scholarly journals LPMX: A pure rootless composable container system

2021 ◽  
Author(s):  
Xu Yang ◽  
Masahiro Kasahara
Keyword(s):  
Genome Analysis ◽  
Genome Research ◽  
New Process ◽  
Order Of Magnitude

Delivering tools for genome analysis to users is often difficult given their complex dependencies and conflicts. Container virtualization systems such as Singularity isolate environments, helping developers avoid conflicts between tools. However, they lack composability, an easy way to integrate multiple tools in different containers or multiple tools both in a container and a host, which compromises the use of container systems in genome research. Another issue is that one may not be able to use a single container system of the same version at all sites they use, which discourages the use of container systems. To this end, we present a pure rootless composable container system, LPMX, that provides composability for letting developers easily integrate tools in different existing containers or on host, allowing researchers to compose existing containers. LPMX is pure rootless, so it does not require root privilege neither during installation nor at runtime, allowing researchers to use LPMX across sites without asking permissions from administrators. LPMX provides a pure userspace layered filesystem with at least an order of magnitude lower overhead for launching a new process than existing container systems. LPMX can import Docker and Singularity images.

scholarly journals Workstation benchmark of Spark Capable Genome Analysis ToolKit 4 Variant Calling

2020 ◽  
Author(s):  
Marcus H. Hansen ◽  
Anita T. Simonsen ◽  
Hans B. Ommen ◽  
Charlotte G. Nyvold
Keyword(s):  
Dna Sequencing ◽  
Genome Analysis ◽  
High Speed ◽  
High Performance ◽  
Variant Calling ◽  
Amplicon Sequencing ◽  
Targeted Sequencing ◽  
Sequencing Analysis ◽  
Genome Analysis Toolkit ◽  
Order Of Magnitude

AbstractBackgroundRapid and practical DNA-sequencing processing has become essential for modern biomedical laboratories, especially in the field of cancer, pathology and genetics. While sequencing turn-over time has been, and still is, a bottleneck in research and diagnostics, the field of bioinformatics is moving at a rapid pace – both in terms of hardware and software development. Here, we benchmarked the local performance of three of the most important Spark-enabled Genome analysis toolkit 4 (GATK4) tools in a targeted sequencing workflow: Duplicate marking, base quality score recalibration (BQSR) and variant calling on targeted DNA sequencing using a modest hyperthreading 12-core single CPU and a high-speed PCI express solid-state drive.ResultsCompared to the previous GATK version the performance of Spark-enabled BQSR and HaplotypeCaller is shifted towards a more efficient usage of the available cores on CPU and outperforms the earlier GATK3.8 version with an order of magnitude reduction in processing time to analysis ready variants, whereas MarkDuplicateSpark was found to be thrice as fast. Furthermore, HaploTypeCallerSpark and BQSRPipelineSpark were significantly faster than the equivalent GATK4 standard tools with a combined ∼86% reduction in execution time, reaching a median rate of ten million processed bases per second, and duplicate marking was reduced ∼42%. The called variants were found to be in close agreement between the Spark and non-Spark versions, with an overall concordance of 98%. In this setup, the tools were also highly efficient when compared execution on a small 72 virtual CPU/18-node Google Cloud cluster.ConclusionIn conclusion, GATK4 offers practical parallelization possibilities for DNA sequence processing, and the Spark-enabled tools optimize performance and utilization of local CPUs. Spark utilizing GATK variant calling is several times faster than previous GATK3.8 multithreading with the same multi-core, single CPU, configuration. The improved opportunities for parallel computations not only hold implications for high-performance cluster, but also for modest laboratory or research workstations for targeted sequencing analysis, such as exome, panel or amplicon sequencing.

A new stereospecific total synthesis of chasmanine and 13-desoxydelphonine

1978 ◽  
Vol 56 (10) ◽  
pp. 1451-1454 ◽  
Author(s):  
Karel Wiesner ◽  
Thomas Y. R. Tsai ◽  
Krishnan P. Nambiar
Keyword(s):  
Total Synthesis ◽  
Vinyl Ether ◽  
Simple Synthesis ◽  
Photochemical Synthesis ◽  
New Process ◽  
Order Of Magnitude

A simple synthesis of the title compounds, which is more than 10 steps shorter and an order of magnitude more efficient than our recent photochemical synthesis of chasmanine, is described. The main feature of the new process is a stereo- and regiospecific addition of benzyl vinyl ether to an o-quinone intermediate masked by a spirolactone group according to the method of Deslongchamps.

A controller for safe, convenient operation of LaB6 emitters on electron-beam instruments

1983 ◽  
Vol 41 ◽  
pp. 408-409
Author(s):  
W. J. Abramson ◽  
H. W. Estry ◽  
L. F. Allard
Keyword(s):  
Electron Beam ◽  
Control System ◽  
Thermal Shock ◽  
Appropriate Care ◽  
Electron Guns ◽  
Tungsten Filaments ◽  
Order Of Magnitude ◽  
Main Components

LaB6 emitters are becoming increasingly popular as direct replacements for tungsten filaments in the electron guns of modern electron-beam instruments. These emitters offer order of magnitude increases in beam brightness, and, with appropriate care in operation, a corresponding increase in source lifetime. They are, however, an order of magnitude more expensive, and may be easily damaged (by improper vacuum conditions and thermal shock) during saturation/desaturation operations. These operations typically require several minutes of an operator's attention, which becomes tedious and subject to error, particularly since the emitter must be cooled during sample exchanges to minimize damage from random vacuum excursions. We have designed a control system for LaBg emitters which relieves the operator of the necessity for manually controlling the emitter power, minimizes the danger of accidental improper operation, and makes the use of these emitters routine on multi-user instruments.Figure 1 is a block schematic of the main components of the control system, and Figure 2 shows the control box.

Novel magneto-optical recording materials: Bi-substituted garnet films

1991 ◽  
Vol 49 ◽  
pp. 776-777
Author(s):  
Takao Suzuki ◽  
Hossein Nuri
Keyword(s):  
Grain Size ◽  
Amorphous Film ◽  
Nitrogen Atmosphere ◽  
Optical Recording ◽  
Garnet Film ◽  
Media Noise ◽  
Garnet Films ◽  
Order Of Magnitude ◽  
A New Technique ◽  
A Current

For future high density magneto-optical recording materials, a Bi-substituted garnet film ((BiDy)3(FeGa)5O12) is an attractive candidate since it has strong magneto-optic effect at short wavelengths less than 600 nm. The signal in read back performance at 500 nm using a garnet film can be an order of magnitude higher than a current rare earth-transition metal amorphous film. However, the granularity and surface roughness of such crystalline garnet films are the key to control for minimizing media noise.We have demonstrated a new technique to fabricate a garnet film which has much smaller grain size and smoother surfaces than those annealed in a conventional oven. This method employs a high ramp-up rate annealing (Γ = 50 ~ 100 C/s) in nitrogen atmosphere. Fig.1 shows a typical microstruture of a Bi-susbtituted garnet film deposited by r.f. sputtering and then subsequently crystallized by a rapid thermal annealing technique at Γ = 50 C/s at 650 °C for 2 min. The structure is a single phase of garnet, and a grain size is about 300A.

Atomic-level imaging of the surface structure of Ag2O

1984 ◽  
Vol 42 ◽  
pp. 656-657
Author(s):  
William Krakow
Keyword(s):  
High Vacuum ◽  
Atomic Level ◽  
Ultra High Vacuum ◽  
Research Groups ◽  
Resolution Electron ◽  
Surface Reconstructions ◽  
Order Of Magnitude ◽  
High Resolution Electron Microscope ◽  
Saturated Structure ◽  
Transmission And Reflection

In recent years electron microscopy has been used to image surfaces in both the transmission and reflection modes by many research groups. Some of this work has been performed under ultra high vacuum conditions (UHV) and apparent surface reconstructions observed. The level of resolution generally has been at least an order of magnitude worse than is necessary to visualize atoms directly and therefore the detailed atomic rearrangements of the surface are not known. The present author has achieved atomic level resolution under normal vacuum conditions of various Au surfaces. Unfortunately these samples were exposed to atmosphere and could not be cleaned in a standard high resolution electron microscope. The result obtained surfaces which were impurity stabilized and reveal the bulk lattice (1x1) type surface structures also encountered by other surface physics techniques under impure or overlayer contaminant conditions. It was therefore decided to study a system where exposure to air was unimportant by using a oxygen saturated structure, Ag2O, and seeking to find surface reconstructions, which will now be described.

Near-field scanning optical microscopy

1986 ◽  
Vol 44 ◽  
pp. 642-643
Author(s):  
E. Betzig ◽  
A. Harootunian ◽  
M. Isaacson ◽  
A. Lewis
Keyword(s):  
Near Field ◽  
Optical Microscope ◽  
Visible Radiation ◽  
Field Methods ◽  
Optical Elements ◽  
Optical Region ◽  
Order Of Magnitude ◽  
Nondestructive Imaging ◽  
Scanning Optical Microscopy ◽  
Near Field Scanning

In general, conventional methods of optical imaging are limited in spatial resolution by either the wavelength of the radiation used or by the aberrations of the optical elements. This is true whether one uses a scanning probe or a fixed beam method. The reason for the wavelength limit of resolution is due to the far field methods of producing or detecting the radiation. If one resorts to restricting our probes to the near field optical region, then the possibility exists of obtaining spatial resolutions more than an order of magnitude smaller than the optical wavelength of the radiation used. In this paper, we will describe the principles underlying such "near field" imaging and present some preliminary results from a near field scanning optical microscope (NS0M) that uses visible radiation and is capable of resolutions comparable to an SEM. The advantage of such a technique is the possibility of completely nondestructive imaging in air at spatial resolutions of about 50nm.

Detection, Averaging, and 3D Reconstruction of Biological Specimens on Hypercubes (Transputer-based) Computers

1990 ◽  
Vol 48 (1) ◽  
pp. 454-455
Author(s):  
Jose-Maria Carazo ◽  
I. Benavides ◽  
S. Marco ◽  
J.L. Carrascosa ◽  
E.L. Zapata
Keyword(s):  
3D Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
Software Tools ◽  
Mapping Method ◽  
Computer Architectures ◽  
Parallel Computer ◽  
Reconstruction Process ◽  
Computing Power ◽  
Order Of Magnitude

Obtaining the three-dimensional (3D) structure of negatively stained biological specimens at a resolution of, typically, 2 - 4 nm is becoming a relatively common practice in an increasing number of laboratories. A combination of new conceptual approaches, new software tools, and faster computers have made this situation possible. However, all these 3D reconstruction processes are quite computer intensive, and the middle term future is full of suggestions entailing an even greater need of computing power. Up to now all published 3D reconstructions in this field have been performed on conventional (sequential) computers, but it is a fact that new parallel computer architectures represent the potential of order-of-magnitude increases in computing power and should, therefore, be considered for their possible application in the most computing intensive tasks.We have studied both shared-memory-based computer architectures, like the BBN Butterfly, and local-memory-based architectures, mainly hypercubes implemented on transputers, where we have used the algorithmic mapping method proposed by Zapata el at. In this work we have developed the basic software tools needed to obtain a 3D reconstruction from non-crystalline specimens (“single particles”) using the so-called Random Conical Tilt Series Method. We start from a pair of images presenting the same field, first tilted (by ≃55°) and then untilted. It is then assumed that we can supply the system with the image of the particle we are looking for (ideally, a 2D average from a previous study) and with a matrix describing the geometrical relationships between the tilted and untilted fields (this step is now accomplished by interactively marking a few pairs of corresponding features in the two fields). From here on the 3D reconstruction process may be run automatically.

Remarkable Art Casting by a New Process

1916 ◽  
Vol 114 (9) ◽  
pp. 225-225
Author(s):  
Robert G. Skerritt
Keyword(s):  
New Process
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