Linux Box Research Articles

K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes.

The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis, or pangenome exploration. Although homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here, we benchmarked a two-step approach, where repeats were first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, with the k-mer-based Repeat Detector (Red) and two repeat libraries (REdat, last updated in 2013, and nrTEplants, curated for this work). Custom libraries produced by RepeatModeler were also tested. We obtained repeated genome fractions that matched those reported in the literature but with shorter repeated elements than those produced directly by sequence homology. Inspection of the masked regions that overlapped genes revealed no preference for specific protein domains. Most Red-masked sequences could be successfully classified by sequence similarity, with the complete protocol taking less than 2 h on a desktop Linux box. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained at https://github.com/Ensembl/plant-scripts.

Gaming with the Throughput and the Latency Benchmarking Measurement Procedures of RFC 2544

In this paper, we investigate three potential issues of the benchmarking measurement procedures defined in RFC 2544 and also used in RFC 5180 and RFC 8219. One of them is the lack of proper timeout usage. We use a Linux box, which can selectively delay a specified ratio of the packets. Using carefully selected parameters based on our preliminary measurements, we demonstrate that the experienced speed of the HTTP download is much less, than what could have been expected on the basis of the throughput results of the RFC 2544 tests. The other critical issue is the strict, absolutely zero loss criterion. We use a Linux box, which drops a specified small ratio of the packets. Whereas the RFC 2544 throughput results tend to be zero, the experienced speed of the HTTP download is quite good. The third problem is the lack of requirement for statistically relevant number of tests in the RFC 2544 benchmarking procedures. We demonstrate its severity with the latency benchmarking procedure defined in RFC 2544 and kept unchanged in RFC 5180 but redefined in RFC 8219.

LocExpress: a web server for efficiently estimating expression of novel transcripts

BackgroundThe temporal and spatial-specific expression pattern of a transcript in multiple tissues and cell types can indicate key clues about its function. While several gene atlas available online as pre-computed databases for known gene models, it’s still challenging to get expression profile for previously uncharacterized (i.e. novel) transcripts efficiently.ResultsHere we developed LocExpress, a web server for efficiently estimating expression of novel transcripts across multiple tissues and cell types in human (20 normal tissues/cells types and 14 cell lines) as well as in mouse (24 normal tissues/cell types and nine cell lines). As a wrapper to RNA-Seq quantification algorithm, LocExpress efficiently reduces the time cost by making abundance estimation calls increasingly within the minimum spanning bundle region of input transcripts. For a given novel gene model, such local context-oriented strategy allows LocExpress to estimate its FPKMs in hundreds of samples within minutes on a standard Linux box, making an online web server possible.ConclusionsTo the best of our knowledge, LocExpress is the only web server to provide nearly real-time expression estimation for novel transcripts in common tissues and cell types. The server is publicly available at http://loc-express.cbi.pku.edu.cn.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3329-3) contains supplementary material, which is available to authorized users.

Brave new RNA world.

Brave new RNA world.

Highly Available XenApp Cloud

In Cloud computing, application and desktop delivery are the two emerging technologies that has reduced application and desktop computing costs and provided greater IT and user flexibility compared to traditional application and desktop management models. Among the various SaaS technologies, XenApp that allow numerous end users to connect to their corporate applications from any device. XenApp enables organizations to improve application management by centralizing applications in the datacenter to reduce costs, controlling and encrypting access to data and applications to improve security and delivering applications instantly to users anywhere by remotely accessing or streaming. As per old architecture we were using the oracle or MS-SQL in the backend of XenApp on Windows Server itself. But as we know for this we have to pay for database especially because we are not using it for any other purpose. And as we know windows is GUI based so running database over it consumes much more resources. So, it can lead to single point of failure. For this, this paper proposes a scheme for removing this problem by using the HA failover cluster based SQL server (mysql or Oracle) which will run over Linux box having concept of VIP (Virtual IP).

Performance Tests of CMSSW on the CernVM

The CERN Virtual Machine (CernVM) Software Appliance is a project developed in CERN with the goal of allowing the execution of the experiment's software on different operating systems in an easy way for the users. To achieve this it makes use of Virtual Machine images consisting of a JEOS (Just Enough Operating System) Linux image, bundled with CVMFS, a distributed file system for software. This image can then be run with a proper virtualizer on most of the platforms available. It also aggressively caches data on the local user's machine so that it can operate disconnected from the network. CMS wanted to compare the performance of the CMS Software running in the virtualized environment with the same software running on a native Linux box. To answer this wish, a series of tests were made on a controlled environment during 2010–2011. This work presents the results of those tests.

Network Security using Linux Intrusion Detection System

Attacks on the nation’s computer infrastructures are becoming an increasingly serious problem. Firewalls provide a certain amount of security, but can be fooled at times by attacks like IP spoofing and the so called authorized users. So an intelligent system that can detect attacks and intrusions is required. The tool GRANT (Global Real-time Analysis of Network Traffic) being a Linux based Intrusion Detection System(LIDs), takes the advantage of the security of a Linux box and secures the other nodes in the perimeter of the network. It is capable of detecting intrusions and probes as and when they occur and capable of responding to “already” successful attacks, thus causing minimal or no damage to the entire network. For better performance, this Linux Intrusion Detection System should be part of a defense in depth strategy such as Firewall and Intrusion Prevention..

Cooperative Maneuvering in Close Environments Among Cybercars and Dual-Mode Cars

This paper describes the results of vehicle-to-vehicle (V2V) and infrastructure-to-vehicle (I2V) experiments implementing cooperative maneuvering for three different vehicles driving automatically. The cars used were cybercars from the Institut National de Recherche en Informatique et Automatique (INRIA), (France), which are fully automated road vehicles, and two mass-produced cars-one a Smart Fortwo car from TNO (Netherlands) equipped with additional actuators and sensors and the other a convertible Citroen C3 from IAI (Spain) that uses sensorial information to manage the actuators. The cars communicate by a wireless mesh network over Wi-Fi using the optimized link state routing (OLSR) ad-hoc protocol. The entire communication task is embedded in a small MIPS Linux Box (4G System Cube) that is transparent for the cars. A standard framework was defined with the parameters needed to perform adaptive cruise control (ACC) and intersection maneuvers among the cars, as well as emergency stops via a signal sent by the infrastructure. The experiments were carried out in La Rochelle (France) during the final demonstration of the European Union (EU) Cybercars-2 Project.

Less is more: the battle of Moore's law against Bremermann's limit on the field of systems biology

Background I run my bioinformatics tasks on two machines. The first one is a Tru64 DS20 AlphaServer, bought in 1999. This has two processors running at 512 MHz with 2 Gb of memory. The second is a custom-built Linux box, purchased in early 2005, which has 8 processors running at 2.7 GHz and 12 Gb of memory. Although performance speed does not quite scale linearly against processor speed, this represents just over a 5-fold increase in computing power over a period of 6 years. This kind of thing has been happening since the 1960s, when Intel-founder Gordon Moore observed that available processing power doubles every 2 years or so. Indeed, my fast Linux box is already quite pedestrian compared to the 3.8 GHz processors that are now routinely available. Under these circumstances, it is easy to become complacent about handling awkward jobs. Large, viral-genome-scale ClustalW jobs that used to run for several days on my DS20 are now finished overnight. Within the horizon of a typical 3-year scientific project, I could conceivably be able to buy a machine that shortens the time to a couple of hours or so. But just because bioinformatics tasks are now becoming increasingly trivial in terms of computer time, does that mean we can expect similar gains in systems biology problems? There is a whole industry of popular science books which attempt to persuade us that Moore's Law will be the basis of a future world in which anything is computable almost instantly, and we will, even within our lifetimes, know everything. How seriously should we take such claims and what relevance do they have to research in the here-and-now?

Circuit design on your Linux box using gEDA

Use Linux to create a circuit board design. Send files to a fabrication house and, voila, what you get back is a professional quality circuit board of your very own design.

Artificial Time, 1998–99

Much of modern life has come to depend on the accurate measurement of time. With the development of the cesium atomic clock, we can now keep time to an accuracy of one millionth of a second per year. This clock is so accurate that it is more precise than the earth’s rotation in measuring the passing of a year. As technology has developed, we have intervened in nature’s timekeeping process with the ultimate goal of improving on its perceived imperfections. In so doing, we have abstracted our sense of time from nature. Artificial Time is an interactive telerobotic installation for the Web that explores our concepts of and relationship to time. A robotic arm, which consists of an armature with a halogen light source on the end, is connected to the Web and acts as a light source that revolves above a sundial. By controlling the movement of the robotic arm, one will be able to control the shadow on the sundial, thereby controlling the representation of time. The sundial represents a contrast of current technology with past technology and an organic awareness of time in a purely mechanical and artificial environment. My “sun” provides 24 hours a day of sunlight, rain or shine, with computer-driven precision. Because the sundial is dependent on location in terms of latitude and longitude position, it becomes a metaphor for location on the Web, a mapping out of different time zones and a sense of place. Our modern clocks dictate the pace of our lives. The precise measurements lead to a tightly scheduled day of hours and minutes. The imprecision of a sundial proposes a different pace; events are scheduled to the hour rather than to minutes. With the coming of the new millennium and the growing importance our modern society places on the measurement of time, it seems appropriate to rethink our relationship to time and propose alternatives to our present system. A video camera transmits the image of the sundial on the Web. While multiple viewers can see the sundial, only one person at a time can have access to the robotic arm, which is timed to one minute. There is a different interface to the arm depending on whether you are influencing the arm or just observing. When one gains control of the arm, the time and location set on one’s computer is sent to the server, which will position the robot accordingly. Others who are connected at that time will be able to see the location of the controller as well as the initial time they connected. A second window with a time map is also part of the Web site. It is a record of the last 24 connection times drawn in shades of gray from black to white, where the last connection is in white. Eventually it will also include a map of time zones or locations. The default time on the dial is the local time of its physical location. The project will be installed at a gallery or space, as it is being manipulated remotely. Only those present at the gallery can see the actual source of light. The entire application is written in Java. It requires a Web server computer (preferably a Windows NT or Linux box) and a second computer serving up the video images (PC or Mac). The total space required is around seven ft. square. Artists’ Statements