Genomics Virtual Laboratory: a practical bioinformatics workbench for the cloud

Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets ; workflow platform(s) enabling accessible, reproducible, portable analyses, through a flexible set of interfaces ; highly available, scalable computational resources ; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise

Path Integral Monte Carlo Approach to the U(1) Lattice Gauge Theory in (2+1) Dimensions

Path Integral Monte Carlo simulations have been performed for U(1) lattice gauge theory in (2+1) dimensions on anisotropic lattices. We extractthe static quark potential, the string tension and the low-lying "glueball" spectrum.The Euclidean string tension and mass gap decrease exponentially at weakcoupling in excellent agreement with the predictions of Polyakov and G{\" o}pfert and Mack, but their magnitudes are five times bigger than predicted. Extrapolations are made to the extreme anisotropic or Hamiltonian limit, and comparisons are made with previous estimates obtained in the Hamiltonian formulation.Comment: 12 pages, 16 figure

Community-driven development for computational biology at Sprints, Hackathons and Codefests

Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. Results: This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. Conclusions: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects

Functional illness in primary care: dysfunction versus disease

<p>Abstract</p> <p>Background</p> <p>The Biopsychosocial Model aims to integrate the biological, psychological and social components of illness, but integration is difficult in practice, particularly when patients consult with medically unexplained physical symptoms or functional illness.</p> <p>Discussion</p> <p>This Biopsychosocial Model was developed from General Systems Theory, which describes nature as a dynamic order of interacting parts and processes, from molecular to societal. Despite such conceptual progress, the biological, psychological, social and spiritual components of illness are seldom managed as an integrated whole in conventional medical practice. This is because the biomedical model can be easier to use, clinicians often have difficulty relinquishing a disease-centred approach to diagnosis, and either dismiss illness when pathology has been excluded, or explain all undifferentiated illness in terms of psychosocial factors. By contrast, traditional and complementary treatment systems describe reversible functional disturbances, and appear better at integrating the different components of illness. Conventional medicine retains the advantage of scientific method and an expanding evidence base, but needs to more effectively integrate psychosocial factors into assessment and management, notably of 'functional' illness. As an aid to integration, pathology characterised by structural change in tissues and organs is contrasted with dysfunction arising from disordered physiology or psychology that may occur independent of pathological change.</p> <p>Summary</p> <p>We propose a classification of illness that includes orthogonal dimensions of pathology and dysfunction to support a broadly based clinical approach to patients; adoption of which may lead to fewer inappropriate investigations and secondary care referrals and greater use of cognitive behavioural techniques, particularly when managing functional illness.</p

Electron correlations in mesoscopic systems.

This thesis deals with electron correlation effects within low-dimensional, mesoscopic systems. We study phenomena within two different types of system in which correlations play an important role. The first involves the spectra and spin structure of small symmetric quantum dots, or &quoteartificial atoms&quote. The second is the&quote0.7 structure&quote, a well-known but mysterious anomalous conductance plateau which occurs in the conductance profile of a quantum point contact.Artificial atoms are manufactured mesoscopic devices: quantum dots which resemble real atoms in that their symmetry gives them a &quoteshell structure&quote. We examine two-dimensional circular artificial atoms numerically, using restricted and unrestricted Hartree-Fock simulation. We go beyond the mean-field approximation by direct calculation of second-order correlation terms; a method which works well for real atoms but to our knowledge has not been used before for quantum dots. We examine the spectra and spin structure of such dots and find, contrary to previous theoretical mean-field studies, that Hund's rule is not followed. We also find, in agreement with previous numerical studies, that the shell structure is fragile with respect to a simple elliptical deformation.The 0.7 structure appears in the conductance of a quantum point contact. The conductance through a ballistic quantum point contact is quantised in units of 2e^2/h. On the lowest conductance step, an anomalous narrow conductance plateau at about G = 0.7 x 2e^2/h isknown to exist, which cannot be explained in the non-interacting picture. Based on suggestive numerical results, we model conductance through the lowest channel of a quantum point contact analytically. The model is based on the screening of the electron-electron interaction outside the QPC, and our observation that the wavefunctions at the Fermi level are peaked within the QPC. We use a kinetic equation approach, with perturbative account of electron-electron backscattering, to demonstrate that these simple features lead to the existence of a 0.7-like structure in the conductance. The behaviour of this structure reproduces experimentally observed features of the 0.7 structure, including the temperature dependence and the behaviour under applied in-plane magnetic fields

Rubra - flexible distributed pipelines

<p>This poster was presented at the Bioinformatics Open Source Conference, 2013 (BOSC2013). It describes:</p> <p>* Rubra, a tool for running analysis pipelines based on the Ruffus framework for Python,</p> <p>* an implemented pipeline for calling variants from next-gen sequencing data.</p> <p>We have released the code for both on github.</p

Bionitio:Demonstrating and facilitating best practices for bioinformatics command-line software

BACKGROUND: Bioinformatics software tools are often created ad hoc, frequently by people without extensive training in software development. In particular, for beginners, the barrier to entry in bioinformatics software development is high, especially if they want to adopt good programming practices. Even experienced developers do not always follow best practices. This results in the proliferation of poorer-quality bioinformatics software, leading to limited scalability and inefficient use of resources; lack of reproducibility, usability, adaptability, and interoperability; and erroneous or inaccurate results. FINDINGS: We have developed Bionitio, a tool that automates the process of starting new bioinformatics software projects following recommended best practices. With a single command, the user can create a new well-structured project in 1 of 12 programming languages. The resulting software is functional, carrying out a prototypical bioinformatics task, and thus serves as both a working example and a template for building new tools. Key features include command-line argument parsing, error handling, progress logging, defined exit status values, a test suite, a version number, standardized building and packaging, user documentation, code documentation, a standard open source software license, software revision control, and containerization. CONCLUSIONS: Bionitio serves as a learning aid for beginner-to-intermediate bioinformatics programmers and provides an excellent starting point for new projects. This helps developers adopt good programming practices from the beginning of a project and encourages high-quality tools to be developed more rapidly. This also benefits users because tools are more easily installed and consistent in their usage. Bionitio is released as open source software under the MIT License and is available at https://github.com/bionitio-team/bionitio

Obesity does not alter endometrial gene expression in women with endometriosis

Research question: Does obesity affect endometrial gene expression in women with endometriosis, specifically women with stage I disease? Design: Differential gene expression analysis was conducted on endometrium from women with and without endometriosis (n = 169). Women were diagnosed after surgical visualization and staged according to the revised American Society for Reproductive Medicine (stage I-IV). Women were grouped by body mass index (BMI) (kg/m) as underweight, normal, pre-obese or obese. After accounting for menstrual cycle stage, endometrial gene expression was analysed by BMI (continuous and grouped) in women with endometriosis, and in non-endometriosis controls. Results: No significant interaction effect was found between BMI and endometriosis status on endometrial gene expression. We have previously reported that obese women with endometriosis have a reduced incidence of stage I disease; however, stratifying our analysis into stage I endometriosis versus combined II, III and IV endometriosis failed to reveal any differentially expressed endometrial genes between normal, pre-obese and obese patients. Conclusions: Despite obesity having deleterious effects on endometrial gene expression in other gynaecological pathologies, e.g. endometrial cancer and polycystic ovary syndrome, our results do not support an association between BMI and altered endometrial gene expression in women with or without endometriosis

A summary of the criteria that would define a general genomics workbench environment, and suggested implications on technical requirements.

<p>A summary of the criteria that would define a general genomics workbench environment, and suggested implications on technical requirements.</p