Open-source Analysis Software Research Articles

Low-cost motility tracking system (LOCOMOTIS) for time-lapse microscopy applications and cell visualisation.

Direct visualisation of cells for the purpose of studying their motility has typically required expensive microscopy equipment. However, recent advances in digital sensors mean that it is now possible to image cells for a fraction of the price of a standard microscope. Along with low-cost imaging there has also been a large increase in the availability of high quality, open-source analysis programs. In this study we describe the development and performance of an expandable cell motility system employing inexpensive, commercially available digital USB microscopes to image various cell types using time-lapse and perform tracking assays in proof-of-concept experiments. With this system we were able to measure and record three separate assays simultaneously on one personal computer using identical microscopes, and obtained tracking results comparable in quality to those from other studies that used standard, more expensive, equipment. The microscopes used in our system were capable of a maximum magnification of 413.6×. Although resolution was lower than that of a standard inverted microscope we found this difference to be indistinguishable at the magnification chosen for cell tracking experiments (206.8×). In preliminary cell culture experiments using our system, velocities (mean µm/min ± SE) of 0.81±0.01 (Biomphalaria glabrata hemocytes on uncoated plates), 1.17±0.004 (MDA-MB-231 breast cancer cells), 1.24±0.006 (SC5 mouse Sertoli cells) and 2.21±0.01 (B. glabrata hemocytes on Poly-L-Lysine coated plates), were measured and are consistent with previous reports. We believe that this system, coupled with open-source analysis software, demonstrates that higher throughput time-lapse imaging of cells for the purpose of studying motility can be an affordable option for all researchers.

AtomicJ: an open source software for analysis of force curves.

We present an open source Java application for analysis of force curves and images recorded with the Atomic Force Microscope. AtomicJ supports a wide range of contact mechanics models and implements procedures that reduce the influence of deviations from the contact model. It generates maps of mechanical properties, including maps of Young's modulus, adhesion force, and sample height. It can also calculate stacks, which reveal how sample's response to deformation changes with indentation depth. AtomicJ analyzes force curves concurrently on multiple threads, which allows for high speed of analysis. It runs on all popular operating systems, including Windows, Linux, and Macintosh.

Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment.

Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation. Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging and laborious activity, and a major hurdle for many small research and clinical laboratories. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. Based on virtual machine technologies, TREVA is a solution for rapid and efficient deployment of complex bioinformatics pipelines to laboratories of all sizes, enabling reproducible results. The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is available at http://bioinformatics.petermac.org/treva/.

The MOLDY short-range molecular dynamics package

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron–carbon alloy. Program summary Program title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as measuring thermodynamic properities, diffusion, radiation damage, fracture, twinning deformation, nucleation and growth of phase transitions, sputtering etc. In the vast majority of materials, the interactions are non-pairwise, and the code must be able to deal with many-body forces. Solution method: Molecular dynamics involves integrating Newtonʼs equations of motion. MOLDY uses verlet (for good energy conservation) or predictor–corrector (for accurate trajectories) algorithms. It is parallelised using open MP. It also includes a static minimisation routine to find the lowest energy structure. Boundary conditions for surfaces, clusters, grain boundaries, thermostat (Nose), barostat (Parrinello–Rahman), and externally applied strain are provided. The initial configuration can be either a repeated unit cell or have all atoms given explictly. Initial velocities are generated internally, but it is also possible to specify the velocity of a particular atom. A wide range of interatomic force models are implemented, including embedded atom, Morse or Lennard-Jones. Thus the program is especially well suited to calculations of metals. Restrictions: The code is designed for short-ranged potentials, and there is no Ewald sum. Thus for long range interactions where all particles interact with all others, the order- N scaling will fail. Different interatomic potential forms require recompilation of the code. Additional comments: There is a set of associated open-source analysis software for postprocessing and visualisation. This includes local crystal structure recognition and identification of topological defects. Running time: A set of test modules for running time are provided. The code scales as order N. The parallelisation shows near-linear scaling with number of processors in a shared memory environment. A typical run of a few tens of nanometers for a few nanoseconds will run on a timescale of days on a multiprocessor desktop.

The THEMIS Mission

The Time History of Events and Macroscale Interactions during Substorms (THEMIS) mission is the fifth NASA Medium-class Explorer (MIDEX), launched on February 17, 2007 to determine the trigger and large-scale evolution of substorms. The mission employs five identical micro-satellites (hereafter termed “probes”) which line up along the Earth’s magnetotail to track the motion of particles, plasma and waves from one point to another and for the first time resolve space–time ambiguities in key regions of the magnetosphere on a global scale. The probes are equipped with comprehensive in-situ particles and fields instruments that measure the thermal and super-thermal ions and electrons, and electromagnetic fields from DC to beyond the electron cyclotron frequency in the regions of interest. The primary goal of THEMIS, which drove the mission design, is to elucidate which magnetotail process is responsible for substorm onset at the region where substorm auroras map (∼10 RE): (i) a local disruption of the plasma sheet current (current disruption) or (ii) the interaction of the current sheet with the rapid influx of plasma emanating from reconnection at ∼25 RE. However, the probes also traverse the radiation belts and the dayside magnetosphere, allowing THEMIS to address additional baseline objectives, namely: how the radiation belts are energized on time scales of 2–4 hours during the recovery phase of storms, and how the pristine solar wind’s interaction with upstream beams, waves and the bow shock affects Sun–Earth coupling. THEMIS’s open data policy, platform-independent dataset, open-source analysis software, automated plotting and dissemination of data within hours of receipt, dedicated ground-based observatory network and strong links to ancillary space-based and ground-based programs. promote a grass-roots integration of relevant NASA, NSF and international assets in the context of an international Heliophysics Observatory over the next decade. The mission has demonstrated spacecraft and mission design strategies ideal for Constellation-class missions and its science is complementary to Cluster and MMS. THEMIS, the first NASA micro-satellite constellation, is a technological pathfinder for future Sun-Earth Connections missions and a stepping stone towards understanding Space Weather.

PhysioNet: an NIH research resource for complex signals

The Research Resource for Complex Physiologic Signals, supported by the National Institutes of Health (NIH), is intended to promote and facilitate investigations in the study of cardiovascular and other complex biomedical signals. The resource website ( www.physionet.org ) has 3 interdependent components: 1) PhysioBank is an archive of well-characterized digital recordings of physiologic signals and related data, including databases of electrocardiogram and heart rate time series from patients with heart failure, coronary disease, sleep apnea syndromes, and cardiac arrhythmias; 2) PhysioToolkit is a library of open-source software for physiologic signal processing and analysis; and 3) PhysioNet, for which the resource is named, is an on-line forum for dissemination and exchange of recorded biomedical signals and open-source software for analyzing them. PhysioNet, in cooperation with the annual Computers in Cardiology conference, hosts a series of challenges inviting participants to tackle clinically interesting problems that are either unsolved or not well solved. PhysioNet invites contributions of databases and software from the biomedical community.

PhysioBank, PhysioToolkit, and PhysioNet: components of a new research resource for complex physiologic signals.

The newly inaugurated Research Resource for Complex Physiologic Signals, which was created under the auspices of the National Center for Research Resources of the National Institutes of Health, is intended to stimulate current research and new investigations in the study of cardiovascular and other complex biomedical signals. The resource has 3 interdependent components. PhysioBank is a large and growing archive of well-characterized digital recordings of physiological signals and related data for use by the biomedical research community. It currently includes databases of multiparameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and from patients with a variety of conditions with major public health implications, including life-threatening arrhythmias, congestive heart failure, sleep apnea, neurological disorders, and aging. PhysioToolkit is a library of open-source software for physiological signal processing and analysis, the detection of physiologically significant events using both classic techniques and novel methods based on statistical physics and nonlinear dynamics, the interactive display and characterization of signals, the creation of new databases, the simulation of physiological and other signals, the quantitative evaluation and comparison of analysis methods, and the analysis of nonstationary processes. PhysioNet is an on-line forum for the dissemination and exchange of recorded biomedical signals and open-source software for analyzing them. It provides facilities for the cooperative analysis of data and the evaluation of proposed new algorithms. In addition to providing free electronic access to PhysioBank data and PhysioToolkit software via the World Wide Web (http://www.physionet. org), PhysioNet offers services and training via on-line tutorials to assist users with varying levels of expertise.