Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

<p>Abstract</p> <p>Background</p> <p>For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly.</p> <p>Results</p> <p>We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform.</p> <p>Conclusions</p> <p>By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.</p

The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon

a key model organism, not only for the study of halophilicity, but also for archaeal biology in general. DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb).

Alpha band prefrontal asymmetry does not underlie pain approach-avoidance: Results from two EEG studies

Pain research is often focused on escape from pain or approach of relief, yet individuals with chronic pain make complex choices to face their pain to satiate other drives (approach-avoidance conflicts). An abundance of research has indicated that prefrontal alpha band asymmetry (PFA) underlies approach-avoidance in general, but there is limited information about whether PFA underlies pain approach-avoidance conflicts. Electroencephalogram activity was recorded while 70 participants with chronic pain (n=33) and without chronic pain (n=37) approached/avoided stimuli containing simultaneous pain (low-high) and monetary reward (low-high). Findings from both studies revealed that approach-avoidance for pain stimuli is not accompanied by prefrontal asymmetry, irrespective of the presence of chronic pain

Equity at sea: Gender and inclusivity in UK sea-going science

Today, we can celebrate a strong representation of women in sea-going science in the United Kingdom, providing positive role models for early-career female marine scientists. However, women continue to face challenges to their progression in their marine science careers, especially those who are also members of other under-represented groups. In this article we consider gender equity and equality in participation and leadership in sea-going marine science in the UK, discussing successes and lessons learned for the future. After a brief history of UK women in ocean science, and a summary of some recent advances in gender equality, we look at further areas in need of improvement, and ask whether successes in improved gender equality can be transferred to tackling other forms of under-representation in sea-going science

WATERS: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

Abstract Background For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly. Results We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform. Conclusions By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions