Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server

BACKGROUND: DNA sequencing is used ubiquitously: from deciphering genomes[1] to determining the primary sequence of small RNAs (smRNAs) [2-5]. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences[6]. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study. RESULTS: Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases. Our laboratory used Ebbie to analyze scores of DNA sequencing data originating from an smRNA cloning project[6]. Through its built-in instant analysis of all inserts using BlastN, we were able to quickly identify 33 groups of smRNAs from ~700 database entries. This clustering allowed the easy identification of novel and highly expressed clusters of smRNAs. Ebbie is available under GNU GPL and currently implemented on CONCLUSION: Ebbie was designed for medium sized smRNA cloning projects with about 1,000 database entries [6-8].Ebbie can be used for any type of sequence analysis where two constant primer regions flank a sequence of interest. The reliable storage of inserts, and their annotation in a MySQL database, BlastN[9] comparison of new inserts to dynamic and static databases make it a powerful new tool in any laboratory using DNA sequencing. Ebbie also prevents manual mistakes during the excision process and speeds up annotation and data-entry. Once the server is installed locally, its access can be restricted to protect sensitive new DNA sequencing data. Ebbie was primarily designed for smRNA cloning projects, but can be applied to a variety of RNA and DNA cloning projects[2,3,10,11]

Multi-dimensional modeling and simulation of semiconductor nanophotonic devices

Self-consistent modeling and multi-dimensional simulation of semiconductor nanophotonic devices is an important tool in the development of future integrated light sources and quantum devices. Simulations can guide important technological decisions by revealing performance bottlenecks in new device concepts, contribute to their understanding and help to theoretically explore their optimization potential. The efficient implementation of multi-dimensional numerical simulations for computer-aided design tasks requires sophisticated numerical methods and modeling techniques. We review recent advances in device-scale modeling of quantum dot based single-photon sources and laser diodes by self-consistently coupling the optical Maxwell equations with semiclassical carrier transport models using semi-classical and fully quantum mechanical descriptions of the optically active region, respectively. For the simulation of realistic devices with complex, multi-dimensional geometries, we have developed a novel hp-adaptive finite element approach for the optical Maxwell equations, using mixed meshes adapted to the multi-scale properties of the photonic structures. For electrically driven devices, we introduced novel discretization and parameter-embedding techniques to solve the drift-diffusion system for strongly degenerate semiconductors at cryogenic temperature. Our methodical advances are demonstrated on various applications, including vertical-cavity surface-emitting lasers, grating couplers and single-photon sources

Projektionsgestützte Assistenzsysteme in der manuellen Montage

Die Anforderungen an die Gestaltung von Montagesystemen verändern sich. Dazu tragen kürzer werdende Innovations- und Produktlebenszyklen sowie eine zunehmende Variantenvielfalt bei, mit der eine Montage von kleinen Losen bis hin zur kundenindividuellen Montage einhergeht

Montageassistenzsysteme - Begriff, Entwicklungstrends und Umsetzungsbeispiele

Informatorische Montageassistenzsysteme können einen entscheidenden Beitrag dazu leisten, Anlernprozesse zu verkürzen, Montagefehler zu vermeiden und die Arbeitsproduktivität zu steigern. Gleichzeitig können sie Unsicherheiten und mentale Belastungen der Beschäftigten reduzieren, indem sie den Beschäftigten die richtigen Informationen zur richtigen Zeit bedarfsgerecht übermitteln. Bei der Gestaltung der Assistenzsysteme sind die Anforderungen von Betrieben und Beschäftigten zu berücksichtigen. Aus diesen Anforderungen lässt sich eine Reihe von Entwicklungstrends ableiten. Zu diesen werden im Beitrag Umsetzungsbeispiele aufgezeigt

Development of Projection Based Assistance System for Manual Assembly

The requirements for the configuration of assembly systems are changing. With innovation times and product life cycles constantly being shortened, as well as an increasing number of variants and small batches contributing to this phenomenon, industries are faced with the challenge to create efficient processes with high process capability. In particular, assembly errors happen because of activities with larger work content and fluctuating demands. In addition, under these conditions often quantity or rather productivity targets are missed. The reasons for this are the insufficient support of learning processes for new employees as well as the missing preparation of assembly information, which should be designed to be spotted quickly and implemented intuitively correct. In a study at the Laboratory of Industrial Engineering of the Ostwestfalen-Lippe University of Applied Sciences, a prototype of a projection based assistance system for manual assembly has been developed and tested. The system contains functionalities for ergonomic display of work instructions. These include, markers and precise positioning representations corresponding with these, a pick-to-light function and other features. By adapting the representation to the context-sensitive information, the complexity of large work contents can be made manageable

Montageassistenzsysteme - Begriff, Entwicklungstrends und Umsetzungsbeispiele

Informatorische Montageassistenzsysteme können einen entscheidenden Beitrag dazu leisten, Anlernprozesse zu verkürzen, Montagefehler zu vermeiden und die Arbeitsproduktivität zu steigern. Gleichzeitig können sie Unsicherheiten und mentale Belastungen der Beschäftigten reduzieren, indem sie den Beschäftigten die richtigen Informationen zur richtigen Zeit bedarfsgerecht übermitteln. Bei der Gestaltung der Assistenzsysteme sind die Anforderungen von Betrieben und Beschäftigten zu berücksichtigen. Aus diesen Anforderungen lässt sich eine Reihe von Entwicklungstrends ableiten. Zu diesen werden im Beitrag Umsetzungsbeispiele aufgezeigt

Projektionsgestützte Assistenzsysteme in der manuellen Montage

Die Anforderungen an die Gestaltung von Montagesystemen verändern sich. Dazu tragen kürzer werdende Innovations- und Produktlebenszyklen sowie eine zunehmende Variantenvielfalt bei, mit der eine Montage von kleinen Losen bis hin zur kundenindividuellen Montage einhergeht

Characterizing multiple exogenous and endogenous small RNA populations in parallel with subfemtomolar sensitivity using a streptavidin gel-shift assay

Here we present a simple and inexpensive gel-shift assay for the detection and quantification of small RNAs. The assay is at least 5–10 times more sensitive than a conventional Northern, and is highly scalable. Total RNA is first size purified to enrich the desired size range, phosphatase treated, and then radiolabeled to high specific activity using polynucleotide kinase. The resulting RNA stock is then hybridized to an excess of biotinylated DNA probe oligonucleotide, prior to mixing with streptavidin and loading on a native gel. The amount of supershifted material was proportional to the amount of labeled target RNA in the sample. We applied this method to verify sequencing data originally obtained from a four-point comparison study on the effect of endogenous expression of HC-Pro on Y-satellite/cucumber mosaic virus infection in tobacco plants. The results of the streptavidin gel-shift assay were consistent with the concentrations of small RNA infected plants inferred by our original cloning data, and rapidly provided information about the relative concentration of a number of viral and endogenous small RNAs. Further straightforward improvements to this simple methodology might be expected to improve the methods sensitivity by as much as another 10-fold

Development of a Projection-Based Assistance System for Maintaining Injection Molding Tools

The maintenance of a tool for injection molding or forming is usually accompanied by its disassembly and assembly. The duration of the assembly activities is often a large part of the total activity time for the maintenance of the tool. The degree of performance of the employees in the execution of these disassembly and assembly activities is often low. In addition, allowances occur (e.g. searching for work equipment). At the Industrial Engineering Lab of the Ostwestfalen-Lippe University of Applied Sciences, a prototype of an assistance system was developed to support the assembly activities in toolmaking. With the help of this system, the operator is guided step by step through the assembly process. The economic potential of the system exists in the reduction of training times, the avoidance of assembly errors and the increase of labor productivity