Graphics by Ritchie King If you follow the headlines, your confidence in science may have taken a hit lately. Peer review? More like self-review. An investigation in November uncovered a scam in wh…
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What to believe in the new world of open access publishing

What to believe in the new world of open access publishing | The science toolbox | Scoop.it
Just as no one ever assumed that everything in print was trustworthy, neither should that be the case for open access content.
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Rescooped by Niklaus Grunwald from MycorWeb Plant-Microbe Interactions
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Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead?

Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead? | The science toolbox | Scoop.it
Global change is altering species distributions and thus interactions among organisms. Organisms live in concert with thousands of other species, some beneficial, some pathogenic, some which have little to no effect in complex communities. Since natural communities are composed of organisms with very different life history traits and dispersal ability it is unlikely they will all respond to climatic change in a similar way. Disjuncts in plant-pollinator and plant-herbivore interactions under global change have been relatively well described, but plant-soil microorganism and soil microbe-microbe relationships have received less attention. Since soil microorganisms regulate nutrient transformations, provide plants with nutrients, allow co-existence among neighbors, and control plant populations, changes in soil microorganism-plant interactions could have significant ramifications for plant community composition and ecosystem function. In this paper we explore how climatic change affects soil microbes and soil microbe-plant interactions directly and indirectly, discuss what we see as emerging and exciting questions and areas for future research, and discuss what ramifications changes in these interactions may have on the composition and function of ecosystems.

Via Francis Martin
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Rescooped by Niklaus Grunwald from MycorWeb Plant-Microbe Interactions
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Forests and global change: what can genetics contribute to the major forest management and policy challenges of the twenty-first century? - Springer

Forests and global change: what can genetics contribute to the major forest management and policy challenges of the twenty-first century? - Springer | The science toolbox | Scoop.it

The conservation and sustainable use of forests in the twenty-first century pose huge challenges for forest management and policy. Society demands that forests provide a wide range of ecosystem services, from timber products, raw materials and renewable energy to sociocultural amenities and habitats for nature conservation. Innovative management and policy approaches need to be developed to meet these often-conflicting demands in a context of environmental change of uncertain magnitude and scale. Genetic diversity is a key component of resilience and adaptability. Overall, forest tree populations are genetically very diverse, conferring them an enormous potential for genetic adaptation via the processes of gene flow and natural selection. Here, we review the main challenges facing our forests in the coming century and focus on how recent progress in genetics can contribute to the development of appropriate practical actions that forest managers and policy makers can adopt to promote forest resilience to climate change. Emerging knowledge will inform and clarify current controversies relating to the choice of appropriate genetic resources for planting, the effect of silvicultural systems and stand tending on adaptive potential and the best ways to harness genetic diversity in breeding and conservation programs. Gaps in our knowledge remain, and we identify where additional information is needed (e.g., the adaptive value of peripheral populations or the genetic determinism of key adaptive traits) and the types of studies that are required to provide this key understanding.


Via Francis Martin
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XSim: Simulation of Descendants from Ancestors with Sequence Data

XSim: Simulation of Descendants from Ancestors with Sequence Data | The science toolbox | Scoop.it

Real or imputed high-density SNP genotypes are routinely used for genomic prediction and genome-wide association studies. Many researchers are moving toward the use of actual or imputed next-generation sequence data in whole-genome analyses. Simulation studies are useful to mimic complex scenarios and test different analytical methods. We have developed the software tool XSim to efficiently simulate sequence data in descendants in arbitrary pedigrees. In this software, a strategy to drop-down origins and positions of chromosomal segments rather than every allele state is implemented to simulate sequence data and to accommodate complicated pedigree structures across multiple generations. Both C++ and Julia versions of XSim have been developed.

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PhyloBotanist: The popularity of phylogenetic programs over the years

PhyloBotanist: The popularity of phylogenetic programs over the years | The science toolbox | Scoop.it

Great blog on: "What is the actual market share of different phylogenetics programs? How has it developed over time? by PhyloBotanist

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Should All Research Papers Be Free?

Following Mr. Swartz’s death, the White House issued a directive requiring agencies that make more than $100 million in research grants to develop plans so that recipients release their findings to the public within a year of publication. Moreover, there is legislation before Congress that requires the same, only shortening the embargo period to six months. Private funders such as the Wellcome Trust, Howard Hughes Medical Institute and the Bill & Melinda Gates Foundation have also begun making grants contingent on open access to resulting articles, as well as possibly to the underlying data.
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Statisticians Found One Thing They Can Agree On: It’s Time To Stop Misusing P-Values

Statisticians Found One Thing They Can Agree On: It’s Time To Stop Misusing P-Values | The science toolbox | Scoop.it
Little p-value What are you trying to say Of significance? — Stephen Ziliak, Roosevelt University economics professor How many statisticians does it take to en…
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RClone: a package to identify MultiLocus Clonal Lineages and handle clonal datasets in R - Bailleul - Methods in Ecology and Evolution - Wiley Online Library

RClone: a package to identify MultiLocus Clonal Lineages and handle clonal datasets in R - Bailleul - Methods in Ecology and Evolution - Wiley Online Library | The science toolbox | Scoop.it
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SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees

SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees | The science toolbox | Scoop.it

We present a fast and flexible software package –SimPhy– for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer –all three potentially leading to species-tree/gene-tree discordance– and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions.SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy’s output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, pre-compiled executables, a detailed manual and example cases. 

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Is There Really A War on Science?

Is There Really A War on Science? | The science toolbox | Scoop.it
People who oppose vaccines, GMOs and climate change evidence may be more anxious than antagonistic
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How to switch quickly to diamond open access: The best journals are free for authors and readers | Free Science Blog

The conventional wisdom among experts is that open access (OA) publication is better in all respects: Publications are not hidden behind paywalls, authors get more citations for their work, and results of publicly funded research are available to the public. This has been widely known for over 12 years, but not much has been happening. Some actors are frustrated, such as Ralf Schimmer, vice-director of the Max Planck Society’s MPDL: Henotes that despite all the pro-OA activities at universities and science organizations, the open access movement is stagnating. While one sixth of all publications is open access by open access, the clear majority for subscription seems to be stable.

 

What explains this strange stability, which defies the politicians’ hopes and the experts’ recommendations? The OA experts do not seem to be interested in finding out.

 
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Sustainable potato that resists blight given green light by USDA, but anti-GMO activists remain opposed | Genetic Literacy Project

Sustainable potato that resists blight given green light by USDA, but anti-GMO activists remain opposed | Genetic Literacy Project | The science toolbox | Scoop.it
Sustainable potato that reduces browning and bruising and lowers presence of potentially cancer-causing chemical now has added benefit of resisting blight that caused Great Irish Potato famine.
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New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation | The science toolbox | Scoop.it

Phylogeographic methods aim to infer migration trends and the history of sampled lineages from genetic data. Applications of phylogeography are broad, and in the context of pathogens include the reconstruction of transmission histories and the origin and emergence of outbreaks. Phylogeographic inference based on bottom-up population genetics models is computationally expensive, and as a result faster alternatives based on the evolution of discrete traits have become popular. In this paper, we show that inference of migration rates and root locations based on discrete trait models is extremely unreliable and sensitive to biased sampling. To address this problem, we introduce BASTA (BAyesian STructured coalescent Approximation), a new approach implemented in BEAST2 that combines the accuracy of methods based on the structured coalescent with the computational efficiency required to handle more than just few populations. We illustrate the potentially severe implications of poor model choice for phylogeographic analyses by investigating the zoonotic transmission of Ebola virus. Whereas the structured coalescent analysis correctly infers that successive human Ebola outbreaks have been seeded by a large unsampled non-human reservoir population, the discrete trait analysis implausibly concludes that undetected human-to-human transmission has allowed the virus to persist over the past four decades. As genomics takes on an increasingly prominent role informing the control and prevention of infectious diseases, it will be vital that phylogeographic inference provides robust insights into transmission history.

 
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Monarch butterfly studies tell a perplexing tale

Monarch butterfly studies tell a perplexing tale | The science toolbox | Scoop.it
Mexico’s winter declines not obvious in summer surveys elsewhere
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Rescooped by Niklaus Grunwald from Genomics and metagenomics of microbes
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Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils

Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils | The science toolbox | Scoop.it
Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS). The following treatments were considered: 1) the amount of soil used in DNA extraction, 2) the inclusion of additional steps (freeze/t

Via Bradford Condon
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Rescooped by Niklaus Grunwald from Complex networks & bioinformatics
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The dangers of default parameters in bioinformatics: lessons from Bowtie and TopHat

The dangers of default parameters in bioinformatics: lessons from Bowtie and TopHat | The science toolbox | Scoop.it

Most bioinformatics tools are equipped with a vast array of command-line options which let the user configure the inputs, outputs, and performance of the software. You may not wish to explore every possible option when using a particular piece of software, but you should always try to have a look at the manual. 


Via Pablo Vicente Munuera
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