The GNU Binary Utilities, or binutils, is a collection of programming tools maintained by the GNU Project for working with executable code including assembly, linking and many other development operations. The tools are originally from Cygnus Solutions. The tools are typically used along with other GNU tools such as GNU Compiler Collection, and the GNU Debugger. == Tools == The tools include: == elfutils == Ulrich Drepper wrote elfutils, to partially replace GNU Binutils, purely for Linux and with support only for ELF and DWARF. It distributes three libraries with it for programmatic access.
Coolgorilla
Coolgorilla was one of the earliest software developers that created 3rd party native applications for Apple iPod devices. Coolgorilla was an early adopter of using a sponsorship business model to enable mobile applications to be given away freely. Coolgorilla developed a series of Talking Phrasebooks for iPods in 2006. They partnered with online travel company lastminute.com who sponsored the applications enabling them to be made available to download completely free of charge. As mobile devices became more sophisticated, Coolgorilla developed the Talking Phrasebooks for Sony Ericsson and Nokia Mobile Devices which at the time were considerably noteworthy since the applications used real voice audio translations. With Apple's introduction of the iPhone in 2007, Coolgorilla developed a Web App before having four of the iPhone Talking Phrasebooks available to download from Apple's App Store on the day it opened in 2008. == Almanac in Chronological Order == On 23 December 2005, CoolGorilla, a new start-up, launched a trivia game for the iPod. It was titled "Rock and Pop Quiz". It was a quiz game that tested users' knowledge on bands such as U2, Metallica, Beyonce, and the Beatles. The quiz contained twenty megabytes of audible trivia questions. The free game was compatible with 3rd, 4th and 5th generation iPods, iPod mini and nano. In March 2006, Coolgorilla released "Movie Quiz for iPods" with a price of $5. It was an audio game narrated by New York's DJ Thomas, a radio and television host, voice over artist and event Master of Ceremonies. There were questions on Star Wars, Spiderman, The Godfather, Pulp Fiction, The Matrix, James Bond, and others. The user could keep track of their score. The game included a secret code for players who answered all questions correctly which enabled users to enter their name on the Coolgorilla Hall of Fame. In May 2006, Coolgorilla launched a World Cup Encyclopedia which was released prior to the 2006 FIFA World Cup. It had information on the World Cup schedule, details of every player from every team, every score from every world cup game ever played, stadium details, and manager profiles. It was a free download. In June 2006, Coolgorilla released a series of iPod Phrasebooks in German, Greek, French and Spanish. They were sponsored by lastminute.com and were free. The phrasebooks included common words and phrases for tourists with 750 sound files. They were accessed through the iPod's Notes feature. In April 2007, Coolgorilla released a downloadable version of the Talking Phrasebooks for Nokia and Sony Ericsson mobile devices. French, Spanish, German, Greek, Italian, and Portuguese were produced. The application provided real voice translations. They initially sold for £3 but 3 months later were offered for free. The branding was lastminute.com branding. Apple's iPhone was released at the end of June 2007. Soon after, Coolgorilla released an online all-in-one version of their Talking Phrasebooks for iPhone (Web App). The Phrasebooks were made available online in the form of a web app as iPhone did not yet allow for the download of additional apps. The app provided both text and audio translations in French, Spanish, Portuguese, Italian, German, and Greek. The iPhone translated the phrases using the recordings of real, native voice-over artists. A text translation on screen was also displayed. Apple's App Store opened in July 2008 with approximately 500 native apps available. Four of these Apps were Coolgorilla's Talking Phrasebooks for iPhone (Native Apps). There was French, German, Italian, and Spanish. These Apps carried lastminute.com branding and were available for free download. In the first three weeks following their release, the phrasebooks had over 350,000 downloads. Subsequently, Dutch, Arabic, Mandarin and Cantonese were also released. In October 2008, Coolgorilla released an iPhone London Travel Guide. Coolgorilla featured on NBC News in August 2009. In 2010, FIAT used the Italian Phrasebook to help promote the release of their FIAT 500 in the US. There has been no further activity since.
Multiple sequence alignment
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences. Alignments highlight mutation events such as point mutations (single amino acid or nucleotide changes), insertion mutations and deletion mutations, and alignments are used to assess sequence conservation and infer the presence and activity of protein domains, tertiary structures, secondary structures, and individual amino acids or nucleotides. Multiple sequence alignments require more sophisticated methodologies than pairwise alignments, as they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. However, heuristic methods generally cannot guarantee high-quality solutions and have been shown to fail to yield near-optimal solutions on benchmark test cases. == Problem statement == Given m {\displaystyle m} sequences S i {\displaystyle S_{i}} , i = 1 , ⋯ , m {\displaystyle i=1,\cdots ,m} similar to the form below: S := { S 1 = ( S 11 , S 12 , … , S 1 n 1 ) S 2 = ( S 21 , S 22 , ⋯ , S 2 n 2 ) ⋮ S m = ( S m 1 , S m 2 , … , S m n m ) {\displaystyle S:={\begin{cases}S_{1}=(S_{11},S_{12},\ldots ,S_{1n_{1}})\\S_{2}=(S_{21},S_{22},\cdots ,S_{2n_{2}})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S_{m}=(S_{m1},S_{m2},\ldots ,S_{mn_{m}})\end{cases}}} A multiple sequence alignment is taken of this set of sequences S {\displaystyle S} by inserting any amount of gaps needed into each of the S i {\displaystyle S_{i}} sequences of S {\displaystyle S} until the modified sequences, S i ′ {\displaystyle S'_{i}} , all conform to length L ≥ max { n i ∣ i = 1 , … , m } {\displaystyle L\geq \max\{n_{i}\mid i=1,\ldots ,m\}} and no values in the sequences of S {\displaystyle S} of the same column consists of only gaps. The mathematical form of an MSA of the above sequence set is shown below: S ′ := { S 1 ′ = ( S 11 ′ , S 12 ′ , … , S 1 L ′ ) S 2 ′ = ( S 21 ′ , S 22 ′ , … , S 2 L ′ ) ⋮ S m ′ = ( S m 1 ′ , S m 2 ′ , … , S m L ′ ) {\displaystyle S':={\begin{cases}S'_{1}=(S'_{11},S'_{12},\ldots ,S'_{1L})\\S'_{2}=(S'_{21},S'_{22},\ldots ,S'_{2L})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S'_{m}=(S'_{m1},S'_{m2},\ldots ,S'_{mL})\end{cases}}} To return from each particular sequence S i ′ {\displaystyle S'_{i}} to S i {\displaystyle S_{i}} , remove all gaps. == Graphing approach == A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. When finding alignments via graph, a complete alignment is created in a weighted graph that contains a set of vertices and a set of edges. Each of the graph edges has a weight based on a certain heuristic that helps to score each alignment or subset of the original graph. === Tracing alignments === When determining the best suited alignments for each MSA, a trace is usually generated. A trace is a set of realized, or corresponding and aligned, vertices that has a specific weight based on the edges that are selected between corresponding vertices. When choosing traces for a set of sequences it is necessary to choose a trace with a maximum weight to get the best alignment of the sequences. == Alignment methods == There are various alignment methods used within multiple sequence to maximize scores and correctness of alignments. Each is usually based on a certain heuristic with an insight into the evolutionary process. Most try to replicate evolution to get the most realistic alignment possible to best predict relations between sequences. === Dynamic programming === A direct method for producing an MSA uses the dynamic programming technique to identify the globally optimal alignment solution. For proteins, this method usually involves two sets of parameters: a gap penalty and a substitution matrix assigning scores or probabilities to the alignment of each possible pair of amino acids based on the similarity of the amino acids' chemical properties and the evolutionary probability of the mutation. For nucleotide sequences, a similar gap penalty is used, but a much simpler substitution matrix, wherein only identical matches and mismatches are considered, is typical. The scores in the substitution matrix may be either all positive or a mix of positive and negative in the case of a global alignment, but must be both positive and negative, in the case of a local alignment. For n individual sequences, the naive method requires constructing the n-dimensional equivalent of the matrix formed in standard pairwise sequence alignment. The search space thus increases exponentially with increasing n and is also strongly dependent on sequence length. Expressed with the big O notation commonly used to measure computational complexity, a naïve MSA takes O(LengthNseqs) time to produce. To find the global optimum for n sequences this way has been shown to be an NP-complete problem. In 1989, based on Carrillo-Lipman Algorithm, Altschul introduced a practical method that uses pairwise alignments to constrain the n-dimensional search space. In this approach pairwise dynamic programming alignments are performed on each pair of sequences in the query set, and only the space near the n-dimensional intersection of these alignments is searched for the n-way alignment. The MSA program optimizes the sum of all of the pairs of characters at each position in the alignment (the so-called sum of pair score) and has been implemented in a software program for constructing multiple sequence alignments. In 2019, Hosseininasab and van Hoeve showed that by using decision diagrams, MSA may be modeled in polynomial space complexity. === Progressive alignment construction === The most widely used approach to multiple sequence alignments uses a heuristic search known as progressive technique (also known as the hierarchical or tree method) developed by Da-Fei Feng and Doolittle in 1987. Progressive alignment builds up a final MSA by combining pairwise alignments beginning with the most similar pair and progressing to the most distantly related. All progressive alignment methods require two stages: a first stage in which the relationships between the sequences are represented as a phylogenetic tree, called a guide tree, and a second step in which the MSA is built by adding the sequences sequentially to the growing MSA according to the guide tree. The initial guide tree is determined by an efficient clustering method such as neighbor-joining or unweighted pair group method with arithmetic mean (UPGMA), and may use distances based on the number of identical two-letter sub-sequences (as in FASTA rather than a dynamic programming alignment). Progressive alignments are not guaranteed to be globally optimal. The primary problem is that when errors are made at any stage in growing the MSA, these errors are then propagated through to the final result. Performance is also particularly bad when all of the sequences in the set are rather distantly related. Most modern progressive methods modify their scoring function with a secondary weighting function that assigns scaling factors to individual members of the query set in a nonlinear fashion based on their phylogenetic distance from their nearest neighbors. This corrects for non-random selection of the sequences given to the alignment program. Progressive alignment methods are efficient enough to implement on a large scale for many (100s to 1000s) sequences. A popular progressive alignment method has been the Clustal family. ClustalW is used extensively for phylogenetic tree construction, in spite of the author's explicit warnings that unedited alignments should not be used in such studies and as input for protein structure prediction by homology modeling. European Bioinformatics Institute (EMBL-EBI) announced that CLustalW2 will expire in August 2015. They recommend Clustal Omega which performs based on seeded guide trees and HMM profile-profile techniques for protein alignments. An alternative tool for progressive DNA alignments is multiple alignment using fast Fourier transform (MAFFT). Another common progressive alignment method named T-Coffee is slower than Clustal and its derivatives but generally produces more accurate alignments for distantly related sequence sets. T-Coffee calculates pairwise alignments by combining the direct alignment of the pair with indirect alignments that aligns each sequence of the pair to a third sequence. It uses the output from Clustal as well as another local alignment program LALIGN, which finds multiple regions of local alignment between two sequences. The resulting alignment and phylogenetic tree are used as a guide to produce new and more accurate w
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Factored language model
The factored language model (FLM) is an extension of a conventional language model introduced by Jeff Bilmes and Katrin Kirchoff in 2003. In an FLM, each word is viewed as a vector of k factors: w i = { f i 1 , . . . , f i k } . {\displaystyle w_{i}=\{f_{i}^{1},...,f_{i}^{k}\}.} An FLM provides the probabilistic model P ( f | f 1 , . . . , f N ) {\displaystyle P(f|f_{1},...,f_{N})} where the prediction of a factor f {\displaystyle f} is based on N {\displaystyle N} parents { f 1 , . . . , f N } {\displaystyle \{f_{1},...,f_{N}\}} . For example, if w {\displaystyle w} represents a word token and t {\displaystyle t} represents a Part of speech tag for English, the expression P ( w i | w i − 2 , w i − 1 , t i − 1 ) {\displaystyle P(w_{i}|w_{i-2},w_{i-1},t_{i-1})} gives a model for predicting current word token based on a traditional Ngram model as well as the Part of speech tag of the previous word. A major advantage of factored language models is that they allow users to specify linguistic knowledge such as the relationship between word tokens and Part of speech in English, or morphological information (stems, root, etc.) in Arabic. Like N-gram models, smoothing techniques are necessary in parameter estimation. In particular, generalized back-off is used in training an FLM.
Robomart
Robomart is an American technology company headquartered in Santa Monica, California that builds autonomous smart shops for cafes, ice cream parlors, and quick-service restaurants. The company’s white label platform gives retailers the option to expand their footprint at a significantly lower cost than traditional brick-and-mortar real-estate. Robomarts are equipped with a proprietary checkout-free system, temperature controlled compartments, sensors for autonomous operation, and external cameras for added security. The company licenses its technology and white label applications to retailers who manage their fleet of stores and deploy them to their consumers’ locations. After consumers have taken goods from the robomart, their order is automatically calculated, their card on file is charged and they are sent a receipt. The company has announced partnerships with Unilever, Mars, and Fatty Mart. == History == Robomart was founded by Ali Ahmed, Tigran Shahverdyan, and Emad Suhail Rahim. The company debuted at CES 2018 where it unveiled its concept of a self-driving store. At GITEX 2018 the company presented its first functional prototype of a fully driverless Robomart. At the 2019 Consumer Electronics Show the company demonstrated the technology behind its autonomous stores and checkout-free shopping experience. In January 2019, Robomart announced its first partnership with U.S. grocery chain Stop & Shop to test its driverless stores. In December 2020, Robomart deployed the Pharmacy Robomart in a trial in West Hollywood. In June 2021, the company launched its commercial service with a fleet of Pharmacy and Snacks Robomarts operating within West Hollywood and Central Hollywood. In August 2023, Robomart announced a $2 million seed round, putting its to-date funding at $3.4 million. == Partnerships == In September 2019, Robomart partnered with Avery Dennison to source the RFID tags used to enable its checkout-free shopping experience. In December 2020, Robomart partnered with Zeeba Vans to provide vehicles for its growing fleet. In June 2021, Robomart partnered with REEF Technology to provide inventory management and restocking services. In addition, REEF's Light Speed grocery division serves as the first merchant selling products through Robomart. == Products == The company currently offers three Robomart types. The frozen Robomart that stocks ice cream, the refrigerated Robomart that stocks perishable foods, and the ambient Robomart that stocks shelf-stable goods.
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