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@book{schaling2011boost,
	Author = {Sch{\"a}ling, Boris},
	Date-Added = {2015-03-05 19:59:56 +0000},
	Date-Modified = {2015-03-05 19:59:56 +0000},
	Publisher = {Boris Sch{\"a}ling},
	Title = {The boost C++ libraries},
	Year = {2011}}

@inproceedings{DBLP:conf/padl/MaldeO09,
	Abstract = {Analysis of biological data often involves large data sets and computationally expensive algorithms. Databases of biological data continue to grow, leading to an increasing demand for improved algorithms and data structures. Despite having many advantages over more traditional indexing structures, the Bloom filter is almost unused in bioinformatics. Here we present a robust and efficient Bloom filter implementation in Haskell, and implement a simple bioinformatics application for indexing and matching sequence data. We use this to index the chromosomes that make up the human genome, and map all available gene sequences to it. Our experiences with developing and tuning our application suggest that for bioinformatics applications, Haskell offers a compelling combination of rapid development, quality assurance, and high performance.},
	Author = {Ketil Malde and Bryan O'Sullivan},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {PADL},
	Crossref = {DBLP:conf/padl/2009},
	Date-Added = {2014-05-06 22:27:05 +0000},
	Date-Modified = {2014-05-06 22:27:05 +0000},
	Pages = {183-194},
	Title = {Using Bloom Filters for Large Scale Gene Sequence Analysis in Haskell},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-540-92995-6_13}}

@proceedings{DBLP:conf/padl/2009,
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {PADL},
	Date-Added = {2014-05-06 22:27:05 +0000},
	Date-Modified = {2014-05-06 22:27:05 +0000},
	Editor = {Andy Gill and Terrance Swift},
	Isbn = {978-3-540-92994-9},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Title = {Practical Aspects of Declarative Languages, 11th International Symposium, PADL 2009, Savannah, GA, USA, January 19-20, 2009. Proceedings},
	Volume = {5418},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-540-92995-6}}

@inproceedings{DBLP:conf/sigmod/CohenM03,
	Abstract = {A Bloom Filter is a space-efficient randomized data structure allowing membership queries over sets with certain allowable errors. It is widely used in many applications which take advantage of its ability to compactly represent a set, and filter out effectively any element that does not belong to the set, with small error probability. This paper introduces the Spectral Bloom Filter (SBF), an extension of the original Bloom Filter to multi-sets, allowing the filtering of elements whose multiplicities are below a threshold given at query time. Using memory only slightly larger than that of the original Bloom Filter, the SBF supports queries on the multiplicities of individual keys with a guaranteed, small error probability. The SBF also supports insertions and deletions over the data set. We present novel methods for reducing the probability and magnitude of errors. We also present an efficient data structure and algorithms to build it incrementally and maintain it over streaming data, as well as over materialized data with arbitrary insertions and deletions. The SBF does not assume any a priori filtering threshold and effectively and efficiently maintains information over the entire data-set, allowing for ad-hoc queries with arbitrary parameters and enabling a range of new applications.},
	Author = {Saar Cohen and Yossi Matias},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {SIGMOD Conference},
	Crossref = {DBLP:conf/sigmod/2003},
	Date-Added = {2014-05-06 22:23:00 +0000},
	Date-Modified = {2014-05-06 22:23:00 +0000},
	Pages = {241-252},
	Title = {Spectral Bloom Filters},
	Year = {2003},
	Bdsk-Url-1 = {http://doi.acm.org/10.1145/872757.872787}}

@proceedings{DBLP:conf/sigmod/2003,
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {SIGMOD Conference},
	Date-Added = {2014-05-06 22:23:00 +0000},
	Date-Modified = {2014-05-06 22:23:00 +0000},
	Editor = {Alon Y. Halevy and Zachary G. Ives and AnHai Doan},
	Isbn = {1-58113-634-X},
	Publisher = {ACM},
	Title = {Proceedings of the 2003 ACM SIGMOD International Conference on Management of Data, San Diego, California, USA, June 9-12, 2003},
	Year = {2003}}

@inproceedings{DBLP:conf/sigcomm/EstanV02,
	Abstract = {Accurate network traffic measurement is required for accounting, bandwidth provisioning and detecting DoS attacks. These applications see the traffic as a collection of flows they need to measure. As link speeds and the number of flows increase, keeping a counter for each flow is too expensive (using SRAM) or slow (using DRAM). The current state-of-the-art methods (Cisco's sampled NetFlow) which log periodically sampled packets are slow, inaccurate and resource-intensive. Previous work showed that at different granularities a small number of heavy hitters accounts for a large share of traffic. Our paper introduces a paradigm shift for measurement by concentrating only on large flows --- those above some threshold such as 0.1% of the link capacity.We propose two novel and scalable algorithms for identifying the large flows: sample and hold and multistage filters, which take a constant number of memory references per packet and use a small amount of memory. If $M$ is the available memory, we show analytically that the errors of our new algorithms are proportional to $1/M$; by contrast, the error of an algorithm based on classical sampling is proportional to $1/sqrtM$, thus providing much less accuracy for the same amount of memory. We also describe further optimizations such as early removal and conservative update that further improve the accuracy of our algorithms, as measured on real traffic traces, by an order of magnitude. Our schemes allow a new form of accounting called threshold accounting in which only flows above a threshold are charged by usage while the rest are charged a fixed fee. Threshold accounting generalizes usage-based and duration based pricing.},
	Author = {Cristian Estan and George Varghese},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {SIGCOMM},
	Crossref = {DBLP:conf/sigcomm/2002},
	Date-Added = {2014-05-06 22:21:14 +0000},
	Date-Modified = {2014-05-06 22:21:14 +0000},
	Pages = {323-336},
	Title = {New directions in traffic measurement and accounting},
	Year = {2002},
	Bdsk-Url-1 = {http://doi.acm.org/10.1145/633025.633056}}

@proceedings{DBLP:conf/sigcomm/2002,
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {SIGCOMM},
	Date-Added = {2014-05-06 22:21:14 +0000},
	Date-Modified = {2014-05-06 22:21:14 +0000},
	Isbn = {1-58113-570-X},
	Publisher = {ACM},
	Title = {Proceedings of the ACM SIGCOMM 2002 Conference on Applications, Technologies, Architectures, and Protocols for Computer Communication, August 19-23, 2002, Pittsburgh, PA, USA},
	Year = {2002}}

@article{flajolet2008hyperloglog,
	Author = {Flajolet, Philippe and Fusy, {\'E}ric and Gandouet, Olivier and Meunier, Fr{\'e}d{\'e}ric},
	Date-Added = {2014-05-03 02:17:23 +0000},
	Date-Modified = {2014-05-03 02:17:23 +0000},
	Journal = {DMTCS Proceedings},
	Number = {1},
	Title = {HyperLogLog: the analysis of a near-optimal cardinality estimation algorithm},
	Year = {2008}}

@article{Fan:2000:SCS:343571.343572,
	Acmid = {343572},
	Address = {Piscataway, NJ, USA},
	Author = {Fan, Li and Cao, Pei and Almeida, Jussara and Broder, Andrei Z.},
	Date-Added = {2014-05-03 02:09:38 +0000},
	Date-Modified = {2014-05-03 02:09:38 +0000},
	Doi = {10.1109/90.851975},
	Issn = {1063-6692},
	Issue_Date = {June 2000},
	Journal = {IEEE/ACM Trans. Netw.},
	Keywords = {ICP, Web cache, Web proxy, bloom filter, cache sharing},
	Month = jun,
	Number = {3},
	Numpages = {13},
	Pages = {281--293},
	Publisher = {IEEE Press},
	Title = {Summary Cache: A Scalable Wide-area Web Cache Sharing Protocol},
	Url = {http://dx.doi.org/10.1109/90.851975},
	Volume = {8},
	Year = {2000},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/90.851975}}

@article{broder2004network,
	Author = {Broder, Andrei and Mitzenmacher, Michael},
	Date-Added = {2014-04-20 17:14:01 +0000},
	Date-Modified = {2014-04-20 17:14:01 +0000},
	Journal = {Internet mathematics},
	Number = {4},
	Pages = {485--509},
	Publisher = {Taylor \& Francis},
	Title = {Network applications of bloom filters: A survey},
	Volume = {1},
	Year = {2004}}

@manual{khmer,
	Author = {Crusoe, Michael and Edvenson, Greg and Fish, Jordan and Howe, Adina and McDonald, Eric and Nahum, Joshua and Nanlohy, Kaben and Ortiz-Zuazaga, Humberto and Pell, Jason and Simpson, Jared and Scott, Camille and Srinivasan, Ramakrishnan and Zhang, Qingpeng and Brown, C. Titus},
	Date-Added = {2014-04-18 23:29:55 +0000},
	Date-Modified = {2014-06-10 21:44:59 +0000},
	Title = {The khmer software package: enabling efficient sequence analysis},
	Url = {http://dx.doi.org/10.6084/m9.figshare.979190},
	Year = {2014},
	Bdsk-Url-1 = {-%20http://figshare.com/articles/The_khmer_software_package_enabling_efficient_sequence_analysis/979190}}

@article{Audano2014,
	Abstract = {MOTIVATION: Converting nucleotide sequences into short overlapping fragments of uniform length, k-mers, is a common step in many bioinformatics applications. While existing software packages count k-mers, few are optimized for speed, offer an API (Application Programming Interface), a graphical interface, or contain features that make it extensible and maintainable. We designed KAnalyze to compete with the fastest k-mer counters, to produce reliable output, and to support future development efforts through well architected, documented, and testable code. Currently, KAnalyze can output k-mer counts in a sorted tab-delimited file or stream k-mers as they are read. KAnalyze can process large data sets with 2GB of memory. This project is implemented in Java 7, and the CLI (Command Line Interface) is designed to integrate into pipelines written in any language.
RESULTS: As a k-mer counter, KAnalyze outperforms Jellyfish (Mar{\c c}ais and Kingsford, 2011), DSK (Rizk et al., 2013), and a pipeline built on a Perl and Linux utilities. Through extensive unit and system testing, we have verified that KAnalyze produces the correct k-mer counts over multiple data sets and k-mer sizes.
AVAILABILITY: KAnalyze is available on SourceForge: https://sourceforge.net/projects/kanalyze/ SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
CONTACT: fredrik.vannberg@biology.gatech.edu.},
	Author = {Audano, Peter and Vannberg, Fredrik},
	Date-Added = {2014-04-18 20:50:07 +0000},
	Date-Modified = {2014-06-10 21:36:18 +0000},
	Doi = {10.1093/bioinformatics/btu152},
	Journal = {Bioinformatics: Advance Access published March 18, 2014},
	Journal-Full = {Bioinformatics (Oxford, England)},
	Month = {Mar},
	Pages = {doi: 10.1093/bioinformatics/btu152},
	Pmid = {24642064},
	Pst = {aheadofprint},
	Title = {KAnalyze: A Fast Versatile Pipelined K-mer Toolkit},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/btu152}}

@article{Roy2014,
	Abstract = {MOTIVATION: Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing data. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a reduced but error-free representation of the experiment, which can inform read error correction or serve as the input to de novo assembly methods. Ideally, the memory requirement for counting should be linear in the number of frequent k-mers and not in the, typically much larger, total number of k-mers in the read library.
RESULTS: We present a novel method that balances time, space and accuracy requirements to efficiently extract frequent k-mers even for high-coverage libraries and large genomes such as human. Our method is designed to minimize cache misses in a cache-efficient manner by using a pattern-blocked Bloom filter to remove infrequent k-mers from consideration in combination with a novel sort-and-compact scheme, instead of a hash, for the actual counting. Although this increases theoretical complexity, the savings in cache misses reduce the empirical running times. A variant of method can resort to a counting Bloom filter for even larger savings in memory at the expense of false-negative rates in addition to the false-positive rates common to all Bloom filter-based approaches. A comparison with the state-of-the-art shows reduced memory requirements and running times.
AVAILABILITY AND IMPLEMENTATION: The tools are freely available for download at http://bioinformatics.rutgers.edu/Software/Turtle and http://figshare.com/articles/Turtle/791582.
CONTACT: rajatroy@cs.rutgers.edu or schliep@cs.rutgers.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
	Author = {Roy, Rajat Shuvro and Bhattacharya, Debashish and Schliep, Alexander},
	Date-Added = {2014-04-18 20:48:21 +0000},
	Date-Modified = {2014-06-10 21:35:20 +0000},
	Doi = {10.1093/bioinformatics/btu132},
	Journal = {Bioinformatics: Advance Access published March 10, 2014},
	Journal-Full = {Bioinformatics (Oxford, England)},
	Month = {Apr},
	Pages = {doi: 10.1093/bioinformatics/btu132},
	Pmid = {24618471},
	Pst = {aheadofprint},
	Title = {Turtle: Identifying frequent k-mers with cache-efficient algorithms},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/btu132}}

@inproceedings{CormodeM05,
	Author = {Graham Cormode and S. Muthukrishnan},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {SDM},
	Crossref = {DBLP:conf/sdm/2005},
	Date-Added = {2014-04-18 20:43:06 +0000},
	Date-Modified = {2014-04-18 20:43:35 +0000},
	Pages = {44-55},
	Title = {Summarizing and Mining Skewed Data Streams},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1137/1.9781611972757.5}}

@proceedings{DBLP:conf/sdm/2005,
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {SDM},
	Date-Added = {2014-04-18 20:43:06 +0000},
	Date-Modified = {2014-04-18 20:43:06 +0000},
	Editor = {Hillol Kargupta and Jaideep Srivastava and Chandrika Kamath and Arnold Goodman},
	Isbn = {978-0-89871-593-4, 978-1-61197-275-7},
	Publisher = {SIAM},
	Title = {Proceedings of the 2005 SIAM International Conference on Data Mining, SDM 2005, Newport Beach, CA, USA, April 21-23, 2005},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1137/1.9781611972757}}

@article{Li2003,
	Abstract = {In shotgun sequencing projects, the genome or BAC length is not always known. We approach estimating genome length by first estimating the repeat structure of the genome or BAC, sometimes of interest in its own right, on the basis of a set of random reads from a genome project. Moreover, we can find the consensus for repeat families before assembly. Our methods are based on the l-tuple content of the reads.},
	Author = {Li, Xiaoman and Waterman, Michael S},
	Date-Added = {2014-04-18 19:55:32 +0000},
	Date-Modified = {2014-04-18 19:55:32 +0000},
	Doi = {10.1101/gr.1251803},
	Journal = {Genome Res},
	Journal-Full = {Genome research},
	Mesh = {Algorithms; Base Composition; Chromosome Mapping; Chromosomes, Artificial, Bacterial; Computational Biology; Computer Simulation; Consensus Sequence; DNA, Bacterial; Mathematical Computing; Poisson Distribution; Repetitive Sequences, Nucleic Acid; Software},
	Month = {Aug},
	Number = {8},
	Pages = {1916-22},
	Pmc = {PMC403783},
	Pmid = {12902383},
	Pst = {ppublish},
	Title = {Estimating the repeat structure and length of DNA sequences using L-tuples},
	Volume = {13},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1101/gr.1251803}}

@article{Howe2014,
	Abstract = {The large volumes of sequencing data required to sample deeply the microbial communities of complex environments pose new challenges to sequence analysis. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires substantial computational resources. We combine two preassembly filtering approaches-digital normalization and partitioning-to generate previously intractable large metagenome assemblies. Using a human-gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes totaling 398 billion bp (equivalent to 88,000 Escherichia coli genomes) from matched Iowa corn and native prairie soils. The resulting assembled contigs could be used to identify molecular interactions and reaction networks of known metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes Orthology database. Nonetheless, more than 60% of predicted proteins in assemblies could not be annotated against known databases. Many of these unknown proteins were abundant in both corn and prairie soils, highlighting the benefits of assembly for the discovery and characterization of novelty in soil biodiversity. Moreover, 80% of the sequencing data could not be assembled because of low coverage, suggesting that considerably more sequencing data are needed to characterize the functional content of soil.},
	Author = {Howe, Adina Chuang and Jansson, Janet K and Malfatti, Stephanie A and Tringe, Susannah G and Tiedje, James M and Brown, C Titus},
	Date-Added = {2014-04-18 18:35:19 +0000},
	Date-Modified = {2014-04-18 18:35:55 +0000},
	Doi = {10.1073/pnas.1402564111},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Month = {Apr},
	Number = {13},
	Pages = {4904-9},
	Pmid = {24632729},
	Pst = {ppublish},
	Title = {Tackling soil diversity with the assembly of large, complex metagenomes},
	Volume = {111},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.1402564111}}

@article{Chikhi:2014aa,
	Abstract = {MOTIVATION: Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically estimate the best k to use and/or quickly generate histograms of k-mer abundances that would allow the user to make an informed decision.
RESULTS: We develop a fast and accurate sampling method that constructs approximate abundance histograms with several orders of magnitude performance improvement over traditional methods. We then present a fast heuristic that uses the generated abundance histograms for putative k values to estimate the best possible value of k. We test the effectiveness of our tool using diverse sequencing datasets and find that its choice of k leads to some of the best assemblies.
AVAILABILITY: Our tool KmerGenie is freely available at: http://kmergenie.bx.psu.edu/.
CONTACT: pashadag@cse.psu.edu.},
	Author = {Chikhi, Rayan and Medvedev, Paul},
	Date-Added = {2014-01-21 16:11:48 +0000},
	Date-Modified = {2014-01-21 16:11:48 +0000},
	Doi = {10.1093/bioinformatics/btt310},
	Journal = {Bioinformatics},
	Journal-Full = {Bioinformatics (Oxford, England)},
	Month = {Jan},
	Number = {1},
	Pages = {31-7},
	Pmid = {23732276},
	Pst = {ppublish},
	Title = {Informed and automated k-mer size selection for genome assembly},
	Volume = {30},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/btt310}}

@article{Jones:2012aa,
	Abstract = {We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we have developed, to our knowledge, the first assembly-based compressor, using a novel de novo assembly algorithm. A probabilistic data structure is used to dramatically reduce the memory required by traditional de Bruijn graph assemblers, allowing millions of reads to be assembled very efficiently. Read sequences are then stored as positions within the assembled contigs. This is combined with statistical compression of read identifiers, quality scores, alignment information and sequences, effectively collapsing very large data sets to <15% of their original size with no loss of information. Availability: Quip is freely available under the 3-clause BSD license from http://cs.washington.edu/homes/dcjones/quip.},
	Author = {Jones, Daniel C and Ruzzo, Walter L and Peng, Xinxia and Katze, Michael G},
	Date-Added = {2014-01-21 16:11:26 +0000},
	Date-Modified = {2014-01-21 16:11:26 +0000},
	Doi = {10.1093/nar/gks754},
	Journal = {Nucleic Acids Res},
	Journal-Full = {Nucleic acids research},
	Mesh = {Algorithms; Data Compression; High-Throughput Nucleotide Sequencing; Probability; Software},
	Month = {Dec},
	Number = {22},
	Pages = {e171},
	Pmc = {PMC3526293},
	Pmid = {22904078},
	Pst = {ppublish},
	Title = {Compression of next-generation sequencing reads aided by highly efficient de novo assembly},
	Volume = {40},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/nar/gks754}}

@article{4160251,
	Author = {P{\'e}rez, F. and Granger, B.E.},
	Journal = {Computing in Science Engineering},
	Number = {3},
	Pages = {21-29},
	Title = {IPython: A System for Interactive Scientific Computing},
	Volume = {9},
	Year = {2007}}

@article{Luo2009,
	Author = {Luo, Weijun and Friedman, Michael S and Shedden, Kerby and Hankenson, Kurt D and Woolf, Peter J},
	Journal = {BMC Bioinformatics},
	Pages = {161},
	Title = {GAGE: generally applicable gene set enrichment for pathway analysis},
	Volume = {10},
	Year = {2009}}

@incollection{McDonald2013,
	Author = {Eric McDonald and C. Titus Brown},
	Booktitle = {The Performance of Open Source Applications},
	Chapter = {12},
	Date-Modified = {2014-06-10 21:39:36 +0000},
	Editor = {Tavish Armstrong},
	Pages = {151},
	Publisher = {lulu.com},
	Title = {Working with Big Data in Bioinformatics},
	Year = {2013}}

@unpublished{Brown2012blog,
	Author = {C. Titus Brown},
	Date-Modified = {2014-06-18 19:54:14 +0000},
	Title = {What does Trinity's In Silico normalization do?},
	Url = {http://dx.doi.org/10.6084/m9.figshare.98198},
	Year = {2012},
	Bdsk-Url-1 = {http://ivory.idyll.org/blog/trinity-in-silico-normalize.html}}

@article{Haas2013,
	Author = {Haas, Brian J and Papanicolaou, Alexie and Yassour, Moran and Grabherr, Manfred and Blood, Philip D and Bowden, Joshua and Couger, Matthew Brian and Eccles, David and Li, Bo and Lieber, Matthias and Macmanes, Matthew D and Ott, Michael and Orvis, Joshua and Pochet, Nathalie and Strozzi, Francesco and Weeks, Nathan and Westerman, Rick and William, Thomas and Dewey, Colin N and Henschel, Robert and Leduc, Richard D and Friedman, Nir and Regev, Aviv},
	Journal = {Nat Protoc},
	Month = {Aug},
	Number = {8},
	Pages = {1494-512},
	Title = {De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis},
	Volume = {8},
	Year = {2013}}

@article{pubmed19997069,
	Author = {ML Metzker},
	Journal = {Nat Rev Genet},
	Number = {1},
	Pages = {31-46},
	Title = {Sequencing technologies - the next generation.},
	Volume = {11},
	Year = {2010}}

@article{pubmed21926975,
	Author = {H Chitsaz and JL Yee-Greenbaum and G Tesler and MJ Lombardo and CL Dupont and JH Badger and M Novotny and DB Rusch and LJ Fraser and NA Gormley and O Schulz-Trieglaff and GP Smith and DJ Evers and PA Pevzner and RS Lasken},
	Journal = {Nat Biotechnol},
	Number = {10},
	Pages = {915-21},
	Title = {Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.},
	Volume = {29},
	Year = {2011}}

@article{Mackelprang2011,
	Author = {Mackelprang, Rachel and Waldrop, Mark P and DeAngelis, Kristen M and David, Maude M and Chavarria, Krystle L and Blazewicz, Steven J and Rubin, Edward M and Jansson, Janet K},
	Journal = {Nature},
	Month = {Dec},
	Number = {7377},
	Pages = {368-71},
	Title = {Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw},
	Volume = {480},
	Year = {2011}}

@article{Kelley2010,
	Author = {Kelley, David R and Schatz, Michael C and Salzberg, Steven L},
	Journal = {Genome Biol},
	Number = {11},
	Pages = {R116},
	Title = {Quake: quality-aware detection and correction of sequencing errors},
	Volume = {11},
	Year = {2010}}

@article{Medvedev2011,
	Author = {Medvedev, Paul and Scott, Eric and Kakaradov, Boyko and Pevzner, Pavel},
	Journal = {Bioinformatics},
	Month = {Jul},
	Number = {13},
	Pages = {i137-41},
	Title = {Error correction of high-throughput sequencing datasets with non-uniform coverage},
	Volume = {27},
	Year = {2011}}

@article{Brown2012,
	Author = {C. Titus Brown and Adina Howe and Qingpeng Zhang and Alexis B. Pyrkosz and Timothy H. Brom},
	Date-Modified = {2014-06-10 21:23:40 +0000},
	Journal = {arXiv},
	Month = {03},
	Pages = {1203.4802},
	Title = {A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data},
	Year = {2012}}

@article{adina2013,
	Author = {Adina Chuang Howe and Jason Pell and Rosangela Canino-Koning and Rachel Mackelprang and Susannah Tringe and Janet Jansson and James M. Tiedje and C. Titus Brown},
	Date-Modified = {2014-06-10 21:26:01 +0000},
	Journal = {arXiv},
	Pages = {1212.0159},
	Title = {Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets},
	Year = {2012}}

@article{Deorowicz2013,
	Author = {Deorowicz, Sebastian and Debudaj-Grabysz, Agnieszka and Grabowski, Szymon},
	Journal = {BMC Bioinformatics},
	Month = {May},
	Number = {1},
	Pages = {160},
	Title = {Disk-based k-mer counting on a PC},
	Volume = {14},
	Year = {2013}}

@article{Minoche2011,
	Author = {Minoche, Andr{\'e} E and Dohm, Juliane C and Himmelbauer, Heinz},
	Journal = {Genome Biol},
	Number = {11},
	Pages = {R112},
	Title = {Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems},
	Volume = {12},
	Year = {2011}}

@article{Rizk2013,
	Author = {Rizk, Guillaume and Lavenier, Dominique and Chikhi, Rayan},
	Journal = {Bioinformatics},
	Month = {Mar},
	Number = {5},
	Pages = {652-3},
	Title = {DSK: k-mer counting with very low memory usage},
	Volume = {29},
	Year = {2013}}

@article{Pell2012,
	Author = {Pell, Jason and Hintze, Arend and Canino-Koning, Rosangela and Howe, Adina and Tiedje, James M and Brown, C Titus},
	Journal = {Proc Natl Acad Sci U S A},
	Month = {Aug},
	Number = {33},
	Pages = {13272-7},
	Title = {Scaling metagenome sequence assembly with probabilistic de Bruijn graphs},
	Volume = {109},
	Year = {2012}}

@article{BroderM03,
	Author = {Andrei Z. Broder and Michael Mitzenmacher},
	Journal = {Internet Mathematics},
	Number = {4},
	Pages = {485-509},
	Title = {Survey: Network Applications of Bloom Filters: A Survey},
	Volume = {1},
	Year = {2003}}

@article{Bloom70,
	Author = {Burton H. Bloom},
	Journal = {Commun. ACM},
	Number = {7},
	Pages = {422-426},
	Title = {Space/Time Trade-offs in Hash Coding with Allowable Errors},
	Volume = {13},
	Year = {1970}}

@article{Li2010,
	Author = {Li, Ruiqiang and Zhu, Hongmei and Ruan, Jue and Qian, Wubin and Fang, Xiaodong and Shi, Zhongbin and Li, Yingrui and Li, Shengting and Shan, Gao and Kristiansen, Karsten and Li, Songgang and Yang, Huanming and Wang, Jian and Wang, Jun},
	Journal = {Genome Res},
	Month = {Feb},
	Number = {2},
	Pages = {265-72},
	Title = {De novo assembly of human genomes with massively parallel short read sequencing},
	Volume = {20},
	Year = {2010}}

@article{Simpson2009,
	Author = {Simpson, Jared T and Wong, Kim and Jackman, Shaun D and Schein, Jacqueline E and Jones, Steven J M and Birol, Inan{\c c}},
	Journal = {Genome Res},
	Month = {Jun},
	Number = {6},
	Pages = {1117-23},
	Title = {ABySS: a parallel assembler for short read sequence data},
	Volume = {19},
	Year = {2009}}

@article{Butler2008,
	Author = {Butler, Jonathan and MacCallum, Iain and Kleber, Michael and Shlyakhter, Ilya A and Belmonte, Matthew K and Lander, Eric S and Nusbaum, Chad and Jaffe, David B},
	Journal = {Genome Res},
	Month = {May},
	Number = {5},
	Pages = {810-20},
	Title = {ALLPATHS: de novo assembly of whole-genome shotgun microreads},
	Volume = {18},
	Year = {2008}}

@article{Zerbino2008,
	Author = {Zerbino, Daniel R and Birney, Ewan},
	Journal = {Genome Res},
	Month = {May},
	Number = {5},
	Pages = {821-9},
	Title = {Velvet: algorithms for de novo short read assembly using de Bruijn graphs},
	Volume = {18},
	Year = {2008}}

@article{Pevzner2001,
	Author = {Pevzner, P A and Tang, H and Waterman, M S},
	Journal = {Proc Natl Acad Sci U S A},
	Month = {Aug},
	Number = {17},
	Pages = {9748-53},
	Title = {An Eulerian path approach to DNA fragment assembly},
	Volume = {98},
	Year = {2001}}

@article{Marcais2011,
	Author = {Mar\c{c}ais, Guillaume and Kingsford, Carl},
	Journal = {Bioinformatics},
	Number = {6},
	Pages = {764--770},
	Title = {{A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.}},
	Volume = {27},
	Year = {2011}}

@article{Qin2010,
	Author = {Qin, Junjie and Li, Ruiqiang and Raes, Jeroen and Arumugam, Manimozhiyan and Burgdorf, Kristoffer Solvsten and Manichanh, Chaysavanh and Nielsen, Trine and Pons, Nicolas and Levenez, Florence and Yamada, Takuji and Mende, Daniel R and Li, Junhua and Xu, Junming and Li, Songgang Shaochuan Shengting and Li, Dongfang and Cao, Jianjun and Wang, Bo and Liang, Huiqing and Zheng, Huisong and Xie, Yinlong and Tap, Julien and Lepage, Patricia and Bertalan, Marcelo and Batto, Jean-Michel and Hansen, Torben and {Le Paslier}, Denis and Linneberg, Allan and Nielsen, H Bj\o rn and Pelletier, Eric and Renault, Pierre and Sicheritz-Ponten, Thomas and Turner, Keith and Zhu, Hongmei and Yu, Chang and Jian, Min and Zhou, Yan and Li, Yingrui and Zhang, Xiuqing and Qin, Nan and Yang, Huanming and Wang, Jun Jian and Brunak, S\o ren and Dor\'{e}, Joel and Guarner, Francisco and Kristiansen, Karsten and Pedersen, Oluf and Parkhill, Julian and Weissenbach, Jean and Bork, Peer and Ehrlich, S Dusko},
	Journal = {Nature},
	Number = {7285},
	Pages = {59--65},
	Title = {{A human gut microbial gene catalogue established by metagenomic sequencing.}},
	Volume = {464},
	Year = {2010}}

@article{Kurtz2008,
	Author = {Kurtz, Stefan and Narechania, Apurva and Stein, Joshua C and Ware, Doreen},
	Journal = {BMC Genomics},
	Number = {1},
	Pages = {517},
	Title = {{A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes}},
	Volume = {9},
	Year = {2008}}

@article{Shi2010,
	Author = {Shi, Haixiang and Schmidt, Bertil and Liu, Weiguo and M\"{u}ller-Wittig, Wolfgang},
	Journal = {Journal of computational biology a journal of computational molecular cell biology},
	Number = {4},
	Pages = {603--615},
	Title = {{A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware.}},
	Volume = {17},
	Year = {2010}}

@article{Davenport2010,
	Author = {Davenport, Colin F and T\"{u}mmler, Burkhard},
	Journal = {PLoS ONE},
	Number = {3},
	Pages = {8},
	Title = {{Abundant Oligonucleotides Common to Most Bacteria}},
	Volume = {5},
	Year = {2010}}

@article{Cormode2005,
	Author = {Cormode, Graham and Muthukrishnan, S},
	Journal = {Journal of Algorithms},
	Month = apr,
	Number = {1},
	Pages = {58--75},
	Title = {{An improved data stream summary: the count-min sketch and its applications}},
	Volume = {55},
	Year = {2005}}

@article{Healy2003,
	Author = {Healy, John and Thomas, Elizabeth E and Schwartz, Jacob T and Wigler, Michael},
	Journal = {Genome Research},
	Number = {10},
	Pages = {2306--2315},
	Title = {{Annotating large genomes with exact word matches.}},
	Volume = {13},
	Year = {2003}}

@article{Miller2010,
	Author = {Miller, Jason R and Koren, Sergey and Sutton, Granger},
	Journal = {Genomics},
	Month = {Jun},
	Number = {6},
	Pages = {315-27},
	Title = {Assembly algorithms for next-generation sequencing data},
	Volume = {95},
	Year = {2010}}

@article{Bar-yossef,
	Author = {Bar-yossef, Ziv and Jayram, T S and Kumar, Ravi and Sivakumar, D},
	Journal = {Memory},
	Title = {{Counting distinct elements in a data stream}}}

@article{Hampson2002,
	Author = {Hampson, Steven and Kibler, Dennis and Baldi, Pierre},
	Journal = {Bioinformatics},
	Number = {4},
	Pages = {513--528},
	Title = {{Distribution patterns of over-represented k-mers in non-coding yeast DNA.}},
	Volume = {18},
	Year = {2002}}

@article{Sindi2008,
	Author = {Sindi, Suzanne S and Hunt, Brian R and Yorke, James A},
	Journal = {Physical Review E - Statistical, Nonlinear and Soft Matter Physics},
	Number = {6 Pt 1},
	Pages = {061912},
	Title = {{Duplication count distributions in DNA sequences.}},
	Volume = {78},
	Year = {2008}}

@article{Melsted2011,
	Author = {Melsted, P\'{a}ll and Pritchard, Jonathan K},
	Journal = {BMC bioinformatics},
	Month = jan,
	Pages = {333},
	Title = {{Efficient counting of k-mers in DNA sequences using a bloom filter.}},
	Volume = {12},
	Year = {2011}}

@article{Hooper2010,
	Author = {Hooper, Sean D and Dalevi, Daniel and Pati, Amrita and Mavromatis, Konstantinos and Ivanova, Natalia N and Kyrpides, Nikos C},
	Journal = {Bioinformatics},
	Number = {3},
	Pages = {295--301},
	Title = {{Estimating DNA coverage and abundance in metagenomes using a gamma approximation}},
	Volume = {26},
	Year = {2010}}

@article{Charikar2004,
	Author = {Charikar, M},
	Journal = {Theoretical Computer Science},
	Month = jan,
	Number = {1},
	Pages = {3--15},
	Title = {{Finding frequent items in data streams}},
	Volume = {312},
	Year = {2004}}

@article{Trifonov2010,
	Author = {Trifonov, Vladimir and Rabadan, Raul},
	Journal = {mBio},
	Number = {3},
	Pages = {1--8},
	Title = {{Frequency Analysis Techniques for Identification of Viral Genetic Data}},
	Volume = {1},
	Year = {2010}}

@article{Chor2009,
	Author = {Chor, Benny and Horn, David and Goldman, Nick and Levy, Yaron and Massingham, Tim},
	Journal = {Genome Biology},
	Number = {10},
	Pages = {R108},
	Title = {{Genomic DNA k-mer spectra: models and modalities}},
	Volume = {10},
	Year = {2009}}

@article{Kirsch2006,
	Author = {Kirsch, Adam and Mitzenmacher, Michael},
	Journal = {Building},
	Pages = {456--467},
	Title = {{Less Hashing , Same Performance : Building a Better Bloom Filter}},
	Year = {2006}}

@article{Hess2011,
	Author = {Hess, M and Sczyrba, A and Egan, R and Kim, T W and Chokhawala, H and Schroth, G and Luo, S and Clark, D S and Chen, F and Zhang, T and Mackie, R I and Pennacchio, L A and Tringe, S G and Visel, A and Woyke, T and Wang, Z and Rubin, E M},
	Journal = {Science},
	Number = {6016},
	Pages = {463--467},
	Title = {{Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen}},
	Volume = {331},
	Year = {2011}}

@article{Richter2008,
	Author = {Richter, Daniel C and Ott, Felix and Auch, Alexander F and Schmid, Ramona and Huson, Daniel H},
	Journal = {PLoS ONE},
	Number = {10},
	Pages = {12},
	Title = {{MetaSim---A Sequencing Simulator for Genomics and Metagenomics}},
	Volume = {3},
	Year = {2008}}

@article{Chen2005,
	Author = {Chen, Yaw-Hwang and Nyeo, Su-Long and Yeh, Chiung-Yuh},
	Journal = {Physical Review E},
	Number = {1},
	Pages = {1--7},
	Title = {{Model for the distributions of k-mers in DNA sequences}},
	Volume = {72},
	Year = {2005}}

@article{Woyke2010,
	Author = {Woyke, Tanja and Tighe, Damon and Mavromatis, Konstantinos and Clum, Alicia and Copeland, Alex and Schackwitz, Wendy and Lapidus, Alla and Wu, Dongying and McCutcheon, John P and McDonald, Bradon R and Moran, Nancy A and Bristow, James and Cheng, Jan-Fang},
	Journal = {PLoS ONE},
	Number = {4},
	Pages = {8},
	Title = {{One Bacterial Cell, One Complete Genome}},
	Volume = {5},
	Year = {2010}}

@article{Kane2010,
	Author = {Kane, Daniel M and Nelson, Jelani and Woodruff, David P and Road, Harry and Jose, San},
	Journal = {PODS '10 P},
	Pages = {41--52},
	Title = {An Optimal Algorithm for the Distinct Elements Problem},
	Year = {2010}}

@article{Campagna2005,
	Author = {Campagna, Davide and Romualdi, Chiara and Vitulo, Nicola and {Del Favero}, Micky and Lexa, Matej and Cannata, Nicola and Valle, Giorgio},
	Journal = {Bioinformatics},
	Number = {5},
	Pages = {582--588},
	Title = {{RAP: a new computer program for de novo identification of repeated sequences in whole genomes.}},
	Volume = {21},
	Year = {2005}}

@article{Yang2011,
	Author = {Yang, Xiao and Aluru, Srinivas and Dorman, Karin S},
	Journal = {BMC Bioinformatics},
	Number = {Suppl 1},
	Pages = {S52},
	Title = {{Repeat-aware modeling and correction of short read errors}},
	Volume = {12},
	Year = {2011}}

@article{Rusu2008,
	Author = {Rusu, Florin and Dobra, Alin},
	Journal = {ACM Transactions on Database Systems},
	Month = aug,
	Number = {3},
	Pages = {1--46},
	Title = {{Sketches for size of join estimation}},
	Volume = {33},
	Year = {2008}}

@article{Do2008,
	Author = {Do, Huy Hoang and Choi, Kwok Pui and Preparata, Franco P and Sung, Wing Kin and Zhang, Louxin},
	Journal = {Journal of computational biology a journal of computational molecular cell biology},
	Number = {5},
	Pages = {469--487},
	Title = {{Spectrum-based de novo repeat detection in genomic sequences.}},
	Volume = {15},
	Year = {2008}}

@article{Conway2011,
	Author = {Conway, Thomas C and Bromage, Andrew J},
	Journal = {Bioinformatics},
	Month = {Feb},
	Number = {4},
	Pages = {479-86},
	Title = {Succinct data structures for assembling large genomes},
	Volume = {27},
	Year = {2011}}

@article{Stein2010,
	Author = {Stein, Lincoln D},
	Journal = {Genome Biol},
	Number = {5},
	Pages = {207},
	Title = {The case for cloud computing in genome informatics},
	Volume = {11},
	Year = {2010}}

@article{Sboner2011,
	Author = {Sboner, Andrea and Mu, Xinmeng Jasmine and Greenbaum, Dov and Auerbach, Raymond K and Gerstein, Mark B},
	Journal = {Genome Biol},
	Number = {8},
	Pages = {125},
	Title = {The real cost of sequencing: higher than you think!},
	Volume = {12},
	Year = {2011}}

@article{McElroy2012,
	Author = {McElroy, Kerensa E and Luciani, Fabio and Thomas, Torsten},
	Journal = {BMC Genomics},
	Pages = {74},
	Title = {GemSIM: general, error-model based simulator of next-generation sequencing data},
	Volume = {13},
	Year = {2012}}

@article{Zhang2014,
	Author = {Qingpeng Zhang and Jason Pell and Rosangela Canino-Koning and Adina Chuang Howe and C. Titus Brown},
	Journal = {PLoS ONE},
	Number = {9},
	Title = {These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure.},
	Volume = {7},
	Year = {2014}}

@article{lighter,
	Author = {Song, L. and Florea, L. and Langmead, B.},
	Journal = {Genome Biol.},
	Number = {11},
	Pages = {509},
	Title = {{{L}ighter: fast and memory-efficient sequencing error correction without counting}},
	Volume = {15},
	Year = {2014}}

@article{quake,
	Author = {Kelley, D. R. and Schatz, M. C. and Salzberg, S. L.},
	Journal = {Genome Biol.},
	Number = {11},
	Pages = {R116},
	Title = {{{Q}uake: quality-aware detection and correction of sequencing errors}},
	Volume = {11},
	Year = {2010}}

@article{bowtie2,
	Author = {Langmead, B. and Salzberg, S. L.},
	Journal = {Nat. Methods},
	Month = {Apr},
	Number = {4},
	Pages = {357--359},
	Title = {{{F}ast gapped-read alignment with {B}owtie 2}},
	Volume = {9},
	Year = {2012}}

@article{jellyfish,
	Author = {Marcais, G. and Kingsford, C.},
	Journal = {Bioinformatics},
	Month = {Mar},
	Number = {6},
	Pages = {764--770},
	Title = {{{A} fast, lock-free approach for efficient parallel counting of occurrences of k-mers}},
	Volume = {27},
	Year = {2011}}

@article{Melsted2014,
	Author = {Melsted, P. and Halldorsson, B. V.},
	Journal = {Bioinformatics},
	Month = {Dec},
	Number = {24},
	Pages = {3541--3547},
	Title = {{{K}mer{S}tream: streaming algorithms for k-mer abundance estimation}},
	Volume = {30},
	Year = {2014}}

@article{drisee,
	Author = {Keegan, K. P. and Trimble, W. L. and Wilkening, J. and Wilke, A. and Harrison, T. and D'Souza, M. and Meyer, F.},
	Journal = {PLoS Comput. Biol.},
	Number = {6},
	Pages = {e1002541},
	Title = {{{A} platform-independent method for detecting errors in metagenomic sequencing data: {D}{R}{I}{S}{E}{E}}},
	Volume = {8},
	Year = {2012}}

@article{Lowe2015,
	Author = {Lowe, E. K. and Swalla, B.J. and Brown, C.T.},
	Journal = {PeerJ Preprints},
	Title = {{{E}valuating a lightweight transcriptome assembly pipeline on two closely related ascidian species.}},
	Url = {http://dx.doi.org/10.7287/peerj.preprints.505v1},
	Volume = {2},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.7287/peerj.preprints.505v1}}

@article{nanopore,
	Author = {Howorka, S. and Cheley, S. and Bayley, H.},
	Journal = {Nat. Biotechnol.},
	Month = {Jul},
	Number = {7},
	Pages = {636--639},
	Title = {{{S}equence-specific detection of individual {D}{N}{A} strands using engineered nanopores}},
	Volume = {19},
	Year = {2001}}

@article{pacbio,
	Author = {Eid, J. and Fehr, A. and Gray, J. and Luong, K. and Lyle, J. and Otto, G. and Peluso, P. and Rank, D. and Baybayan, P. and Bettman, B. and Bibillo, A. and Bjornson, K. and Chaudhuri, B. and Christians, F. and Cicero, R. and Clark, S. and Dalal, R. and Dewinter, A. and Dixon, J. and Foquet, M. and Gaertner, A. and Hardenbol, P. and Heiner, C. and Hester, K. and Holden, D. and Kearns, G. and Kong, X. and Kuse, R. and Lacroix, Y. and Lin, S. and Lundquist, P. and Ma, C. and Marks, P. and Maxham, M. and Murphy, D. and Park, I. and Pham, T. and Phillips, M. and Roy, J. and Sebra, R. and Shen, G. and Sorenson, J. and Tomaney, A. and Travers, K. and Trulson, M. and Vieceli, J. and Wegener, J. and Wu, D. and Yang, A. and Zaccarin, D. and Zhao, P. and Zhong, F. and Korlach, J. and Turner, S.},
	Journal = {Science},
	Month = {Jan},
	Number = {5910},
	Pages = {133--138},
	Title = {{{R}eal-time {D}{N}{A} sequencing from single polymerase molecules}},
	Volume = {323},
	Year = {2009}}

@article{Feigenbaum2005,
	Acmid = {1132638},
	Address = {Essex, UK},
	Author = {Feigenbaum, Joan and Kannan, Sampath and McGregor, Andrew and Suri, Siddharth and Zhang, Jian},
	Doi = {10.1016/j.tcs.2005.09.013},
	Issn = {0304-3975},
	Issue_Date = {8 December 2005},
	Journal = {Theor. Comput. Sci.},
	Keywords = {articulation point, girth, graph, matching, spanner, streaming},
	Month = dec,
	Number = {2},
	Numpages = {10},
	Pages = {207--216},
	Publisher = {Elsevier Science Publishers Ltd.},
	Title = {On Graph Problems in a Semi-streaming Model},
	Url = {http://dx.doi.org/10.1016/j.tcs.2005.09.013},
	Volume = {348},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tcs.2005.09.013}}

@article{podar,
	Author = {Shakya, M. and Quince, C. and Campbell, J. H. and Yang, Z. K. and Schadt, C. W. and Podar, M.},
	Journal = {Environ. Microbiol.},
	Month = {Jun},
	Number = {6},
	Pages = {1882--1899},
	Title = {{{C}omparative metagenomic and r{R}{N}{A} microbial diversity characterization using archaeal and bacterial synthetic communities}},
	Volume = {15},
	Year = {2013}}

@article{chitsaz,
	Author = {Chitsaz, H. and Yee-Greenbaum, J. L. and Tesler, G. and Lombardo, M. J. and Dupont, C. L. and Badger, J. H. and Novotny, M. and Rusch, D. B. and Fraser, L. J. and Gormley, N. A. and Schulz-Trieglaff, O. and Smith, G. P. and Evers, D. J. and Pevzner, P. A. and Lasken, R. S.},
	Journal = {Nat. Biotechnol.},
	Month = {Oct},
	Number = {10},
	Pages = {915--921},
	Title = {{{E}fficient de novo assembly of single-cell bacterial genomes from short-read data sets}},
	Volume = {29},
	Year = {2011}}

@article{trinityrna,
	Author = {Grabherr, M. G. and Haas, B. J. and Yassour, M. and Levin, J. Z. and Thompson, D. A. and Amit, I. and Adiconis, X. and Fan, L. and Raychowdhury, R. and Zeng, Q. and Chen, Z. and Mauceli, E. and Hacohen, N. and Gnirke, A. and Rhind, N. and di Palma, F. and Birren, B. W. and Nusbaum, C. and Lindblad-Toh, K. and Friedman, N. and Regev, A.},
	Journal = {Nat. Biotechnol.},
	Month = {Jul},
	Number = {7},
	Pages = {644--652},
	Title = {{{F}ull-length transcriptome assembly from {R}{N}{A}-{S}eq data without a reference genome}},
	Volume = {29},
	Year = {2011}}

@article{hll,
	Author = {Flajolet, Philippe and Fusy, {\'E}ric and Gandouet, Olivier and Meunier, Fr{\'e}d{\'e}ric},
	Journal = {DMTCS Proceedings},
	Number = {1},
	Title = {HyperLogLog: the analysis of a near-optimal cardinality estimation algorithm},
	Year = {2008}}

@article{waterman,
	Author = {Lander, E. S. and Waterman, M. S.},
	Journal = {Genomics},
	Month = {Apr},
	Number = {3},
	Pages = {231--239},
	Title = {{{G}enomic mapping by fingerprinting random clones: a mathematical analysis}},
	Volume = {2},
	Year = {1988}}

@article{seecer,
	Author = {Le, H. S. and Schulz, M. H. and McCauley, B. M. and Hinman, V. F. and Bar-Joseph, Z.},
	Journal = {Nucleic Acids Res.},
	Month = {May},
	Number = {10},
	Pages = {e109},
	Title = {{{P}robabilistic error correction for {R}{N}{A} sequencing}},
	Volume = {41},
	Year = {2013}}

@article{freclu,
	Author = {Qu, W. and Hashimoto, S. and Morishita, S.},
	Journal = {Genome Res.},
	Month = {Jul},
	Number = {7},
	Pages = {1309--1315},
	Title = {{{E}fficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing}},
	Volume = {19},
	Year = {2009}}

@article{Roberts2011,
	Author = {Roberts, A. and Pachter, L.},
	Journal = {Genome Med},
	Number = {11},
	Pages = {74},
	Title = {{{R}{N}{A}-{S}eq and find: entering the {R}{N}{A} deep field}},
	Volume = {3},
	Year = {2011}}

@article{biases,
	Author = {Dohm, J. C. and Lottaz, C. and Borodina, T. and Himmelbauer, H.},
	Journal = {Nucleic Acids Res.},
	Month = {Sep},
	Number = {16},
	Pages = {e105},
	Title = {{{S}ubstantial biases in ultra-short read data sets from high-throughput {D}{N}{A} sequencing}},
	Volume = {36},
	Year = {2008}}


text:
SUMMARY = "Atmel wilc1000 firmware files for use with Linux kernel"
SECTION = "kernel"

LICENSE = "CLOSED"

SRCREV = "${AUTOREV}"
PV = "0.0+git${SRCPV}"

SRC_URI = "git://github.com/linux4sc/wireless-firmware.git;protocol=git \
          "
S = "${WORKDIR}/git"

inherit allarch

do_compile() {
	:
}

do_install() {
	install -d  ${D}/lib/firmware/atmel/
	cp -r * ${D}/lib/firmware/atmel/

	# remove unneeded file
	rm -f ${D}/lib/firmware/atmel/README.md
	chmod -x ${D}/lib/firmware/atmel/*
}

FILES_${PN} = " \
  /lib/firmware/atmel/wilc100*_*.bin \
"
# TODO: use ALTERNATIVE like in "linux-firmware" package

license: MIT

repository: rousis/meta-atmel

license_type: permissive

repo_name: rousis/meta-atmel

branch_name: refs/heads/master

extension: bb


text:
inherit esw_examples features_check

REQUIRED_MACHINE_FEATURES = "usb"

ESW_COMPONENT_SRC = "/XilinxProcessorIPLib/drivers/usb/examples/"

repository: Xilinx/meta-xilinx

repo_name: Xilinx/meta-xilinx

gha_license_id: MIT

gha_language: C


text:
@inproceedings{he-etal-2020-learning-tag,
    title = "Learning to Tag {OOV} Tokens by Integrating Contextual Representation and Background Knowledge",
    author = "He, Keqing  and
      Yan, Yuanmeng  and
      Xu, Weiran",
    booktitle = "Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics",
    month = jul,
    year = "2020",
    address = "Online",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2020.acl-main.58",
    doi = "10.18653/v1/2020.acl-main.58",
    pages = "619--624",
    abstract = "Neural-based context-aware models for slot tagging have achieved state-of-the-art performance. However, the presence of OOV(out-of-vocab) words significantly degrades the performance of neural-based models, especially in a few-shot scenario. In this paper, we propose a novel knowledge-enhanced slot tagging model to integrate contextual representation of input text and the large-scale lexical background knowledge. Besides, we use multi-level graph attention to explicitly model lexical relations. The experiments show that our proposed knowledge integration mechanism achieves consistent improvements across settings with different sizes of training data on two public benchmark datasets.",
}

extension: bib


text:
# Copyright (C) 2016 David Brown <davidb@davidb.org>
# Released under the MIT license (see COPYING.MIT for the terms)

SUMMARY = "qemu terminal utility"
LICENSE = "BSD"

inherit native

# TODO: Put this upstream instead of like this.
LIC_FILES_CHKSUM = "file://LICENSE;md5=8276d74bfe4bafd148ef0507ad386949"

SRCREV = "5493a6e7c264536f5ca63fe7511e5eed991e4f20"
SRC_URI = "git://github.com/linaro-swg/soc_term.git;protocol=https"
PV = "0.0+git${SRCPV}"

S = "${WORKDIR}/git"

do_configure () {
    :
}

do_compile () {
    oe_runmake -C ${S} || die "make failed"
}

do_install () {
    install -d ${D}/${prefix}/bin/
    install ${S}/soc_term ${D}/${prefix}/bin
}

repository: Zondax/meta-zondax-qemu

repo_name: Zondax/meta-zondax-qemu

branch_name: refs/heads/honister

gha_language: PHP


text:
require xorg-driver-video.inc

DESCRIPTION = "X.org X server -- Trident display driver"
DEPENDS += " xf86dgaproto"
PE = "1"
SRC_URI[archive.md5sum] = "e89799579d0cf3858362bd751469e0bf"
SRC_URI[archive.sha256sum] = "a4f66c9f46f6e93c2c1f10e782a211ddc338b0ff9f0a2ccd2d660db031d3ddb5"


text:
SUMMARY = "openpower-occ-control: install phosphor-logging yaml"
PR = "r1"
PV = "1.0+git${SRCPV}"
LICENSE = "Apache-2.0"
LIC_FILES_CHKSUM = "file://${COREBASE}/meta/files/common-licenses/Apache-2.0;md5=89aea4e17d99a7cacdbeed46a0096b10"

inherit phosphor-logging-yaml-provider
require openpower-occ-control.inc

S = "${WORKDIR}/git"

repository: openbmc/openbmc

repo_name: openbmc/openbmc

gha_license_id: NOASSERTION

gha_language: Python


text:
@article{RN538,
 author = {Davis, J. S. and Yeo, T. W. and Thomas, J. H. and McMillan, M. and Darcy, C. J. and McNeil, Y. R. and Cheng, A. C. and Celermajer, D. S. and Stephens, D. P. and Anstey, N. M.},
 doi = {10.1186/cc8055},
 issn = {1466-609X (Electronic)
1364-8535 (Linking)},
 journal = {Crit Care},
 number = {5},
 pages = {R155},
 title = {Sepsis-associated microvascular dysfunction measured by peripheral arterial tonometry: an observational study},
 type = {Journal Article},
 volume = {13},
 year = {2009}
}


text:
inherit qmake2

require qt-5.0.0.inc

DEPENDS += "qt5-x11-free"

SRC_URI = "git://gitorious.org/qt/qtbase.git;protocol=git"

PR = "r2"

FILES_${PN} += "/usr/local/qt5/examples/qtbase/widgets/wiggly/wiggly"
FILES_${PN}-dbg += "/usr/local/qt5/examples/qtbase/widgets/wiggly/.debug"
FILES_${PN}-dev += "/usr/local/qt5/examples/qtbase/widgets/wiggly"

do_configure () {
    :
}

do_compile () {
    pushd examples/widgets/wiggly
    qmake2
    oe_runmake
    popd
}

do_install() {
    pushd examples/widgets/wiggly
    oe_runmake install INSTALL_ROOT="${D}"
    popd
}


text:
@article{
    UnROOT-2022,
    doi = {10.21105/joss.04452},
    url = {https://doi.org/10.21105/joss.04452},
    year = {2022},
    publisher = {The Open Journal},
    volume = {7},
    number = {76},
    pages = {4452},
    author = {Tamás Gál and Jerry (Jiahong) Ling and Nick Amin},
    title = {UnROOT: an I/O library for the CERN ROOT file format written in Julia},
    journal = {Journal of Open Source Software}
}

gha_language: Julia


text:
DESCRIPTION = "DMI (Desktop Management Interface) table related utilities"
SECTION = "console/utils"
HOMEPAGE = "http://www.nongnu.org/dmidecode/"
LICENSE = "GPLv2"
PR = "r1"

SRC_URI = "http://savannah.nongnu.org/download/dmidecode/${P}.tar.bz2"

COMPATIBLE_HOST = "(i.86|x86_64).*-linux"

do_install() {
	oe_runmake DESTDIR="${D}" install
}

SRC_URI[md5sum] = "3c9c4d55a40b78600f3b43bfa64616f9"
SRC_URI[sha256sum] = "4d74a3e93353320317a424816f9a045df06d9ed4b5b80881e16fdfcc74c9e2c0"

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD


text:
@article{Gardner2020a,
 author = {Gardner, Paul and Liu, Xuanang and Worden, Keith},
 doi = {https://doi.org/10.1016/j.ymssp.2019.106550},
 journal = {Mechanical Systems and Signal Processing},
 pages = {106550},
 title = {On the application of domain adaptation in structural health monitoring},
 url = {http://www.sciencedirect.com/science/article/pii/S088832701930771X},
 volume = {138},
 year = {2020}
}

repository: pagard/academic-kickstart

repo_name: pagard/academic-kickstart


text:
@misc{hemedinger-2016,
  abstract = {We've just celebrated Earth Day, but I'm here to talk about Jupyter -- and the SAS open source project that opens the door for more learning. With this new project on the github.com/sassoftware page, SAS contributes new support for running SAS from within Jupyter Notebooks -- a popular browser-based environment used by professors and data scientists. My colleague Amy Peters announced this during a SAS Tech Talk show at SAS Global Forum 2016. If you want to learn more about Jupyter and see the SAS support in action, then you can watch the video here.},
  annote = {A bit dated, but a nice guide to running SAS in a Jupyter notebook.}
  author = {Hemedinger, Chris},
  mendeley-tags = {SAS programming},
  title = {How to run SAS programs in Jupyter Notebook, The SAS Dummy blog, 2016-04-24},
  source = {19/06/hemedinger-2016},
  url = {https://blogs.sas.com/content/sasdummy/2016/04/24/how-to-run-sas-programs-in-jupyter-notebook/},
  urldate = {2019-06-04}
}

repository: pmean/build-website

repo_name: pmean/build-website


text:
@article{verstegen:2012,
    author = "Judith Anne Verstegen and Derek Karssenberg and Floor van
        der Hilst and André Faaij",
    doi = "10.1016/j.compenvurbsys.2011.08.003",
    issn = "0198-9715",
    journal = "Computers, Environment and Urban Systems",
    keywords = "Spatial Decision Support Systems, Uncertainty, Spatial
        modeling, Visualization, Land use change, Bioenergy",
    number = "1",
    pages = "30–42",
    title = "Spatio-temporal uncertainty in Spatial Decision Support
        Systems: A case study of changing land availability for bioenergy
        crops in Mozambique",
    url = "http://www.sciencedirect.com/science/article/pii/S0198971511000883",
    volume = "36",
    year = "2012"
}

@article{hilst:2012,
    author = {Hilst, Floor and Verstegen, Judith A and Karssenberg, Derek
        and Faaij, André P C},
    title = {{Spatiotemporal land use modelling to assess land availability
        for energy crops – illustrated for Mozambique}},
    issn = {1757-1707},
    doi = {10.1111/j.1757-1707.2011.01147.x},
    pages = {859--874},
    number = {6},
    volume = {4},
    journal = {GCB Bioenergy},
    year = {2012}
}

@article{verstegen:2014,
    author = {Verstegen, J.A. and Karssenberg, D. and van der Hilst,
        F. and Faaij, A.P.C.},
    doi = {10.1016/j.envsoft.2013.11.009},
    journal = {Environmental Modelling and Software},
    pages = {121–136},
    title = {Identifying a land use change cellular automaton by Bayesian
        data assimilation},
    volume = {53},
    year = {2014}
}

repository: OliverSchmitz/lue

repo_name: OliverSchmitz/lue


text:
# Copyright (c) 2012-2013 LG Electronics, Inc.

SUMMARY = "Enyo 1.0 Browser application"
SECTION = "webos/apps"
LICENSE = "Apache-2.0"
LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/Apache-2.0;md5=89aea4e17d99a7cacdbeed46a0096b10"

# isis-project components don't have submissions
PE = "1"
PV = "0.21+wop+gitr${SRCPV}"
SRCREV = "57f91972e6d1abc8c32e476920e1683d026b4d3e"

inherit webos_public_repo
inherit webos_arch_indep

WEBOS_REPO_NAME = "isis-browser"
SRC_URI = "${ISIS_PROJECT_GIT_REPO_COMPLETE}"

inherit webos-ports-repo
S = "${WORKDIR}/git"

do_install() {
    # WEBOS_INSTALL_WEBOS_COREAPPSDIR
    install -d ${D}${webos_applicationsdir}/${PN}
    #INSTALL DB/KINDS
    install -d ${D}${webos_sysconfdir}/db/kinds
    #INSTALL DB/PERSMISSIONS
    install -d ${D}${webos_sysconfdir}/db/permissions

    cp -vrf ${S}/* ${D}${webos_applicationsdir}/${PN}

    if [ -d db/kinds ]; then
        install -v -m 644 db/kinds/* ${D}${webos_sysconfdir}/db/kinds
    fi
    rm -vrf ${D}${webos_applicationsdir}/${PN}/db/kinds

    if [ -d db/permissions ]; then
        install -v -m 644 db/permissions/* ${D}${webos_sysconfdir}/db/permissions
    fi
    rm -vrf ${D}${webos_applicationsdir}/${PN}/db/permissions
}

FILES_${PN} += "${webos_applicationsdir}"

repository: nizovn/meta-webos-ports

repo_name: nizovn/meta-webos-ports


text:
SUMMARY = "Tensorflow models with example scripts, credit to NVIDIA and JK Jung"
LICENSE = "Proprietary"
LIC_FILES_CHKSUM = "file://LICENSE.md;md5=720c330bf4f4d0300ad6642ec1a89893"

SRCREV = "${AUTOREV}"
SRC_URI = "gitsm://github.com/jkjung-avt/tf_trt_models.git \
           file://0001-Hard-code-the-gstreamer-pipeline-to-use-nvarguscamer.patch \
           file://0002-Update-camera_tf_trt-script-to-allow-headless-stream.patch \
           file://0003-Turn-off-help-menu-when-in-stealth-mode.patch \
          "

S = "${WORKDIR}/git"

do_configure[noexec] = "1"
do_compile[noexec] = "1"

RDEPENDS_${PN} += " bash python "

do_install() {
	install -d ${D}/usr/local/tensorflow-tools/tf_trt_models

	cp -r ${S}/data ${D}/usr/local/tensorflow-tools/tf_trt_models
	cp -r ${S}/examples ${D}/usr/local/tensorflow-tools/tf_trt_models
	cp -r ${S}/scripts ${D}/usr/local/tensorflow-tools/tf_trt_models
	cp -r ${S}/tf_trt_models ${D}/usr/local/tensorflow-tools/tf_trt_models
	cp -r ${S}/third_party ${D}/usr/local/tensorflow-tools/tf_trt_models
	cp -r ${S}/utils ${D}/usr/local/tensorflow-tools/tf_trt_models
	cp -r ${S}/camera_tf_trt.py ${D}/usr/local/tensorflow-tools/tf_trt_models
	cp -r ${S}/install.sh ${D}/usr/local/tensorflow-tools/tf_trt_models
	cp -r ${S}/setup.py ${D}/usr/local/tensorflow-tools/tf_trt_models

	rm ${D}/usr/local/tensorflow-tools/tf_trt_models/third_party/models/research/domain_adaptation/domain_separation/_grl_ops.so
	rm ${D}/usr/local/tensorflow-tools/tf_trt_models/third_party/models/research/syntaxnet/tensorflow/tensorflow/compiler/aot/codegen_test_o.golden
}

FILES_${PN} += "/usr/local/tensorflow-tools/tf_trt_models/* "

INHIBIT_PACKAGE_STRIP = "1"
INHIBIT_PACKAGE_DEBUG_SPLIT = "1"

repository: gumstix/meta-gumstix-extras

repo_name: gumstix/meta-gumstix-extras

branch_name: refs/heads/warrior


text:
# Distributed under the OSI-approved BSD 3-Clause License.  See accompanying
# file Copyright.txt or https://cmake.org/licensing for details.

# This module is shared by multiple languages; use include blocker.

if(__GHSMULTI)
  return()
endif()
set(__GHSMULTI 1)

set(GHSMULTI 1)

set(CMAKE_FIND_LIBRARY_PREFIXES "")
set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")

include(Platform/WindowsPaths)

branch_name: refs/heads/main

extension: cmake


text:
include chromium-browser-gn.inc

PR = "dev0"

do_configure_prepend () {
        # Ninja complains if this is not correctly set.
        echo 'LASTCHANGE='ac0ab56fdfe6edad161caa4c657a068390cbba83' > build/util/LASTCHANGE
        echo 'LASTCHANGE='ac0ab56fdfe6edad161caa4c657a068390cbba83-refs/heads/master@{#481962}' > build/util/LASTCHANGE.blink
}

SRC_URI = "\
        https://tmp.igalia.com/chromium-tarballs/chromium-wayland-ac0ab56.tar.xz \
        file://google-chrome \
        ${@bb.utils.contains('PACKAGECONFIG', 'disable-api-keys-info-bar', 'file://api-keys.patch;patchdir=${WORKDIR}', '', d)} \
        file://google-chrome.desktop \
        file://0004-Create-empty-i18n_process_css_test.html-file-to-avoi.patch \
        file://chromium-wayland/0001-Fix-wayland-window-show-hide.patch \
        ${@bb.utils.contains('PACKAGECONFIG', 'ignore-lost-context', 'file://0001-Remove-accelerated-Canvas-support-from-blacklist.patch', '', d)} \
"

S = "${WORKDIR}/src"

LIC_FILES_CHKSUM = "file://LICENSE;md5=0fca02217a5d49a14dfe2d11837bb34d"
SRC_URI[md5sum] = "5edcffee9339fa4e885aadffb14b5a00"
SRC_URI[sha256sum] = "2aacd00b95429a68cb3ce9d5077527c27bb7292cd59eab86ae0210b1876aada5"

INSANE_SKIP_${PN}_arm = "already-stripped"

repository: KurtSchluss/meta-browser

repo_name: KurtSchluss/meta-browser


text:
DESCRIPTION = "Customized settings to use the right fonts in XFCE."
SECTION = "x11"
LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://${COREBASE}/LICENSE;md5=3f40d7994397109285ec7b81fdeb3b58 \
                    file://${COREBASE}/meta/COPYING.MIT;md5=3da9cfbcb788c80a0384361b4de20420"
RDEPENDS_${PN} = "fontconfig"
PR = "r1"
S = "${WORKDIR}"

SRC_URI = "file://48-nilrt-override.conf"

FILES_${PN} = "${sysconfdir}/fonts"

do_install () {
	install -d ${D}/${sysconfdir}/fonts/conf.d
	install -d ${D}/${sysconfdir}/fonts/conf.avail
	install -m 0644 48-nilrt-override.conf ${D}/${sysconfdir}/fonts/conf.avail/48-nilrt-override.conf
	ln -sf ${sysconfdir}/fonts/conf.avail/48-nilrt-override.conf ${D}/${sysconfdir}/fonts/conf.d/48-nilrt-override.conf
}

repository: bmouring/meta-nilrt

repo_name: bmouring/meta-nilrt


text:
DESCRIPTION = "RetroArch full image"
LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/MIT;md5=0835ade698e0bcf8506ecda2f7b4f302"

inherit retro-core-image

IMAGE_INSTALL_append = " \
  packagegroup-standalone-emulators \
  retroarch-assets-xmb-monochrome \
  retroarch-assets-xmb-pixel \
  retroarch-assets-xmb-systematic \
  retroarch-autoconfig \
  retroarch-database-cheats \
  retroarch-database-cursors \
  retroarch-database-titles \
  retroarch-libretro-info \
  retroarch-overlays \
  retroarch-shaders \
"

repository: hansenlabs/meta-retro

repo_name: hansenlabs/meta-retro


text:
SUMMARY = "Wireless Display Software For Linux OS (WDS)"
HOMEPAGE = "https://01.org/wds"
BUGTRACKER = "https://github.com/01org/wds/issues"
LICENSE = "LGPLv2.1"
LIC_FILES_CHKSUM = "file://COPYING;md5=cb8aedd3bced19bd8026d96a8b6876d7"

DEPENDS = "gstreamer1.0"

inherit cmake lib_package

SRCREV = "a488b169d724d6b4cfcd7037dbab1f1c2bf04f3b"
SRC_URI = "git://github.com/01org/wds.git"

S = "${WORKDIR}/git"

EXTRA_OECMAKE += "-DCMAKE_SKIP_RPATH=ON"

do_install_append() {
    install -Dm 0755 ${B}/desktop_source/desktop-source-test ${D}${bindir}/wds-examples/desktop-source-test
    install -Dm 0755 ${B}/libwds/rtsp/tests/test-wds ${D}${bindir}/wds-examples/test-wds
    install -Dm 0755 ${B}/mirac_network/gst-test ${D}${bindir}/wds-examples/gst-test
    install -Dm 0755 ${B}/mirac_network/network-test ${D}${bindir}/wds-examples/network-test
    install -Dm 0755 ${B}/p2p/register-peer-service ${D}${bindir}/wds-examples/register-peer-service
    install -Dm 0755 ${B}/p2p/test-ie ${D}${bindir}/wds-examples/test-ie
    install -Dm 0755 ${B}/sink/sink-test ${D}${bindir}/wds-examples/sink-test
}

PACKAGES =+ "${PN}-examples"
FILES_${PN}-examples += "${bindir}/wds-examples/*"

RDEPENDS_${PN} += " \
    connman-client \
    wpa-supplicant \
    gstreamer1.0-libav \
    gstreamer1.0-plugins-bad \
    gstreamer1.0-plugins-base \
    gstreamer1.0-plugins-good \
"


text:
@proceedings{ws-2019-celtic,
    title = "Proceedings of the Celtic Language Technology Workshop",
    editor = "Lynn, Teresa  and
      Prys, Delyth  and
      Batchelor, Colin  and
      Tyers, Francis",
    month = aug,
    year = "2019",
    address = "Dublin, Ireland",
    publisher = "European Association for Machine Translation",
    url = "https://www.aclweb.org/anthology/W19-6900",
}
@inproceedings{spasic-etal-2019-unsupervised,
    title = "Unsupervised multi-word term recognition in Welsh",
    author = "Spasi{\'c}, Irena  and
      Owen, David  and
      Knight, Dawn  and
      Artemiou, Andreas",
    booktitle = "Proceedings of the Celtic Language Technology Workshop",
    month = aug,
    year = "2019",
    address = "Dublin, Ireland",
    publisher = "European Association for Machine Translation",
    url = "https://www.aclweb.org/anthology/W19-6901",
    pages = "1--6",
}
@inproceedings{batchelor-2019-universal,
    title = "Universal dependencies for {S}cottish Gaelic: syntax",
    author = "Batchelor, Colin",
    booktitle = "Proceedings of the Celtic Language Technology Workshop",
    month = aug,
    year = "2019",
    address = "Dublin, Ireland",
    publisher = "European Association for Machine Translation",
    url = "https://www.aclweb.org/anthology/W19-6902",
    pages = "7--15",
}
@inproceedings{bell-2019-speech,
    title = "Speech technology and Argentinean Welsh",
    author = "Bell, Elise",
    booktitle = "Proceedings of the Celtic Language Technology Workshop",
    month = aug,
    year = "2019",
    address = "Dublin, Ireland",
    publisher = "European Association for Machine Translation",
    url = "https://www.aclweb.org/anthology/W19-6903",
    pages = "16--20",
}
@inproceedings{heinecke-tyers-2019-development,
    title = "Development of a Universal Dependencies treebank for Welsh",
    author = "Heinecke, Johannes  and
      Tyers, Francis M.",
    booktitle = "Proceedings of the Celtic Language Technology Workshop",
    month = aug,
    year = "2019",
    address = "Dublin, Ireland",
    publisher = "European Association for Machine Translation",
    url = "https://www.aclweb.org/anthology/W19-6904",
    pages = "21--31",
}
@inproceedings{lynn-scannell-2019-code,
    title = "Code-switching in Irish tweets: A preliminary analysis",
    author = "Lynn, Teresa  and
      Scannell, Kevin",
    booktitle = "Proceedings of the Celtic Language Technology Workshop",
    month = aug,
    year = "2019",
    address = "Dublin, Ireland",
    publisher = "European Association for Machine Translation",
    url = "https://www.aclweb.org/anthology/W19-6905",
    pages = "32--40",
}
@inproceedings{prys-jones-2019-embedding,
    title = "Embedding {E}nglish to Welsh {MT} in a Private Company",
    author = "Prys, Myfyr  and
      Jones, Dewi Bryn",
    booktitle = "Proceedings of the Celtic Language Technology Workshop",
    month = aug,
    year = "2019",
    address = "Dublin, Ireland",
    publisher = "European Association for Machine Translation",
    url = "https://www.aclweb.org/anthology/W19-6906",
    pages = "41--47",
}
@inproceedings{mccrae-doyle-2019-adapting,
    title = "Adapting Term Recognition to an Under-Resourced Language: the Case of Irish",
    author = "McCrae, John P.  and
      Doyle, Adrian",
    booktitle = "Proceedings of the Celtic Language Technology Workshop",
    month = aug,
    year = "2019",
    address = "Dublin, Ireland",
    publisher = "European Association for Machine Translation",
    url = "https://www.aclweb.org/anthology/W19-6907",
    pages = "48--57",
}
@inproceedings{dowling-etal-2019-leveraging,
    title = "Leveraging backtranslation to improve machine translation for Gaelic languages",
    author = "Dowling, Meghan  and
      Lynn, Teresa  and
      Way, Andy",
    booktitle = "Proceedings of the Celtic Language Technology Workshop",
    month = aug,
    year = "2019",
    address = "Dublin, Ireland",
    publisher = "European Association for Machine Translation",
    url = "https://www.aclweb.org/anthology/W19-6908",
    pages = "58--62",
}
@inproceedings{raghallaigh-etal-2019-improving,
    title = "Improving full-text search results on d{\'u}chas.ie using language technology",
    author = "Raghallaigh, Brian {\'O}  and
      Scannell, Kevin  and
      Dowling, Meghan",
    booktitle = "Proceedings of the Celtic Language Technology Workshop",
    month = aug,
    year = "2019",
    address = "Dublin, Ireland",
    publisher = "European Association for Machine Translation",
    url = "https://www.aclweb.org/anthology/W19-6909",
    pages = "63--69",
}
@inproceedings{doyle-etal-2019-character,
    title = {A Character-Level {LSTM} Network Model for Tokenizing the Old Irish text of the W{\"u}rzburg Glosses on the Pauline Epistles},
    author = "Doyle, Adrian  and
      McCrae, John P.  and
      Downey, Clodagh",
    booktitle = "Proceedings of the Celtic Language Technology Workshop",
    month = aug,
    year = "2019",
    address = "Dublin, Ireland",
    publisher = "European Association for Machine Translation",
    url = "https://www.aclweb.org/anthology/W19-6910",
    pages = "70--79",
}
@inproceedings{ward-etal-2019-green,
    title = "A Green Approach for an Irish App (Refactor, reuse and keeping it real)",
    author = "Ward, Monica  and
      Mozgovoy, Maxim  and
      Purgina, Marina",
    booktitle = "Proceedings of the Celtic Language Technology Workshop",
    month = aug,
    year = "2019",
    address = "Dublin, Ireland",
    publisher = "European Association for Machine Translation",
    url = "https://www.aclweb.org/anthology/W19-6911",
    pages = "80--88",
}

repository: emorynlp/nlprankings

repo_name: emorynlp/nlprankings

gha_language: TeX


text:
require recipes-graphics/xorg-driver/xorg-driver-video.inc

LIC_FILES_CHKSUM = "file://COPYING;md5=aabff1606551f9461ccf567739af63dc"

SUMMARY = "X.Org X server -- ATI Radeon video driver"

DESCRIPTION = "Open-source X.org graphics driver for ATI Radeon graphics"

DEPENDS += "virtual/libx11 libxvmc drm xf86driproto glproto \
            virtual/libgl xineramaproto libpciaccess"

COMPATIBLE_HOST = '(i.86|x86_64).*-linux'

SRC_URI = "git://anongit.freedesktop.org/xorg/driver/xf86-video-ati"
SRCREV = "38797a33117222dadbc89e5f21ed8cd5deef9bea"
S = "${WORKDIR}/git"

EXTRA_OECONF_qt5022-open += "--enable-glamor"
EXTRA_OECONF += "--disable-glamor"

RDEPENDS_${PN} += "xserver-xorg-module-exa xserver-xorg-extension-glx"
#Glamor running dependency
RDEPENDS_${PN}_append_qt5022-open = " libegl"
RRECOMMENDS_${PN} += "linux-firmware-radeon"

repository: qtec/meta-qtec-core

repo_name: qtec/meta-qtec-core


text:
@book{wigham-stemle:2019:cmc17volume,
 abstract = {Communication between humans via networked devices has become an everyday part of people's lives across generations, cultures, geographical areas, and social classes. Shaped by the specific social and technical context in which it is produced, synchronous and asynchronous computer-mediated communication (CMC) has become increasingly participatory, interactive, and multimodal. User interactions and user-generated social media content offer a wide range of research opportunities for a growing multidisciplinary research community. This edited volume combines methodological papers that focus on building and annotating CMC corpora and papers that offer a sociolinguistic analysis of different CMC corpora. The diversity of languages represented in the corpora include Arabic, French, German, Italian, English and Slovenian. In fact, the increasingly multilingual nature of CMC data is a recurring theme throughout the volume, as are the references to the importance of and compliance with standards for CMC corpora development in order to facilitate (the?) re-examination of corpora for reproducibility, and for other areas and objectives of investigation. All but one paper are extended papers from the 2017 edition of the CMC and Social Media Corpora Conference held in Bolzano, Italy where the community met to discuss themes that related to the interaction between language, CMC, and society.},
 date = {2019-06-13},
 editor = {Wigham, Ciara R. and Stemle, Egon W.},
 isbn = {978-2-84516-860-2},
 langid = {english},
 location = {Clermont-Ferrand, FR},
 pagetotal = {155},
 publisher = {Presses Universitaires Blaise Pascal},
 series = {Cahiers du laboratoire de recherche sur le langage},
 title = {Building Computer-Mediated Communication Corpora for sociolinguistic Analysis},
 url = {http://pubp.giantchair.com/livre/?GCOI=28451100141150&language=en},
 urltype = {publisher}
}


text:
@inproceedings{Clark2020ELECTRA:,
title={ELECTRA: Pre-training Text Encoders as Discriminators Rather Than Generators},
author={Kevin Clark and Minh-Thang Luong and Quoc V. Le and Christopher D. Manning},
booktitle={International Conference on Learning Representations},
year={2020},
url={https://openreview.net/forum?id=r1xMH1BtvB}
}

url: https://raw.githubusercontent.com/Hugh-Shi/DL-NLP-Readings/924e4d189e5660c5b5d4854278f3df755ae2231d/Bibtex/ELECTRA - Pre-training Text Encoders as Discriminators Rather Than Generators.bib

repository: Hugh-Shi/DL-NLP-Readings

repo_name: Hugh-Shi/DL-NLP-Readings


text:
DESCRIPTION = "PETALINUX image definition for Xilinx boards"
LICENSE = "MIT"

require recipes-core/images/petalinux-image-common.inc

inherit extrausers
IMAGE_LINGUAS = " "

IMAGE_INSTALL = "\
		kernel-modules \
		sudo \
		dbus-glib \
		dbus-glib-dev \
		modutils-initscripts \
		mtd-utils \
		bash \
		tar \
		canutils \
		curl \
		libcurl \
		dropbear \
		dropbear-openssh-sftp-server \
		lrzsz \
		rsync \
		wget \
		alsa-utils \
		alsa-utils-aconnect \
		alsa-utils-alsaloop \
		alsa-utils-aseqdump \
		alsa-utils-aplay \
		alsa-utils-iecset \
		alsa-utils-alsaucm \
		alsa-utils-alsamixer \
		alsa-utils-amixer \
		alsa-utils-speakertest \
		alsa-utils-alsactl \
		alsa-utils-midi \
		bash-completion \
		git \
		git-bash-completion \
		gitweb \
		git-perltools \
		grep \
		lsb \
		pciutils \
		pkgconfig \
		unzip \
		vim \
		vim-syntax \
		vim-help \
		vim-common \
		vim-vimrc \
		vim-tools \
		zip \
		autoconf \
		automake \
		binutils \
		intltool \
		make \
		run-postinsts \
		ffmpeg \
		gdbm \
		gdbm-dev \
		gettext \
		libgettextlib \
		glib-networking \
		glib-networking-dev \
		gtk+ \
		gtk+-dev \
		gtk+3 \
		gtk+3-dev \
		libxml2 \
		alsa-lib \
		alsa-server \
		libasound \
		alsa-conf-base \
		alsa-conf \
		libsndfile1 \
		libsndfile1-bin \
		pulseaudio \
		pulseaudio-misc \
		libpulse-mainloop-glib \
		libpulsecommon \
		pulseaudio-module-console-kit \
		pulseaudio-bash-completion \
		libpulse-simple \
		libpulsecore \
		libpulse \
		pulseaudio-server \
		taglib \
		ncurses \
		alsa-state \
		alsa-states \
		udev-extraconf \
		libstdc++ \
		libstdc++-dev \
		gcc-sanitizers \
		gdb \
		gdb-dev \
		glib-2.0 \
		glib-2.0-utils \
		glib-2.0-dev \
		glibc \
		glibc-dev \
		ldd \
		gnutls \
		packagegroup-core-boot \
		packagegroup-core-buildessential \
		packagegroup-core-buildessential-dev \
		packagegroup-core-buildessential-dbg \
		packagegroup-core-ssh-dropbear \
		packagegroup-petalinux \
		packagegroup-petalinux-dev \
		packagegroup-petalinux-self-hosted \
		packagegroup-petalinux-self-hosted-dev \
		packagegroup-self-hosted \
		packagegroup-self-hosted-dev \
		rpm \
		rpm-build \
		python-rpm \
		rpm-libs \
		rpm-common \
		tcf-agent \
		v4l-utils \
		libv4l \
		media-ctl \
		yavta \
		alsa-plugins \
		alsa-plugins-pulseaudio-conf \
		gstreamer \
		gstreamer1.0 \
		bridge-utils \
		patch \
		gpioutil \
		pwmdemo \
		libgpio \
		libpwm \
		libuio \
		aravis \
		bbexample \
		"
EXTRA_USERS_PARAMS = "usermod -P root root;"

repository: lsplf/RealTimeVideo

repo_name: lsplf/RealTimeVideo


text:
SUMMARY = "OpenRC init scripts for udev"
HOMEPAGE = "https://gitweb.gentoo.org/proj/udev-gentoo-scripts.git/"
LICENSE = "GPL-2.0-only"
LIC_FILES_CHKSUM = "file://init.d/udev;md5=14c7d7d983a7bc708cc23e88e7cdd856;beginline=2;endline=3"

SRC_URI = "https://gitweb.gentoo.org/proj/udev-gentoo-scripts.git/snapshot/udev-gentoo-scripts-${PV}.tar.gz"
SRC_URI[sha256sum] = "51eef30ef99f7f184aa403d190c105c5565e48c1c2d35b1b9f9f052c099fe366"

S = "${WORKDIR}/udev-gentoo-scripts-${PV}"

do_configure[noexec] = "1"

do_install() {
    oe_runmake DESTDIR=${D} install
}

RDEPENDS:${PN} = "openrc"

repository: jsbronder/meta-openrc

repo_name: jsbronder/meta-openrc

gha_language: Shell


text:
SUMMARY = "Altera GSRD customization"
DESCRIPTION = "Altera GSRD lighttpd configuration customization to enable cgi and set 404 page"
AUTHOR = "Tien Hock Loh <thloh@altera.com>"
SECTION = "gsrd"
LICENSE = "BSD-3-Clause"
LIC_FILES_CHKSUM="file://${COMMON_LICENSE_DIR}/BSD-3-Clause;md5=550794465ba0ec5312d6919e203a55f9"

inherit allarch
ALLOW_EMPTY_${PN} = "1"

# Post process the lighttpd.conf file to enable cgi module, sets home page and update 404 page
pkg_postinst_${PN}() {
#!/bin/sh
sed -ir 's:#\(.*mod_cgi\"\,\):\1:' $D/etc/lighttpd.conf
sed -ir 's:\(index-file.names *\=\).*\(,\):\1 ("\/cgi-bin\/index.sh"\2:' $D/etc/lighttpd.conf
echo 'server.error-handler-404   = "/not_found.html"' >> $D/etc/lighttpd.conf
echo 'cgi.assign = ( ".sh"  => "/bin/sh" )' >> $D/etc/lighttpd.conf
}

RDEPENDS_{PN} = "lighttpd-module-cgi"

repository: arrow-socfpga/meta-arrow-sockit

repo_name: arrow-socfpga/meta-arrow-sockit


text:
@Article{Cecil2005322,
  author = {D.J. Cecil and S.J. Goodman and D.J. Boccippio and E.J. Zipser and S.W. Nesbitt},
  title = {Lightning observations from TRMM},
  journal = {Bulletin of the American Meteorological Society},
  year = {2005},
  volume = {86},
  number = {3},
  note = {cited By 0},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-17644389220&partnerID=40&md5=486f07ecaa045f0d2765525d9e5922d8},
  document_type = {Article},
  source = {Scopus},
  pages = {322-323},
  date = {2005-01-01},
}

repository: swnesbitt/academic-kickstart

repo_name: swnesbitt/academic-kickstart


text:
@InProceedings{goes14,
  title = {{Robust Stochastic Principal Component Analysis}},
  author = {Goes, John and Zhang, Teng and Arora, Raman and Lerman, Gilad},
  pages = {266-274},
  abstract = {We consider the problem of finding lower dimensional subspaces in the presence of outliers and noise in the online setting. In particular, we extend previous batch formulations of robust PCA to the stochastic setting with minimal storage requirements and runtime complexity. We introduce three novel stochastic approximation algorithms for robust PCA that are extensions of standard algorithms for PCA - the stochastic power method, incremental PCA and online PCA using matrix-exponentiated-gradient (MEG) updates. For robust online PCA we also give a sub-linear convergence guarantee. Our numerical results demonstrate the superiority of the the robust online method over the other robust stochastic methods and the advantage of robust methods over their non-robust counterparts in the presence of outliers in artificial and real scenarios.},
}

repository: mreid/papersite

repo_name: mreid/papersite


text:
@misc{ wiki:Mereotopology,
    author = "{Wikipedia contributors}",
    title = "Mereotopology --- {Wikipedia}{,} The Free Encyclopedia",
    year = "2018",
    url = "{https://en.wikipedia.org/w/index.php?title=Mereotopology&oldid=863532843}",
    note = "[Online; accessed 3-January-2020]"
  }

repository: palisades-lakes/xfp

repo_name: palisades-lakes/xfp


text:
SUMMARY = "INITRD able to resize the mmc paritions"
LICENSE = "MIT"

IMAGE_FSTYPES = "${INITRAMFS_FSTYPES}"
inherit core-image

IMAGE_ROOTFS_EXTRA_SPACE = "0"

# Reset IMAGE_LINGUAS to empty
IMAGE_LINGUAS = ""

# Disable partition image for InitRD image to avoid circular dependancy
# If we keep enable this feature, when building the InitRD image a dependancy
# will be added for the completion of bootfs image while we're just expecting
# to add the InitRD inside bootfs...
ENABLE_PARTITIONS_IMAGE = "0"

# Disable flashlayout generation for this particular image as this is supposed
# to be done only for complete image (bootloader binaries, bootfs, rootfs...))
ENABLE_FLASHLAYOUT_CONFIG = "0"

# Disable image license summary generation for this particular image as this is
# supposed to be done only for complete image
ENABLE_IMAGE_LICENSE_SUMMARY = "0"

# Disable generation of multi volume ubifs  for this particular image as this is
# supposed to be done only for complete image
ENABLE_MULTIVOLUME_UBI = "0"

PACKAGE_INSTALL = " \
    busybox \
    e2fsprogs \
    e2fsprogs-e2fsck \
    e2fsprogs-resize2fs \
    e2fsprogs-tune2fs \
    e2fsprogs-mke2fs \
    initramfs-module-rootfs \
    initramfs-module-udev \
    initrd-boot \
    "

NO_RECOMMENDATIONS = "1"

repository: STMicroelectronics/meta-st-openstlinux

repo_name: STMicroelectronics/meta-st-openstlinux

branch_name: refs/heads/kirkstone


text:
# depending only on LOCAL_BASE allows CMAKE_MODULE_PATH use
# of this FindGLM.cmake without any special environment, other
# than LOCAL_BASE

set(GLM_PREFIX "$ENV{LOCAL_BASE}/opticks/externals/glm")

set(GLM_LIBRARIES "")
set(GLM_INCLUDE_DIRS "${GLM_PREFIX}/glm")
set(GLM_DEFINITIONS "")

repository: recepkandemir/opticks

repo_name: recepkandemir/opticks


text:
/**
 * Created by rzsavilla on 28/08/2016.
 */

Text.prototype = new Transformable();
Text.prototype.constructor=Text;
function Text(x,y,setString,setFont) {
    Transformable.call(this);   //Super
    var string = setString;
    var font = setFont;
    this.colour = "red";

    this.setString = function(newString) {
        string = newString;
    }
    this.setFont = function(newFont) {
        font = newFont;
    }

    this.draw = function(c) {
        c.font = font;
        c.fillStyle = this.colour;
        ctx.textAlign = "center";
        c.fillText(string,x,y);
    }
}

function LoadingScreen() {
    var text = new Text(canvas.width / 2, canvas.height / 2,"LOADING","100px Arial");
    text.colour = ("white");
    this.draw = function(c) {
        c.fillStyle = "black"
        c.fillRect(0,0,canvas.width,canvas.height);
        text.draw(c);
    }
}

function PauseScreen() {
    var text = new Text(canvas.width / 2, canvas.height / 2,"PAUSED","100px Arial");
    text.colour = "white";
    this.draw = function(c) {
        c.fillStyle = "black"
        c.fillRect(0,0,canvas.width,canvas.height);
        text.draw(c);
    }
}

function EndScreen() {
    var text = new Text(canvas.width / 2, canvas.height / 2,"Thanks for Playing","50px Arial");
    text.colour = "white";
    this.draw = function(c) {
        c.fillStyle = "black"
        c.fillRect(0,0,canvas.width,canvas.height);
        text.draw(c);
    }
}

extension: js


text:
import React from 'react';
import SvgIcon from '@material-ui/core/SvgIcon';
/**
 * IiifIcon ~
*/
export default function IiifIcon(props) {
  return (
    <SvgIcon {...props}>
      <svg width="100%" height="100%" viewBox="0 0 350 312" xmlns="http://www.w3.org/2000/svg">
        <path d="M349.914,153.001c-7.226,2.462 -14.526,4.735 -21.608,7.558c-1.292,0.515 -2.384,3.264 -2.397,4.99c-0.158,19.829 -0.086,39.659 -0.085,59.489c0.001,19.33 -0.045,38.66 0.023,57.99c0.01,2.729 -0.365,4.639 -3.374,5.734c-20.773,7.564 -41.488,15.288 -62.229,22.942c-0.274,0.102 -0.64,-0.043 -1.375,-0.111c-0.149,-1.154 -0.45,-2.396 -0.45,-3.639c0.016,-72.654 0.053,-145.308 0.098,-217.962c0.025,-40.429 27.685,-76.061 66.956,-85.815c8,-1.987 16.288,-2.814 24.442,-4.177c0,20.333 0,40.667 0,61c-2.107,-0.355 -4.21,-0.746 -6.323,-1.062c-8.942,-1.335 -16.88,3.769 -17.504,12.61c-0.766,10.846 -0.183,21.787 -0.183,33.631c8.451,-2.879 16.23,-5.529 24.01,-8.18c-0.001,18.335 -0.001,36.669 -0.001,55.002Z" style={{ fill: '#e92428' }} />
        <path d="M158.345,106.616c0.095,2.047 0.222,3.505 0.222,4.962c0.006,56.487 -0.047,112.975 0.094,169.461c0.01,4.037 -1.195,5.712 -5.008,7.072c-18.773,6.697 -37.406,13.788 -56.104,20.701c-1.672,0.618 -3.446,0.961 -5.603,1.549c0,-15.906 0.068,-31.381 -0.013,-46.854c-0.22,-42.298 -0.448,-84.595 -0.846,-126.891c-0.039,-4.124 1.115,-5.928 5.188,-7.368c19.113,-6.76 38.054,-14.008 57.064,-21.062c1.501,-0.557 3.057,-0.963 5.006,-1.57Z" style={{ fill: '#e92428' }} />
        <path d="M72.704,310.583c-21.884,-8.075 -43.084,-15.836 -64.189,-23.845c-1.203,-0.457 -2.324,-2.935 -2.331,-4.478c-0.133,-30.819 -0.096,-61.641 -0.095,-92.461c0.002,-27.481 0,-54.964 0,-83.259c7.621,2.723 14.854,5.241 22.039,7.889c13.548,4.992 27.043,10.129 40.621,15.037c2.829,1.022 4.258,2.165 4.251,5.547c-0.119,57.476 -0.092,114.952 -0.104,172.429c0,0.81 -0.096,1.621 -0.192,3.141Z" style={{ fill: '#0f7ca8' }} />
        <path d="M242.875,310.627c-10.717,-3.889 -20.829,-7.533 -30.923,-11.227c-10.59,-3.875 -21.133,-7.88 -31.761,-11.644c-2.84,-1.006 -4.221,-2.192 -4.214,-5.565c0.114,-57.781 0.078,-115.563 0.084,-173.345c0,-0.487 0.111,-0.975 0.261,-2.192c8.077,2.919 15.972,5.699 23.812,8.624c12.915,4.817 25.729,9.919 38.735,14.473c3.397,1.189 4.157,2.731 4.15,6.016c-0.118,54.617 -0.118,109.234 -0.145,163.853c0,3.312 0.001,6.625 0.001,11.007Z" style={{ fill: '#0f7ca8' }} />
        <path d="M111.35,104.374c-15.571,-0.313 -25.599,-10.227 -25.676,-25.962c-0.062,-12.442 4.396,-23.427 11.943,-33.128c9.449,-12.147 21.068,-20.831 36.801,-23.46c17.646,-2.948 31.024,10.385 30.038,28.301c-1.324,24.035 -23.423,48.431 -44.776,52.94c-2.746,0.58 -5.552,0.879 -8.33,1.309Z" style={{ fill: '#e92428' }} />
        <path d="M170.345,48.635c-0.675,-20.953 16.457,-32.623 38.345,-24.484c22.334,8.304 36.075,24.972 39.608,48.417c3.056,20.271 -8.947,33.757 -29.851,30.963c-24.911,-3.33 -48.113,-29.833 -48.102,-54.896Z" style={{ fill: '#0f7ca8' }} />
        <path d="M0.019,48.81c-0.675,-20.953 16.457,-32.623 38.345,-24.484c22.334,8.304 36.075,24.972 39.608,48.417c3.056,20.271 -8.947,33.757 -29.851,30.963c-24.911,-3.33 -48.112,-29.832 -48.102,-54.896Z" style={{ fill: '#0f7ca8' }} />
      </svg>
    </SvgIcon>
  );
}


text:
PR = "r0"
PV = "2.0+cvs-${CVSDATE}"

SRC_URI = "cvs://anonymous@cvs.sourceforge.net/cvsroot/gaim;module=gaim \
	file://no-superimposed-version-on-logo.patch;patch=1 \
	file://desktop-name-2.0.0.patch;patch=1 \
	"

include gaim.inc

S = "${WORKDIR}/gaim"

CFLAGS += "-D_GNU_SOURCE"

DEPENDS += "startup-notification"

#include autopoint (gettext)
EXTRA_AUTORECONF = ""

#disable "X Session Management"... It is EVIL
EXTRA_OECONF += "--disable-sm --enable-startup-notification"

repository: Terentyev/familiar-linux

repo_name: Terentyev/familiar-linux


text:
@article{Daneshi-2021-Modelling,
    title = "Modelling the impacts of climate and land use change on water security in a semi-arid forested watershed using InVEST",
    author = "Daneshi, Alireza  and
      Brouwer, Roy  and
      Najafinejad, Ali  and
      Panahi, Mostafa  and
      Zarandian, Ardavan  and
      Maghsood, Fatemeh Fadia",
    journal = "Journal of Hydrology, Volume 593",
    volume = "593",
    year = "2021",
    publisher = "Elsevier BV",
    url = "https://aclanthology.org/G21-143001",
    doi = "10.1016/j.jhydrol.2020.125621",
    pages = "125621",
}
@article{Shook-2021-Quantifying,
    title = "Quantifying the effects of Prairie depressional storage complexes on drainage basin connectivity",
    author = "Shook, Kevin  and
      Papalexiou, Simon  and
      Pomeroy, John W.",
    journal = "Journal of Hydrology, Volume 593",
    volume = "593",
    year = "2021",
    publisher = "Elsevier BV",
    url = "https://aclanthology.org/G21-28001",
    doi = "10.1016/j.jhydrol.2020.125846",
    pages = "125846",
}

repository: gwf-uwaterloo/gwf-publications

repo_name: gwf-uwaterloo/gwf-publications


text:
@article{hunter_matplotlib_2007,
  Author    = {Hunter, J. D.},
  Title     = {Matplotlib: A 2D graphics environment},
  Journal   = {Computing in Science \& Engineering},
  Volume    = {9},
  Number    = {3},
  Pages     = {90--95},
  abstract  = {Matplotlib is a 2D graphics package used for Python for
  application development, interactive scripting, and publication-quality
  image generation across user interfaces and operating systems.},
  publisher = {IEEE COMPUTER SOC},
  doi       = {10.1109/MCSE.2007.55},
  year      = 2007
}

@article{turk_yt_2011,
   author = {{Turk}, M.~J. and {Smith}, B.~D. and {Oishi}, J.~S. and {Skory}, S. and
{Skillman}, S.~W. and {Abel}, T. and {Norman}, M.~L.},
    title = "{yt: A Multi-code Analysis Toolkit for Astrophysical Simulation Data}",
  journal = {The Astrophysical Journal Supplement Series},
archivePrefix = "arXiv",
   eprint = {1011.3514},
 primaryClass = "astro-ph.IM",
 keywords = {cosmology: theory, methods: data analysis, methods: numerical},
     year = 2011,
    month = jan,
   volume = 192,
      eid = {9},
    pages = {9},
      doi = {10.1088/0067-0049/192/1/9},
   adsurl = {http://adsabs.harvard.edu/abs/2011ApJS..192....9T},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@article{perez_ipython_2007,
	title = {{IPython}: {A} {System} for {Interactive} {Scientific} {Computing}},
	volume = {9},
	issn = {1521-9615},
	shorttitle = {{IPython}},
	url = {http://ieeexplore.ieee.org/document/4160251/},
	doi = {10.1109/MCSE.2007.53},
	number = {3},
	urldate = {2019-09-06},
	journal = {Computing in Science \& Engineering},
	author = {Perez, Fernando and Granger, Brian E.},
	year = {2007},
	pages = {21--29}
}

@misc{munk_widgyts_2019,
	title = {widgyts},
	copyright = {BSD-3-Clause},
	url = {https://github.com/data-exp-lab/widgyts},
	urldate = {2019-09-06},
	publisher = {Data Exploration Lab},
	author = {Munk, Madicken and Turk, Matthew J.},
	month = jul,
	year = {2019},
	note = {original-date: 2018-03-06T17:47:21Z}
}

@misc{grout_ipywidgets_2019,
	title = {ipywidgets},
	copyright = {BSD-3-Clause},
	url = {https://github.com/jupyter-widgets/ipywidgets},
	urldate = {2019-09-06},
	publisher = {Jupyter Widgets},
	author = {Grout, Jason and Frederic, Jonathan and Corlay, Sylvain and Ragan-Kelley, Min},
	month = sep,
	year = {2019},
	note = {original-date: 2015-04-17T20:29:25Z},
	keywords = {jupyterlab-extension}
}

@misc{jupyter-matplotlib_2019,
	title = {jupyter-matplotlib},
	copyright = {BSD-3-Clause},
	url = {https://github.com/matplotlib/jupyter-matplotlib},
	abstract = {Matplotlib Jupyter Extension. Contribute to matplotlib/jupyter-matplotlib development by creating an account on GitHub.},
	urldate = {2019-11-19},
	publisher = {{Matplotlib Developers}},
    author = {Sylvain Corlay and
              Steven Silvester and
              martinRenou and
              Kyle Boone and
              Thomas A Caswell and
              Jens Hedegaard Nielsen and
              Erik Sundell and
              Greg and
              Jason Grout and
              Matt McCormick and
              Nathan Dunfield and
              Tim Paine and
              Todd},
	month = nov,
	year = {2019},
	note = {original-date: 2016-07-21T14:38:56Z},
	keywords = {jupyterlab-extension}
}

@Manual{bokeh_2019,
	title = {Bokeh: Python library for interactive visualization},
	copyright = {BSD-3-Clause},
	url = {https://bokeh.org/},
	urldate = {2019-11-19},
	year = {2019},
    author = {{Bokeh Development Team}},
	publisher = {Bokeh},
}

@misc{bqplot_2019,
	title = {bqplot: Plotting for Jupyter},
	copyright = {Apache-2.0},
	url = {https://github.com/bloomberg/bqplot},
	abstract = {Plotting library for IPython/Jupyter Notebooks.},
	urldate = {2019-11-19},
	author = {Corlay, Sylvain and Sunkara, Srinivas and Madeka, Dhruv and Menegaux, Romain and Cherukuri, Chakri and Grout, Jason and Mabille, Johan},
	publisher = {Bloomberg},
	month = nov,
	year = {2019},
	note = {original-date: 2015-09-26T04:02:18Z}
}

@software{itk_2019,
  author       = {Luis Ibanez and
                  Bill Lorensen and
                  Matt McCormick and
                  Brad King and
                  Daniel Blezek and
                  Hans Johnson and
                  Bradley Lowekamp and
                  jjomier and
                  Kitware, Inc. and
                  Gaëtan Lehmann and
                  Arnaud Gelas and
                  karthikkrishnan and
                  Mathieu Malaterre and
                  Bill Hoffman and
                  Dženan Zukić and
                  Will and
                  Stephen R. Aylward and
                  Xiaoxiao Liu and
                  stnava and
                  Michka Popoff and
                  Nick Tustison and
                  gabehart and
                  Niels Dekker and
                  alex gouaillard and
                  Sean and
                  andinet enquobahrie and
                  Brian Helba and
                  Tom Vercauteren and
                  Pablo Hernandez-Cerdan and
                  David Doria},
  title        = {InsightSoftwareConsortium/ITK: ITK 5.0.1},
  month        = jul,
  year         = 2019,
  publisher    = {Zenodo},
  version      = {v5.0.1},
  doi          = {10.5281/zenodo.3351620},
  url          = {https://doi.org/10.5281/zenodo.3351620}
}

@software{itkwidgets_2020,
  author       = {Matt McCormick and
                  Marco Musy and
                  Kevin Mader and
                  Dave Chen and
                  Bane Sullivan and
                  Ramraj Chandradevan and
                  Jean-Christophe Fillion-Robin and
                  Jean Francois Pambrun and
                  Hadrien Mary and
                  Genevieve Buckley and
                  Erik Sundell and
                  David Haberthür},
  title        = {{InsightSoftwareConsortium/itkwidgets: itkwidgets
                   0.24.2}},
  month        = jan,
  year         = 2020,
  publisher    = {Zenodo},
  version      = {v0.24.2},
  doi          = {10.5281/zenodo.3603359},
  url          = {https://doi.org/10.5281/zenodo.3603359}
}

repository: yt-project/widgyts

repo_name: yt-project/widgyts


text:
@inproceedings{kurzinger2020ctc,
  title={CTC-segmentation of large corpora for german end-to-end speech recognition},
  author={K{\"u}rzinger, Ludwig and Winkelbauer, Dominik and Li, Lujun and Watzel, Tobias and Rigoll, Gerhard},
  booktitle={International Conference on Speech and Computer},
  pages={267--278},
  year={2020},
  organization={Springer}
}

@article{ebden2015kestrel,
  title={The Kestrel TTS text normalization system},
  author={Ebden, Peter and Sproat, Richard},
  journal={Natural Language Engineering},
  volume={21},
  number={3},
  pages={333},
  year={2015},
  publisher={Cambridge University Press}
}

@article{sproat2016rnn,
  title={RNN approaches to text normalization: A challenge},
  author={Sproat, Richard and Jaitly, Navdeep},
  journal={arXiv preprint arXiv:1611.00068},
  year={2016}
}

@book{taylor2009text,
  title={Text-to-speech synthesis},
  author={Taylor, Paul},
  year={2009},
  publisher={Cambridge university press}
}

@Inbook{mohri2009,
author="Mohri, Mehryar",
editor="Droste, Manfred
and Kuich, Werner
and Vogler, Heiko",
title="Weighted Automata Algorithms",
bookTitle="Handbook of Weighted Automata",
year="2009",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="213--254",
abstract="Weighted automata and transducers are widely used in modern applications in bioinformatics and text, speech, and image processing. This chapter describes several fundamental weighted automata and shortest-distance algorithms including composition, determinization, minimization, and synchronization, as well as single-source and all-pairs shortest distance algorithms over general semirings. It presents the pseudocode of these algorithms, gives an analysis of their running time complexity, and illustrates their use in some simple cases. Many other complex weighted automata and transducer algorithms used in practice can be obtained by combining these core algorithms.",
isbn="978-3-642-01492-5",
doi="10.1007/978-3-642-01492-5_6",
url="https://doi.org/10.1007/978-3-642-01492-5_6"
}

repository: Jimmy-INL/NeMo

repo_name: Jimmy-INL/NeMo


text:
# base recipe: meta/recipes-graphics/wayland/wayland-protocols_1.17.bb
# base branch: warrior
# base commit: 8e211c9a6187d859eec1fa7607503d77e459daaf

SUMMARY = "Collection of additional Wayland protocols"
DESCRIPTION = "Wayland protocols that add functionality not \
available in the Wayland core protocol. Such protocols either add \
completely new functionality, or extend the functionality of some other \
protocol either in Wayland core, or some other protocol in \
wayland-protocols."
HOMEPAGE = "http://wayland.freedesktop.org"
LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://COPYING;md5=c7b12b6702da38ca028ace54aae3d484 \
                    file://stable/presentation-time/presentation-time.xml;endline=26;md5=4646cd7d9edc9fa55db941f2d3a7dc53"

inherit debian-package
require recipes-debian/sources/${BPN}.inc

DEBIAN_QUILT_PATCHES = ""

UPSTREAM_CHECK_URI = "https://wayland.freedesktop.org/releases.html"

inherit allarch autotools pkgconfig

PACKAGES = "${PN}"
FILES_${PN} += "${datadir}/pkgconfig/wayland-protocols.pc"

repository: miraclelinux/meta-debian-extended

repo_name: miraclelinux/meta-debian-extended

gha_language: BitBake


text:
require ti-framework-components.inc

PV = "2_25_00_04"

# Full-FC
#SRC_URI[cetarball.md5sum] = "729ede0fd24210d3c5439511fa859d51"
#SRC_URI[cetarball.sha256sum] = "81f815159f3dfda0525be6da543644b02c3610bcb080df170cbd27e2d8420ba2"

# Lite-FC
SRC_URI[fctarball.md5sum] = "9b186aa6b431be08bd8b91926cd91c95"
SRC_URI[fctarball.sha256sum] = "733737f5a0d0ca251993d8c7138378fb9481867a5d6c77ffa7d133673916c30f"

SRC_URI[md5sum] = "11410b5cf4142ae415b683af0e9929b5"
SRC_URI[sha256sum] = "161432f5cf184f96de290f807a4a6fddf11f2612d5b2efd91f8187c0ac612a40"

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty