These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure

K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation. We present the khmer software package for fast and memory efficient online counting of k-mers in sequencing data sets. Unlike previous methods based on data structures such as hash tables, suffix arrays, and trie structures, khmer relies entirely on a simple probabilistic data structure, a Count-Min Sketch. The Count-Min Sketch permits online updating and retrieval of k-mer counts in memory which is necessary to support online k-mer analysis algorithms. On sparse data sets this data structure is considerably more memory efficient than any exact data structure. In exchange, the use of a Count-Min Sketch introduces a systematic overcount for k-mers; moreover, only the counts, and not the k-mers, are stored. Here we analyze the speed, the memory usage, and the miscount rate of khmer for generating k-mer frequency distributions and retrieving k-mer counts for individual k-mers. We also compare the performance of khmer to several other k-mer counting packages, including Tallymer, Jellyfish, BFCounter, DSK, KMC, Turtle and KAnalyze. Finally, we examine the effectiveness of profiling sequencing error, k-mer abundance trimming, and digital normalization of reads in the context of high khmer false positive rates. khmer is implemented in C++ wrapped in a Python interface, offers a tested and robust API, and is freely available under the BSD license at github.com/ged-lab/khmer

How Early Is Early Enough: Correlating Student Performance With Final Grades

Student retention is one of the greatest challenges facing computer science programs. Difficulties in an introductory programming class often snowball, resulting in poor student performance or dropping the major completely. In this paper, we present an analysis of 197 students over 6 semesters from 11 sections of an introductory programming class at a private four-year liberal arts university in the southeastern United States. The goal of this research was to find the earliest point in the assessment sequence which could predict final grade outcomes. Accordingly, we measured the degree of correlation between student performance on quizzes, labs, programs, and tests compared to final course grade. Overall, the results show a strong positive correlation for all four assessment modalities. These results hold significance for educators and researchers insofar as the body of computing education research is extended by evaluating the relative effectiveness of early semester subsets of each of the four categories of student data to model class outcomes

PERANCANGAN ENTERPRISE ARCHITECTURE MENGGUNAKAN ZACHMAN FRAMEWORK PADA PERUSAHAAN JEWELRY

Jewelry Company merupakan perusahaan yang memproduksi perhiasan dengan memberikan kualitas yang terbaik kepada konsumennya. Dalam perkembangannya, jewelry Company memiliki sebuah pabrik yang memproduksi berbagai jenis perhiasan diantaranya emas, perak, ruby, permata, topaz dan sapphire. Namun, dalam perencanaan SI/TI di dalam perusahaan tersebut masih terbilang kurang memaksimalkan penggunaan SI/TI yang seharusnya diterapkan di dalam sebuah perusahaan. Oleh sebab itu, perusahaan ini memerlukan sebuah perencanaan yang lebih strategis untuk mendukung tujuan bisnis yang selaras dengan strategi bisnis dan strategi SI/TI. Enterprise Architecture Planning dipilih sebagai panduan dan Zachman Framework sebagai metode dalam perancangan yang terdiri dari enam baris yaitu scope, enterprise model, system model, technology constrained model, retailed representations, dan functioning enterprise, serta enam kolom yang terdiri dari what, how, where, who, when, dan why. Hasil dari penelitian ini adalah sebuah usulan rancangan arsitektur yang disarankan kepada perusahaan diharapkan dapat mendukung penuh kegiatan bisnis yang berjalan agar lebih optimal dan efektif

Reflow: Automatically Improving Touch Interactions in Mobile Applications through Pixel-based Refinements

Touch is the primary way that users interact with smartphones. However, building mobile user interfaces where touch interactions work well for all users is a difficult problem, because users have different abilities and preferences. We propose a system, Reflow, which automatically applies small, personalized UI adaptations, called refinements -- to mobile app screens to improve touch efficiency. Reflow uses a pixel-based strategy to work with existing applications, and improves touch efficiency while minimally disrupting the design intent of the original application. Our system optimizes a UI by (i) extracting its layout from its screenshot, (ii) refining its layout, and (iii) re-rendering the UI to reflect these modifications. We conducted a user study with 10 participants and a heuristic evaluation with 6 experts and found that applications optimized by Reflow led to, on average, 9% faster selection time with minimal layout disruption. The results demonstrate that Reflow's refinements useful UI adaptations to improve touch interactions

230 GHz VLBI OBSERVATIONS OF M87: EVENT‐HORIZON‐SCALE STRUCTURE DURING AN ENHANCED VERY‐HIGH‐ENERGY γ‐RAY STATE IN 2012

We report on 230 GHz (1.3 mm) very long baseline interferometry (VLBI) observations of M87 with the Event Horizon Telescope using antennas on Mauna Kea in Hawaii, Mt. Graham in Arizona, and Cedar Flat in California. For the first time, we have acquired 230 GHz VLBI interferometric phase information on M87 through measurement of the closure phase on the triangle of long baselines. Most of the measured closure phases are consistent with 0° as expected by physically motivated models for 230 GHz structure such as jet models and accretion disk models. The brightness temperature of the event-horizon-scale structure is ~1 X 10[superscript 10] K derived from the compact flux density of ~1 Jy and the angular size of ~40 µas ~ 5.5 R[subscript s], which is broadly consistent with the peak brightness of the radio cores at 1–86 GHz located within ~10[superscript 2] R[subscript s]. Our observations occurred in the middle of an enhancement in very-high-energy (VHE) γ-ray flux, presumably originating in the vicinity of the central black hole. Our measurements, combined with results of multi-wavelength observations, favor a scenario in which the VHE region has an extended size of ~20–60 R[subscript s]

AUDIT APLIKASI DEVELOP INTERNAL DENGAN COBIT 4.1 (STUDI KASUS : PT CENTRAL MEGA KENCANA)

Information technology is an important part for companies or institutions as a thing that can support the achievement of strategic plans to achieve the goals of vision, mission and corporate goals PT.Central Mega Kencana. By increasing the role of information technology, investment in information technology is getting bigger and more complex in its management. Therefore To organize, evaluate the required information technology governance by using standardized obeject approach. The governance of this information system audit is done using the AI (acquired and implemented) Cobit 4.1 framework and the final result of this analysis yields how far the level of maturity level governance maturity and recommendations for PT. Central Mega Kencana proposed

1.3 mm Wavelength VLBI of Sagittarius A*: Detection of Time-Variable Emission on Event Horizon Scales

Sagittarius A*, the ~4 x 10^6 solar mass black hole candidate at the Galactic Center, can be studied on Schwarzschild radius scales with (sub)millimeter wavelength Very Long Baseline Interferometry (VLBI). We report on 1.3 mm wavelength observations of Sgr A* using a VLBI array consisting of the JCMT on Mauna Kea, the ARO/SMT on Mt. Graham in Arizona, and two telescopes of the CARMA array at Cedar Flat in California. Both Sgr A* and the quasar calibrator 1924-292 were observed over three consecutive nights, and both sources were clearly detected on all baselines. For the first time, we are able to extract 1.3 mm VLBI interferometer phase information on Sgr A* through measurement of closure phase on the triangle of baselines. On the third night of observing, the correlated flux density of Sgr A* on all VLBI baselines increased relative to the first two nights, providing strong evidence for time-variable change on scales of a few Schwarzschild radii. These results suggest that future VLBI observations with greater sensitivity and additional baselines will play a valuable role in determining the structure of emission near the event horizon of Sgr A*.Comment: 8 pages, submitted to ApJ

The influence of tumor regression, solar elastosis, and patient age on pathologists\u27 interpretation of melanocytic skin lesions.

It is not known whether patient age or tumor characteristics such as tumor regression or solar elastosis influence pathologists\u27 interpretation of melanocytic skin lesions (MSLs). We undertook a study to determine the influence of these factors, and to explore pathologist\u27s characteristics associated with the direction of diagnosis. To meet our objective, we designed a cross-sectional survey study of pathologists\u27 clinical practices and perceptions. Pathologists were recruited from diverse practices in 10 states in the United States. We enrolled 207 pathologist participants whose practice included the interpretation of MSLs. Our findings indicated that the majority of pathologists (54.6%) were influenced toward a less severe diagnosis when patients were70 years of age, or by the presence of tumor regression or solar elastosis (58.5%, 71.0%, and 57.0%, respectively). Generally, pathologists with dermatopathology board certification and/or a high caseload of MSLs were more likely to be influenced, whereas those with more years\u27 experience interpreting MSL were less likely to be influenced. Our findings indicate that the interpretation of MSLs is influenced by patient age, tumor regression, and solar elastosis; such influence is associated with dermatopathology training and higher caseload, consistent with expertise and an appreciation of lesion complexity