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FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections.

High-throughput sequence (HTS) analysis of combinatorial selection populations accelerates lead discovery and optimization and offers dynamic insight into selection processes. An underlying principle is that selection enriches high-fitness sequences as a fraction of the population, whereas low-fitness sequences are depleted. HTS analysis readily provides the requisite numerical information by tracking the evolutionary trajectory of individual sequences in response to selection pressures. Unlike genomic data, for which a number of software solutions exist, user-friendly tools are not readily available for the combinatorial selections field, leading many users to create custom software. FASTAptamer was designed to address the sequence-level analysis needs of the field. The open source FASTAptamer toolkit counts, normalizes and ranks read counts in a FASTQ file, compares populations for sequence distribution, generates clusters of sequence families, calculates fold-enrichment of sequences throughout the course of a selection and searches for degenerate sequence motifs. While originally designed for aptamer selections, FASTAptamer can be applied to any selection strategy that can utilize next-generation DNA sequencing, such as ribozyme or deoxyribozyme selections, in vivo mutagenesis and various surface display technologies (peptide, antibody fragment, mRNA, etc.). FASTAptamer software, sample data and a user's guide are available for download at http://burkelab.missouri.edu/fastaptamer.html.

업무문서 중앙화 서비스 제공을 위한 클라우드 시스템 운영방안

Submitted:October 28, 2014 1 Revision:December 2, 2014 Accepted:December 7, 2014 * 본 논문은 인하대학교의 지원에 의해 연구되었습니다. ** 인하대학교 경영대학 산학협력교수 *** 인하대학교 경영대학 경영학과 교수 This case study focuses on the preparing a guide for the plan to the companies that want to build a business document system for the centralized services under the cloud computing. Total 3 Operating companies with regard to cloud computing issues are introduced for this purpose. Analyzing the usage and development direction of the selected companies were performed to set up plans. Through this in-depth needs of the user's point of view for the management of business documents, The necessary improvements in the process of collaboration and document sharing were derived. Business documents centralized service plans were proposed based on cloud computing models. Practical experiences of the companies were helpful to present the details of the operational strategy and operational plans. Especially with minimal staff input and verification process, Sample method for the automatic generating of the new document file name is introduced. A test bed before operating the enterprise-wide system were presented with information that is to be considered when building systems. Keyword:Cloud Computing, VDI, End User Computing, Business Documents, Test-Bed 韓國IT서비스學會誌 第13卷 第4號 2014年 12月, pp.309-324 310 Yong Yoon.Younsung Kim

Cueing others' memories.

Many situations require us to generate external cues to support later retrieval from memory. For instance, we create file names in order to cue our memory to a file's contents, and instructors create lecture slides to remember what points to make during classes. We even generate cues for others when we remind friends of shared experiences or send colleagues a computer file that is named in such a way so as to remind them of its contents. Here we explore how and how well learners tailor retrieval cues for different intended recipients. Across three experiments, subjects generated verbal cues for a list of target words for themselves or for others. Learners generated cues for others by increasing the normative cue-to-target associative strength but also by increasing the number of other words their cues point to, relative to cues that they generated for themselves. This strategy was effective: such cues supported higher levels of recall for others than cues generated for oneself. Generating cues for others also required more time than generating cues for oneself. Learners responded to the differential demands of cue generation for others by effortfully excluding personal, episodic knowledge and including knowledge that they estimate to be broadly shared.

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Collateral Revelation

Our work of investigating experience is rarely directed at personal transformation. The impact we seek to create is not specific to our participants or intended for them alone, if at all.We don't go into the field to midwife individual discovery or revelation, and this may be why we don't notice how often it happens. We change people. We change their minds, their behaviors, their understanding of themselves.We use the tools of our trade – curiosity and empathy, questioning and watching and listening – to cultivate the conditions of discovery that serve our objectives. But what gets discovered and by whom is not bound by our intent, and what results can be surprising.This Pecha Kucha uses the experiences of participants and practitioners to examine our role as incidental change agents and explore what this says about the value of our work.Save entire document in MS Word with the following file name: yourlastname_EPIC‐2014‐PechaKucha_proceedings.

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Digital data repositories in chemistry and their integration with journals and electronic notebooks.

We discuss the concept of recasting the data-rich scientific journal article into two components, a narrative and separate data components, each of which is assigned a persistent digital object identifier. Doing so allows each of these components to exist in an environment optimized for purpose. We make use of a poorly-known feature of the handle system for assigning persistent identifiers that allows an individual data file from a larger file set to be retrieved according to its file name or its MIME type. The data objects allow facile visualization and retrieval for reuse of the data and facilitates other operations such as data mining. Examples from five recently published articles illustrate these concepts.

Improved High-Speed Data Recorder for Superconducting Digital-RF Receivers

A superconducting digital-RF receiver with high-ingest-rate data recording capability has been developed. The data recorder unit uses standard PC components with state-of-the-art solid-state drives (SSDs) and interfaces with the superconductor analog-to-digital converter (ADC) through a commercial FPGA board. High-speed data ingest rates exceeding 3.2 Gbps have been demonstrated successfully with single-bit ADCs clocked up to 27.52 GHz. A continuous recording of 2.5 TB has been achieved using a bank of 12 SSDs. A new graphical user interface featuring single button operation and automatic file naming, as well as convenient configuration setting, has been developed.

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A digital file inventory of the Queens College Special Collections and Archives

Purpose – This paper aimed to conduct an inventory of digital resources for the Queens College Special Collections and Archives and had two purposes. The first was to assess the digital resources for a department too understaffed to address digital preservation and to provide a step-by-step program for them to start thinking in the long-term. The second was to show how these steps can be generalized for many institutions just starting to have digital holdings and looking to create a long-term digital preservation plan. Design/methodology/approach – The main method for research involved taking a significant sampling of the department’s digital holdings and conducting an inventory of them, analyzing such characteristics as file size, names, formats and metadata. After the inventory was conducted, recommendations were made to the department based on best practices in the field of digital preservation. Findings – We found that while the department generally does not follow industry-best practices for preservation, the files were relatively new and, therefore, many issues could still be fixed. With a concrete plan and a bit of effort, their digital files can be more easily accessible and protected against future threats. Originality/value – The issues that the Department of Special Collections had with their digital holdings are similar to those at many other institutions – especially educational ones where staff turnover is high. This case study could help similar small organizations start to access their digital holdings and start formulating a plan for long-term preservation.

File System

A file is a named collection of related information that is recorded on secondary storage such as magnetic disks, magnetic tapes and optical disks. In general, a file is a sequence of bits, bytes, lines or records whose meaning is defined by the files creator and user. In our research paper we’re going to focus on File Structure, File Type, File Names, Pathnames. File Structure - It is a structure, which is according to a required format that operating system can understand. File types also can be used to indicate the internal structure of the file. File Type – It refers to the ability of the operating system to distinguish different types of file such as text files, source files and the binary files etc .Many Operating system supports many types of files .Operating system like MS-DOS and UNIX have following types of files:

Methodologies for Geotagging in FAT and ExFAT File Systems for Smart Phones

Methodologies for Geotagging in FAT and ExFAT File Systems for Smart Phones

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PsyPad: A platform for visual psychophysics on the iPad

This article introduces PsyPad, a customizable, open-source platform for configuring and conducting visual psychophysics experiments on iPads without the need for any code development for the iPad. Stimuli for experiments are created off-line as a library of images. The PsyPad app (obtainable from the Apple App Store) presents the images according to either built-in, customizable staircase or method of constant stimuli procedures, mapping stimuli levels to images based on the image file names. On-screen buttons for responses are configurable and matched to "correct" using the image file name of any given stimulus. All actions are logged into a text file and sent to a specified server at the end of the test if an Internet connection is available. If the iPad is not connected, the results are uploaded the next time the iPad is online. We provide a secure server for this purpose, but the server-side software is also open source if researchers choose to run their own server.

Implementation of a Hybrid Encryption Scheme for SMS/Multimedia Messages on Android

messages are one of the popular ways of communication. Sending an SMS/MMS is cheap, fast and simple. Because of mobile networks attack or smartphones hackers, the GSM networks are not secure, so that all information or SMS/MMS messages are vulnerable. This paper describe an android application that helps the user to encrypt the message (SMS/Multimedia files) before it is transmitted over the mobile network. The new idea of the program is to transmit encrypted messages and multimedia files via mobile networks or the internet as an alternative mean. To maintain intensive security, the program uses a Hybrid encryption algorithm based on Blowfish and S-Boxes of DES encryption. Moreover, it uses a private key encrypts the files and another private key encrypts file name. The transferring media is maintained online in the absence of mobile network coverage.

Semi-Automatic Segmentation and Classification of Pap Smear Cells

Cytologic screening has been widely used for detecting the cervical cancers. In this study, a semiautomatic PC-based cellular image analysis system was developed for segmenting nuclear and cytoplasmic contours and for computing morphometric and textual features to train support vector machine (SVM) classifiers to classify four different types of cells and to discriminate dysplastic from normal cells. A software program incorporating function, including image reviewing and standardized denomination of file names, was also designed to facilitate and standardize the workflow of cell analyses. Two experiments were conducted to verify the classification performance. The cross-validation results of the first experiment showed that average accuracies of 97.16% and 98.83%, respectively, for differentiating four different types of cells and in discriminating dysplastic from normal cells have been achieved using salient features (8 for four-cluster and 7 for two-cluster classifiers) selected with SVM recursive feature addition. In the second experiment, 70% (837) of the cell images were used for training and 30% (361) for testing, achieving an accuracy of 96.12% and 98.61% for four-cluster and two-cluster classifiers, respectively. The proposed system provides a feasible and effective tool in evaluating cytologic specimens.

English

Building 3-dimensional (3D) molecules is the starting point in molecular modeling. Conformer search and identification of a global energy minimum structure are often performed computationally during spectral analysis of data from NMR, IR, and VCD or during rational drug design through ligand-based, structure-based, and QSAR approaches. I herein report a convenient script that allows for automated building of 3D structures and conformer searching from 2-dimensional (2D) drawing of chemical structures. With this Bash shell script, which runs on Mac OS X and the Linux platform, the tasks are consecutively and iteratively executed without a 3D molecule builder via the command line interface of the free (academic) software OpenBabel, Balloon, and MOPAC2012. A large number of 2D chemical drawing files can be processed simultaneously, and the script functions with stereoisomers. Semi-empirical quantum chemical calculation ensures reliable ranking of the generated conformers on the basis of energy. In addition to an energy-sorted list of file names of the conformers, their Gaussian input files are provided for ab initio and density functional theory calculations to predict rigorous electronic energies, structures, and properties. This script is freely available to all scientists.