Filling the gap between biology and computer science

This editorial introduces BioData Mining, a new journal which publishes research articles related to advances in computational methods and techniques for the extraction of useful knowledge from heterogeneous biological data. We outline the aims and scope of the journal, introduce the publishing model and describe the open peer review policy, which fosters interaction within the research community

Linking de novo assembly results with long DNA reads by dnaasm-link application

Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from next-generation and third-generation sequencing. Herein, we present a new application called dnaasm-link for linking contigs, a result of \textit{de novo} assembly of second-generation sequencing data, with long DNA reads. Our tool includes an integrated module to fill gaps with a suitable fragment of appropriate long DNA read, which improves the consistency of the resulting DNA sequences. This feature is very important, in particular for complex DNA regions, as presented in the paper. Finally, our implementation outperforms other state-of-the-art tools in terms of speed and memory requirements, which may enable the usage of the presented application for organisms with a large genome, which is not possible in~existing applications. The presented application has many advantages as (i) significant memory optimization and reduction of computation time (ii) filling the gaps through the appropriate fragment of a specified long DNA read (iii) reducing number of spanned and unspanned gaps in the existing genome drafts. The application is freely available to all users under GNU Library or Lesser General Public License version 3.0 (LGPLv3). The demo application, docker image and source code are available at http://dnaasm.sourceforge.net.Comment: 16 pages, 5 figure

Dictionary Matching with One Gap

The dictionary matching with gaps problem is to preprocess a dictionary $D$ of $d$ gapped patterns $P_1,\ldots,P_d$ over alphabet $\Sigma$, where each gapped pattern $P_i$ is a sequence of subpatterns separated by bounded sequences of don't cares. Then, given a query text $T$ of length $n$ over alphabet $\Sigma$, the goal is to output all locations in $T$ in which a pattern $P_i\in D$, $1\leq i\leq d$, ends. There is a renewed current interest in the gapped matching problem stemming from cyber security. In this paper we solve the problem where all patterns in the dictionary have one gap with at least $\alpha$ and at most $\beta$ don't cares, where $\alpha$ and $\beta$ are given parameters. Specifically, we show that the dictionary matching with a single gap problem can be solved in either $O(d\log d + |D|)$ time and $O(d\log^{\varepsilon} d + |D|)$ space, and query time $O(n(\beta -\alpha )\log\log d \log ^2 \min \{ d, \log |D| \} + occ)$, where $occ$ is the number of patterns found, or preprocessing time and space: $O(d^2 + |D|)$, and query time $O(n(\beta -\alpha ) + occ)$, where $occ$ is the number of patterns found. As far as we know, this is the best solution for this setting of the problem, where many overlaps may exist in the dictionary.Comment: A preliminary version was published at CPM 201

Generalized crystallography

X-ray crystal structure analysis can now be seen as a special kind of microscopy which is being extended to the recognition and examination of many kinds of ordered structure more general than crystals and which leads to their synthesis or construction by various methods. Electron microscopy and many other techniques now combine to give a coherent science of structure at the scale range of Ångstroms to microns, atoms to assemblies visible to the eye, which should continue to be called crystallography although it overlaps with nanotechnology, molecular biology, and solid state physics. Most generally, a crystal is a structure the description of which is much smaller than the structure itself and this view leads to the consideration of structures as carriers of information and on to wider concerns with growth, form, morphogenesis, and life itself

The Chlamydomonas genome project: A decade on

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes

L-systems in Geometric Modeling

We show that parametric context-sensitive L-systems with affine geometry interpretation provide a succinct description of some of the most fundamental algorithms of geometric modeling of curves. Examples include the Lane-Riesenfeld algorithm for generating B-splines, the de Casteljau algorithm for generating Bezier curves, and their extensions to rational curves. Our results generalize the previously reported geometric-modeling applications of L-systems, which were limited to subdivision curves.Comment: In Proceedings DCFS 2010, arXiv:1008.127

The Role of the Private Sector in Training the Next Generation of Biomedical Scientists

Summarizes the proceedings of a conference to address the unique contribution that private funders can make in ensuring that appropriate and adequate training programs are available for basic and clinical research. Offers conclusions and recommendations

Spontaneous Formation of Stable Capillary Bridges for Firming Compact Colloidal Microstructures in Phase Separating Liquids: A Computational Study

Computer modeling and simulations are performed to investigate capillary bridges spontaneously formed between closely packed colloidal particles in phase separating liquids. The simulations reveal a self-stabilization mechanism that operates through diffusive equilibrium of two-phase liquid morphologies. Such mechanism renders desired microstructural stability and uniformity to the capillary bridges that are spontaneously formed during liquid solution phase separation. This self-stabilization behavior is in contrast to conventional coarsening processes during phase separation. The volume fraction limit of the separated liquid phases as well as the adhesion strength and thermodynamic stability of the capillary bridges are discussed. Capillary bridge formations in various compact colloid assemblies are considered. The study sheds light on a promising route to in-situ (in-liquid) firming of fragile colloidal crystals and other compact colloidal microstructures via capillary bridges

A coupled mitral valve -- left ventricle model with fluid-structure interaction

Understanding the interaction between the valves and walls of the heart is important in assessing and subsequently treating heart dysfunction. With advancements in cardiac imaging, nonlinear mechanics and computational techniques, it is now possible to explore the mechanics of valve-heart interactions using anatomically and physiologically realistic models. This study presents an integrated model of the mitral valve (MV) coupled to the left ventricle (LV), with the geometry derived from in vivo clinical magnetic resonance images. Numerical simulations using this coupled MV-LV model are developed using an immersed boundary/finite element method. The model incorporates detailed valvular features, left ventricular contraction, nonlinear soft tissue mechanics, and fluid-mediated interactions between the MV and LV wall. We use the model to simulate the cardiac function from diastole to systole, and investigate how myocardial active relaxation function affects the LV pump function. The results of the new model agree with in vivo measurements, and demonstrate that the diastolic filling pressure increases significantly with impaired myocardial active relaxation to maintain the normal cardiac output. The coupled model has the potential to advance fundamental knowledge of mechanisms underlying MV-LV interaction, and help in risk stratification and optimization of therapies for heart diseases.Comment: 25 pages, 6 figure