Apparatus for using a time interval counter to measure frequency stability

An apparatus for measuring the relative stability of two signals is disclosed comprising a means for mixing the two signals down to a beat note sine wave and for producing a beat note square wave whose upcrossings are the same as the sine wave. A source of reference frequency is supplied to a clock divider and interval counter to synchronize them and to generate a picket fence for providing a time reference grid of period shorter than the beat period. An interval counter is employed to make a preliminary measurement between successive upcrossings of the beat note square wave for providing an approximate time interval therebetween as a reference. The beat note square wave and the picket fence are then provided to the interval counter to provide an output consisting of the time difference between the upcrossing of each beat note square wave cycle and the next picket fence pulse such that the counter is ready for each upcrossing and dead time is avoided. A computer containing an algorithm for calculating the exact times of the beat note upcrossings then computes the upcrossing times

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

The Omega Counter, a Frequency Counter Based on the Linear Regression

This article introduces the {\Omega} counter, a frequency counter -- or a frequency-to-digital converter, in a different jargon -- based on the Linear Regression (LR) algorithm on time stamps. We discuss the noise of the electronics. We derive the statistical properties of the {\Omega} counter on rigorous mathematical basis, including the weighted measure and the frequency response. We describe an implementation based on a SoC, under test in our laboratory, and we compare the {\Omega} counter to the traditional {\Pi} and {\Lambda} counters. The LR exhibits optimum rejection of white phase noise, superior to that of the {\Pi} and {\Lambda} counters. White noise is the major practical problem of wideband digital electronics, both in the instrument internal circuits and in the fast processes which we may want to measure. The {\Omega} counter finds a natural application in the measurement of the Parabolic Variance, described in the companion article arXiv:1506.00687 [physics.data-an].Comment: 8 pages, 6 figure, 2 table

Scheduling Optimisations for SPIN to Minimise Buffer Requirements in Synchronous Data Flow

Synchronous Data flow (SDF) graphs have a simple and elegant semantics (essentially linear algebra) which makes SDF graphs eminently suitable as a vehicle for studying scheduling optimisations. We extend related work on using SPIN to experiment with scheduling optimisations aimed at minimising buffer requirements.We show that for a benchmark of commonly used case studies the performance of our SPIN based scheduler is comparable to that of state of the art research tools. The key to success is using the semantics of SDF to prove when using (even unsound and/or incomplete) optimisations are justified. The main benefit of our approach lies in gaining deep insight in the optimisations at relatively low cost

Scintillation Counters for the D0 Muon Upgrade

We present the results of an upgrade to the D0 muon system. Scintillating counters have been added to the existing central D0 muon system to provide rejection for cosmic ray muons and out-of-time background, and to provide additional fast timing information for muons in an upgraded Tevatron. Performance and results from the 1994-1996 Tevatron run are presented.Comment: 30 pages, 25 postscript figure