tag:blogger.com,1999:blog-10187046349643484242024-02-07T21:34:31.835+11:00The Organisation of Really Contrived AcronymsRichard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.comBlogger60125tag:blogger.com,1999:blog-1018704634964348424.post-22223473506446175942015-05-30T11:03:00.000+10:002015-05-30T11:03:01.331+10:00IRENE - Image, Reconstruct, Erase Noise, Etc. <p>This month’s <a href="http://www.nature.com/nature/podcast/index-audiofile-2015-05-26.html">Nature Audio file</a> features a device, <a href="http://irene.lbl.gov/">IRENE</a>, designed to:</p>
<blockquote>
<p><em>acquire digital maps of the surface of the media, without contact, and then apply image analysis methods to recover the audio data and reduce noise.</em> </p>
</blockquote>
<p><a href="http://irene.lbl.gov/"><strong>IRENE</strong></a> stands for <strong>I</strong>mage, <strong>R</strong>econstruct, <strong>E</strong>rase <strong>N</strong>oise, <strong>E</strong>tc. and was named after one of the first reconstructed audio recordings: “Goodnight Irene”, written by H. Ledbetter and J. Lomax, performed by the Weavers (1950). This earns IRENE the much prized <a href="http://orcacronyms.blogspot.com.au/p/acronym-classification-acronyms-in-orca.html">pre-hoc classification</a>.</p>
<p>Here more about IRENE <a href="http://www.nature.com/nature/podcast/index-audiofile-2015-05-26.html">here</a>.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-52282341310934399712015-04-15T08:34:00.001+10:002015-04-15T08:35:39.439+10:00FUBAR - Fast Unconstrained Bayesian AppRoximation<p>From the authors that brought you <a href="http://orcacronyms.blogspot.com.au/2015/02/busted-branch-site-unrestricted.html">BUSTED (Branch-site Unrestricted Statistical Test for Episodic Diversification)</a>, behold <strong>FUBAR</strong>: <strong>F</strong>ast <strong>U</strong>nconstrained <strong>B</strong>ayesian <strong>A</strong>pp<strong>R</strong>oximation. (Doubly from the authors in this case, as the first author gave the tip-off.) </p>
<p>Despite it’s intranym status, FUBAR gets an extra geek hat-tip for being a homonym of “<a href="http://en.wikipedia.org/wiki/Foobar">foo bar</a>”. (Although in looking that up, I came across the original <a href="http://en.wikipedia.org/wiki/Military_slang#FUBAR">FUBAR</a> acronym, which is hopefully <em>not</em> reflective of their method!)</p>
<h2 id="abstract">Abstract</h2>
<blockquote>
<p>Model-based analyses of natural selection often categorize sites into a relatively small number of site classes. Forcing each site to belong to one of these classes places unrealistic constraints on the distribution of selection parameters, which can result in misleading inference due to model misspecification. We present an approximate hierarchical Bayesian method using a Markov chain Monte Carlo (MCMC) routine that ensures robustness against model misspecification by averaging over a large number of predefined site classes. This leaves the distribution of selection parameters essentially unconstrained, and also allows sites experiencing positive and purifying selection to be identified orders of magnitude faster than by existing methods. We demonstrate that popular random effects likelihood methods can produce misleading results when sites assigned to the same site class experience different levels of positive or purifying selection–an unavoidable scenario when using a small number of site classes. Our Fast Unconstrained Bayesian AppRoximation (FUBAR) is unaffected by this problem, while achieving higher power than existing unconstrained (fixed effects likelihood) methods. The speed advantage of FUBAR allows us to analyze larger data sets than other methods: We illustrate this on a large influenza hemagglutinin data set (3,142 sequences). FUBAR is available as a batch file within the latest HyPhy distribution (http://www.hyphy.org), as well as on the Datamonkey web server (http://www.datamonkey.org/).</p>
</blockquote>
<ul>
<li>Murrell B, Moola S, Mabona A, Weighill T, Sheward D, Kosakovsky Pond SL & Scheffler K (2013). FUBAR: a fast, unconstrained bayesian approximation for inferring selection. <em>Mol Biol Evol.</em> <strong>30(5):</strong>1196-205. PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/23420840">23420840</a></li>
</ul>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-71808091832695406222015-02-26T11:57:00.000+11:002015-02-26T11:57:30.282+11:00BUSTED - Branch-site Unrestricted Statistical Test for Episodic Diversification<p>This paper popped up in my PubCrawler feed today:</p>
<p>Murrell B et al. (2015). Gene-wide identification of episodic selection. <a href="http://mbe.oxfordjournals.org/content/early/2015/02/19/molbev.msv035.long">Mol Biol Evol. 2015 Feb 19. pii: msv035</a>.</p>
<blockquote>
<p>We present BUSTED, a new approach to identifying gene-wide evidence of episodic positive selection, where the non-synonymous substitution rate is transiently greater than the synonymous rate. BUSTED can be used either on an entire phylogeny (without requiring an a priori hypothesis regarding which branches are under positive selection) or on a pre-specified subset of foreground lineages (if a suitable a priori hypothesis is available). Selection is modeled as varying stochastically over branches and sites, and we propose a computationally inexpensive evidence metric for identifying sites under episodic positive selection on any foreground branches. We compare BUSTED to existing models on simulated and empirical data. An implementation is available on www.datamonkey.org/busted, with a widget allowing the interactive specification of foreground branches.</p>
</blockquote>
<p>From the Introduction, we find that BUSTED is indeed an orca-worthy contrived acronym: <b>BUSTED</b> - <b>B</b>ranch-site <b>U</b>nrestricted <b>S</b>tatistical <b>T</b>est for <b>E</b>pisodic <b>D</b>iversification.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com2tag:blogger.com,1999:blog-1018704634964348424.post-6528164585071045872014-12-20T22:57:00.001+11:002014-12-20T22:57:39.820+11:00SANTA - Spatial Analysis of NeTwork Associations<p>A festive bioinformatics acronym today: <b>SANTA</b> - <b>S</b>patial <b>A</b>nalysis of <b>N</b>e<b>T</b>work <b>A</b>ssociations. The authors don't make a big deal of the acronym in the paper but it seemed contrived enough for a Christmas ORCA entry.</p>
<h2 id="abstract">Abstract</h2>
<blockquote>
<p>Linking networks of molecular interactions to cellular functions and phenotypes is a key goal in systems biology. Here, we adapt concepts of spatial statistics to assess the functional content of molecular networks. Based on the guilt-by-association principle, our approach (called SANTA) quantifies the strength of association between a gene set and a network, and functionally annotates molecular networks like other enrichment methods annotate lists of genes. As a general association measure, SANTA can (i) functionally annotate experimentally derived networks using a collection of curated gene sets and (ii) annotate experimentally derived gene sets using a collection of curated networks, as well as (iii) prioritize genes for follow-up analyses. We exemplify the efficacy of SANTA in several case studies using the S. cerevisiae genetic interaction network and genome-wide RNAi screens in cancer cell lines. Our theory, simulations, and applications show that SANTA provides a principled statistical way to quantify the association between molecular networks and cellular functions and phenotypes. SANTA is available from <a href="http://bioconductor.org/packages/release/bioc/html/SANTA.html">http://bioconductor.org/packages/release/bioc/html/SANTA.html</a>.</p>
</blockquote>
<p>Ref: Cornish AJ & Markowetz F (2014) SANTA: Quantifying the Functional Content of Molecular Networks. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003808">PLoS Comput Biol 10(9): e1003808</a>.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-46724082600786079182014-11-05T23:12:00.000+11:002014-12-20T22:59:14.946+11:00REACH - Registration, Evaluation, Authorisation and Restriction of Chemicals<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjo2gvZ-Dia2HqD2YwHlpf1wHmcaQF6ez7gCZbPPK4XMEQyTl0xHR9xD2I1K8gtYH9a7caXx9kwbA-PGr23DdvwHy3vDpDvuMvJysb2tIvYnQqXNQRocg1_EBfQjxoQqsR14hNstgeilvU/s1600/reach.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjo2gvZ-Dia2HqD2YwHlpf1wHmcaQF6ez7gCZbPPK4XMEQyTl0xHR9xD2I1K8gtYH9a7caXx9kwbA-PGr23DdvwHy3vDpDvuMvJysb2tIvYnQqXNQRocg1_EBfQjxoQqsR14hNstgeilvU/s200/reach.jpg" align="right" style="margin-left:25px" /></a><a href="http://ec.europa.eu/enterprise/sectors/chemicals/reach/index_en.htm"><strong>REACH</strong> - <strong>R</strong>egistration, <strong>E</strong>valuation, <strong>A</strong>uthorisation and Restriction of <strong>Ch</strong>emicals</a> is a fine example of acronym contrivance (although lacking the panache of a good <em>pre hoc</em> concoction). Not got the right words for something catchy? Just ignore the inconvenient word!</p>
<blockquote>
<p><em>“[REACH] streamlines and improves the former legislative framework on chemicals of the European Union (EU). The main aims of REACH are to ensure a high level of protection of human health and the environment from the risks that can be posed by chemicals, the promotion of alternative test methods, the free circulation of substances on the internal market and enhancing competitiveness and innovation.”</em></p>
</blockquote>
<p>I guess you can’t blame them for trying to make it more interesting.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-91612433387042071052014-10-14T20:26:00.000+11:002014-10-14T20:26:04.682+11:00MUSIC - MUltiScale enrIchment Calling<p><a href="http://www.acgt.me/blog/2013/6/23/introducing-jabba-just-another-bogus-bioinformatics-acronym.html" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHK6pNKLkQ9S1rW93GiDjrCbc2evXkhw1jnBEgosUS7hgoaq1TTTgpIOI368y7k69lPmjqV98TQgPxeAE352aj_D9JeCKDqJ0bwOsDTgao3FG5zt8ieJGl5UanP6ur2DEG3wZ5jLsZ6MM/s180/jabba.png" align="right" style="margin-left:20px" /></a>Over on <a href="http://www.acgt.me/">the ACGT blog</a>, Keith Bradnam has another <a href="http://orcacronyms.blogspot.com.au/2013/08/jabba-just-another-bogus-bioinformatics.html">JABBA Award</a> (and a nice new JABBA logo):</p>
<blockquote>
<p><a href="http://www.acgt.me/blog/2014/10/9/if-music-be-the-food-of-bioinformatics-play-on-time-for-a-new-jabba-award"><strong>MUSIC</strong> - <strong>Mu</strong>lti<strong>s</strong>cale Enr<strong>i</strong>chment <strong>C</strong>alling</a>.</p>
</blockquote>
<p>I'm not sure what the connection between MUSIC and ChIP-Seq is but the authors seemed pretty determined. His post is actually a twofer, as it also draws attention to an equally contrived an unfathomable intranym:</p>
<blockquote>
<p><a href="http://bioinformatics.oxfordjournals.org/content/20/14/2309.full.pdf+html"><strong>MuSiC</strong> - <strong>Mu</strong>ltiple <strong>S</strong>equence Al<strong>i</strong>gnment with <strong>C</strong>onstraints</a></p>
</blockquote>
<p>Read more at <a href="http://www.acgt.me/blog/2014/10/9/if-music-be-the-food-of-bioinformatics-play-on-time-for-a-new-jabba-award">Keith’s blog</a>!</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-40313027184422891162014-10-06T23:14:00.002+11:002014-10-06T23:14:58.431+11:00DREAM - Dialogue for Reverse Engineering Assessments and Methods<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiW73BOxzH_I3HmvuoW7R0G6grUhK1dvkK_GEQRXbNNUTKuMWjKNH9X8a7NWmLkkEL4ge0HYNuFPC3F7FIImxjM01fC1zPAPGOrrUiHXiF8EoMFbHGnmkWsWBW6Qn6nGt8libLz2ejMdpc/s1600/DREAM.png" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiW73BOxzH_I3HmvuoW7R0G6grUhK1dvkK_GEQRXbNNUTKuMWjKNH9X8a7NWmLkkEL4ge0HYNuFPC3F7FIImxjM01fC1zPAPGOrrUiHXiF8EoMFbHGnmkWsWBW6Qn6nGt8libLz2ejMdpc/s113/DREAM.png" align="right" style="margin-left:10px"/></a>According to <a href="http://www.the-dream-project.org/">the website</a>, <strong>DREAM</strong> is a <strong>D</strong>ialogue for <strong>R</strong>everse <strong>E</strong>ngineering <strong>A</strong>ssessments and <strong>M</strong>ethods: </p>
<blockquote>
<p><em>“The main objective is to catalyze the interaction between experiment and theory in the area of cellular network inference and quantitative model building in systems biology.”</em></p>
</blockquote>
<p>Not clear?</p>
<blockquote>
<p><em>“DREAM (Dialogue for Reverse Engineering Assessments and Methods) poses fundamental questions about systems biology, and invites participants to propose solutions. The main objective is to catalyze the interaction between theory and experiment, specifically in the area of cellular network inference and quantitative model building. DREAM challenges address how we can assess the quality of our descriptions of networks that underlie biological systems, and of our predictions of the outcomes of novel experiments. These are not simple questions. Researchers have used a variety of algorithms to deduce the structure of biological networks and/or to predict the outcome of perturbations to their systems. They have also evaluated the success of their methodologies using a diverse set of non-standardised metrics. What is still needed, and what DREAM aims to achieve, is a fair comparison of the strengths and weaknesses of these methods and a clear sense of the reliability of the models that researchers create.”</em></p>
</blockquote>
<p>I know a bit about Systems Biology but I must admit to being confused about the “Assessment and Methods” part of DREAM. I <i>think</i> it means that DREAM is about assessing methods and models for reverse engineering biological systems (<i>i.e.</i> Systems Biology), even though it reads that they are trying to reverse engineer assessments and methods. Such dedication to the acronym over clarity makes DREAM a worthy ORCA entry.</p>
Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-82275827493165109832014-10-05T22:46:00.001+11:002014-10-05T22:46:30.868+11:00ILIaD - Institute for Learning Innovation and Development<p>The learning and teaching unit at the University of Southampton has had a few different names over the years but its latest incarnation is ORCA-worthy with some selective use of prepositions: <strong>ILIaD</strong> - the <strong>I</strong>nstitute for <strong>L</strong>earning <strong>I</strong>nnovation <strong>a</strong>nd <strong>D</strong>evelopment. Find out more at <a href="http://www.southampton.ac.uk/aboutus/professionalservices/iliad.html">the ILIaD website</a>. (Although ILIaD is undoubtedly replete with heroes, I think this is <i>ad hoc</i>.)</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-75878947913800838292014-09-22T20:00:00.000+10:002014-10-05T22:51:35.868+11:00MAGIC - the Meta-Analyses of Glucose and Insulin-related traits Consortium<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhqyYvqZVNC4k0xo53ys56EL2937Vcy8_JI3IP9tqF0oxJD1yucQ19Bvn9IOv4GouSS_W8F5B8wJyWSqwFE3_B467f08ssw2WBLbg_9HZNXi5rwIONPjf5fbDXkmwVI5pOZPt7mR0YDo7Y/s1600/magic_logo.png" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhqyYvqZVNC4k0xo53ys56EL2937Vcy8_JI3IP9tqF0oxJD1yucQ19Bvn9IOv4GouSS_W8F5B8wJyWSqwFE3_B467f08ssw2WBLbg_9HZNXi5rwIONPjf5fbDXkmwVI5pOZPt7mR0YDo7Y/s320/magic_logo.png" align="left" style="margin-right:10px"/></a>The final human genetics <a href="http://orcacronyms.blogspot.com.au/search/label/consortium">consortium</a> (for now) is <a href="http://www.magicinvestigators.org/"><strong>MAGIC</strong></a> - the <strong>M</strong>eta-<strong>A</strong>nalyses of <strong>G</strong>lucose and <strong>I</strong>nsulin-related traits <strong>C</strong>onsortium, another co-author of the DIAGRAM consortium. This is probably the most contrived of the lot, in that it failed to use all its words but did include “Consortium”. At the same time, being part of MAGIC has a certain appeal above <a href="http://orcacronyms.blogspot.com.au/2014/09/charge-cohorts-for-heart-and-aging.html">CHARGE</a>, <a href="http://orcacronyms.blogspot.com.au/2014/09/diagram-diabetes-genetics-replication.html">DIAGRAM</a> or <a href="http://orcacronyms.blogspot.com.au/2014/09/giant-genetic-investigation-of.html">GIANT</a>.</p>
<blockquote>
<p><em>“MAGIC (the Meta-Analyses of Glucose and Insulin-related traits Consortium) represents a collaborative effort to combine data from multiple GWAS to identify additional loci that impact on glycemic and metabolic traits.</em></p>
<p><em>MAGIC investigators have initially studied fasting glucose, fasting insulin, 2h glucose and HBA1c, as well as performed meta-analysis of more sophisticated measures of insulin secretion and sensitivity. Through these efforts, dozens of loci influencing these traits have been idenified, a subset of which also influence risk of type 2 diabetes.”</em></p>
</blockquote>
<p>There is a certain degree of magic involved in a good genome-wide association study (GWAS) but I still rate this one <em>ad hoc</em>.</p>
<p>If contrived consortium acronyms are your thing, you can probably do a lot worse than sign up to the Table of Contents alerts for the journal <a href="http://www.nature.com/ng/index.html"><em>Nature Genetics</em></a>.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-76924202521018707672014-09-21T20:00:00.000+10:002014-09-21T20:00:00.707+10:00GIANT - Genetic Investigation of ANthropometric Traits<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKKJvLFapyjSa-b7ndSpGzo-1JNpXtw63qkneCkMcqsESibGfZd27I2XeGavo5Ooo_VULHt0TQE9TQgxON4tXjmVT41ehVKmDR7_JTex7oZYihH1TnTkU9EZ3XkCAFWXRuR8LgIabH5GU/s1600/GIANTlogo.png" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKKJvLFapyjSa-b7ndSpGzo-1JNpXtw63qkneCkMcqsESibGfZd27I2XeGavo5Ooo_VULHt0TQE9TQgxON4tXjmVT41ehVKmDR7_JTex7oZYihH1TnTkU9EZ3XkCAFWXRuR8LgIabH5GU/s320/GIANTlogo.png" align="left" style="margin-right:10px" /></a>
Human genetics <a href="http://orcacronyms.blogspot.com.au/search/label/consortium">consortium</a> number three is the <a href="http://www.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium"><strong>GIANT</strong></a> - <strong>G</strong>enetic <strong>I</strong>nvestigation of <strong>AN</strong>thropometric <strong>T</strong>raits - consortium, a co-author of one of the recent DIAGRAM papers in <a href="http://www.nature.com/ng/index.html"><i>Nature Genetics</i></a>.</p>
<blockquote>
<p><em>“The Genetic Investigation of ANthropometric Traits (GIANT) consortium is an international collaboration that seeks to identify genetic loci that modulate human body size and shape, including height and measures of obesity. The GIANT consortium is a collaboration between investigators from many different groups, institutions, countries, and studies, and the results represent their combined efforts. The primary approach has been meta-analysis of genome-wide association data and other large-scale genetic data sets. Anthropometric traits that have been studied by GIANT include body mass index (BMI), height, and traits related to waist circumference (such as waist-hip ratio adjusted for BMI, or WHRadjBMI). Thus far, the GIANT consortium has identified common genetic variants at hundreds of loci that are associated with anthropometric traits.”</em></p>
</blockquote>
<p>Genome-wide association studies are big by nature, and GIANT does have a lot of <a href="http://www.broadinstitute.org/collaboration/giant/index.php/GIANT_Cohorts_and_Groups">participating cohorts and groups on their webpage</a>, so I think that GIANT can be given a <em>post hoc</em> rating.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-40004013552105655842014-09-20T20:00:00.000+10:002014-09-20T20:00:02.022+10:00DIAGRAM - DIAbetes Genetics Replication And Meta-analysis<p><a href="http://diagram-consortium.org/index.html" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhXzJxe50pY09jyd2HjJo0DLCyO0RNcKlRjdKpns58UwK2ruxDkq3d4C31fFuEDzMcH_ucXzkAFTxuaLT58YIFIbP-K1HVVoDLFrVhpK2soVDbokzFTEKqSjCkiz-r1d3UKPH1V4SMUO2w/s280/diagram_logo.jpg" align="left" style="margin-right:10px"/></a>The <a href="http://diagram-consortium.org/index.html"><strong>DIAGRAM</strong></a> - <strong>DIA</strong>betes <strong>G</strong>enetics <strong>R</strong>eplication <strong>A</strong>nd <strong>M</strong>eta-analysis - consortium is the second ORCA entry this month for human genetics <a href="http://orcacronyms.blogspot.com.au/search/label/consortium">consortia</a>, which seem to be almost as productive a source of contrived acronyms as <a href="http://orcacronyms.blogspot.com.au/search/label/bioinformatics">bioinformatics</a>. </p>
<blockquote>
<p><em>“The DIAGRAM (DIAbetes Genetics Replication And Meta-analysis) consortium is a grouping of researchers with shared interests in performing large-scale studies to characterise the genetic basis of type 2 diabetes, and a principal focus on samples of European descent.”</em> </p>
</blockquote>
<p>You can read more on <a href="http://diagram-consortium.org/about.html">their website</a>, which features an array of additional acronyms (including some future ORCA entries).</p>
Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-13633169131419095342014-09-19T21:56:00.000+10:002014-09-19T21:56:34.048+10:00CHARGE - Cohorts for Heart and Aging Research in Genomic Epidemiology<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjn9lYMZDTKgidwHrSOHlyCEEMqkHxk973YHD0GqjTpWAaTiSw9Q8B6FqNfGFXo_2IC9CKRKM4JIrcJrKo6KwmT30BFB6HEH3PQehY4hzoXDWS_hIrDRVCcHl-kq3QrzKNoMMzN4xUGjys/s1600/charge_logo.png" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYjbwXa2p01evHwFy5luovKcnsjV9-DYaTxBTStx_nPVfEMitJuLY5RW1mYvdySDmbm1BBOAUaC6ATIXAdvtV5PqRd3KMUmLyTUPkfZ-8gx6OwmlW8Rc2M17mYEKH0md_a3qxettPcWZE/s320/charge_logo.png" align="left" style="margin-right:10px"/></a>The <a href="http://www.chargeconsortium.com/"><strong>CHARGE</strong></a> - <strong>C</strong>ohorts for <strong>H</strong>eart and <strong>A</strong>ging <strong>R</strong>esearch in <strong>G</strong>enomic <strong>E</strong>pidemiology - consortium is the first of four human genetics consortia to hit ORCA this month.</p>
<p>I’m not really sure what tigers have to do with hearts or aging, or even charging for that matter, but it’s a nice logo. Coordinating research with that many participants must be challenging enough - I am not sure how you contrive an acronym and logo that everyone agrees with!</p>
<p>According to <a href="http://www.chargeconsortium.com/">the CHARGE consortium website</a>:</p>
<blockquote>
<p><i>"The Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium was formed to facilitate genome-wide association study meta-analyses and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies."</i></p>
</blockquote>
<ul>
<li>Psaty BM, O’Donnell CJ, Gudnason V, Lunetta KL, Folsom AR, Rotter JI, Uitterlinden AG, Harris TB, Witteman JCM, Boerwinkle E, on behalf of the CHARGE Consortium (2009) Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium: Design of prospective meta-analyses of genome-wide association studies from five cohorts. <a href="http://circgenetics.ahajournals.org/cgi/content/full/2/1/73"><em>Circ Cardiovasc Genet.</em> 2:73-80</a>. </li>
</ul>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-50537977281122225792014-09-18T13:47:00.001+10:002014-09-18T13:47:13.318+10:00PEPPER - Protein complex Expansion using Protein-Protein intERactions<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhw5EL8nBPFffVjSTM8xDhm0g0W9JpoH_jSg1rUDLkUW9vAOZUpn9PZF9_31b2T3F4CgZYQHlU3NpuALkI3Pd5SMvj27ftvfN71Eu1GXHapGuay5YONlO9e9AWXkRqu_NuwSZFqAUawSuU/s1600/pepper_logo.png" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhw5EL8nBPFffVjSTM8xDhm0g0W9JpoH_jSg1rUDLkUW9vAOZUpn9PZF9_31b2T3F4CgZYQHlU3NpuALkI3Pd5SMvj27ftvfN71Eu1GXHapGuay5YONlO9e9AWXkRqu_NuwSZFqAUawSuU/s320/pepper_logo.png" align="left" style="margin-right:20px"/></a>Another offering from the ever-fruitful world of bioinformatics today - with a fruit, fittingly enough.</p>
<p><strong>PEPPER</strong> - <strong>P</strong>rotein complex <strong>E</strong>xpansion using <strong>P</strong>rotein-<strong>P</strong>rotein int<strong>ER</strong>actions - pulls out all the stops when it comes to contriving a functional word, skipping words and using internal letters. </p>
<p>For the curious, PEPPER is <a href="http://apps.cytoscape.org/apps/pepper">available from the Cytoscape App Store</a> and is:</p>
<blockquote>
<p><em>“designed to identify protein complexes as densely connected subnetworks from seed lists of proteins derived from proteomic studies. Pepper identifies connected subgraph by using multi-objective optimization involving two functions: (i) the coverage, a solution must contain as many proteins from the seed as possible, (ii) the density, the proteins of a solution must be as connected as possible, using only interactions from a proteome-wide interaction network.”</em></p>
</blockquote>
<p>Despite its use of “seed lists”, I don’t think there is a direct connection with peppers, so PEPPER is being <a href="http://orcacronyms.blogspot.com.au/p/acronym-classification-acronyms-in-orca.html">classified</a> as an <em>ad hoc</em> intranym.</p>
<p>I’m not sure if there’s a bigger version of the logo available but if you look carefully, you can see the little chilli peppers.</p>
<blockquote>
<p>Winterhalter C <em>et al.</em> (2014) <a href="http://www.ncbi.nlm.nih.gov/pubmed/25138169?dopt=Abstract">PEPPER: cytoscape app for protein complex expansion using protein-protein interaction networks</a>. <i>Bioinformatics.</i> Aug 18. pii: btu517. [<a href="http://bioinformatics.oxfordjournals.org/content/early/2014/09/01/bioinformatics.btu517.long">Epub ahead of print</a>]</p>
</blockquote>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-965441738763886092014-07-04T22:25:00.000+10:002014-07-04T22:25:08.600+10:00WImpiBLAST - Web Interface for mpiBLAST<p>Although <a href="http://orcacronyms.blogspot.com.au/2014/07/blast-basic-local-alignment-search-tool.html">BLAST</a> is a deserved ORCAcronym in its own right, it is also notable for the number of spin-offs and add-ons that it has produced. One such program is <a href="http://www.mpiblast.org/">mpiBLAST</a>, an open-source parallelisation of BLAST. This is turn has spawned <strong>WImpiBLAST</strong> - <strong>W</strong>eb <strong>I</strong>nterface for <strong>mpiBLAST</strong>. I’m not sure if WImpiBLAST deserves a new “anti hoc” class of acronym, as parallelisation of BLAST on a supercomputer is anything but wimpy. <em>Ad hoc</em> will do for now.</p>
<p>You can find out more at <a href="http://www.rna-seqblog.com/wimpiblast-web-interface-for-mpiblast-to-help-biologists-perform-large-scale-annotation/">RNA-Seq Blog</a> or the paper:</p>
<ul>
<li>Sharma P & Mantri SS (2014) “<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0101144">WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing.</a>” <i>PLoS ONE</i> <b>9(6):</b> e101144.</li>
</ul>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-60857694029492601132014-07-04T22:12:00.000+10:002014-07-04T22:12:17.142+10:00BLAST - Basic Local Alignment Search Tool<p>If there is one bioinformatics program that every biologist has heard of, it is <a href="http://en.wikipedia.org/wiki/BLAST"><strong>BLAST</strong>: <strong>B</strong>asic <strong>L</strong>ocal <strong>A</strong>lignment <strong>S</strong>earch <strong>T</strong>ool</a>. In fact, BLAST is so popular and famous that many people probably don’t know that it is an acronym nor what it stands for; “to BLAST” has become a verb in common use. For non-biologists, BLAST is a homology search tool, which means that it finds similarities between biological (nucleotide or protein) sequences, and biologists will frequently “BLAST a sequence against a database” to find similar sequences.</p>
<p>The original BLAST algorithm is pretty old, which is part of the reason for its widespread fame. I’m not sure of the stats but the original Altschul <em>et al.</em> (1990) paper must be one of the most cited of all time.</p>
<ul>
<li>Altschul S, Gish W, Miller W, Myers E & Lipman D (1990). “<a href="http://www.ncbi.nlm.nih.gov/pubmed/2231712">Basic local alignment search tool</a>”. <i>Journal of Molecular Biology</i> <b>215 (3):</b> 403–410.</li>
</ul>
<p>Certainly a worth addition to ORCA. (Although the main motivation for adding it is for the next post!) Given that BLAST works by fragmenting the query sequence into pieces for the initial search, I think that it rates at least as a <em>post hoc</em>.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-91467477065026826892014-06-16T14:10:00.000+10:002014-06-16T14:10:46.853+10:00MFSPSSMpred - Masked, Filtered and Smoothed Position-Specific Scoring Matrix-based predictor<p>Today’s post is a bit odd, as it is an anti-ORCA acronym. There is a reason why contrived acronyms exist, and I think that <a href="http://www.biomedcentral.com/1471-2105/14/300">MFSPSSMpred</a> is a prime example. The acronym itself is <em>almost</em> informative, although it fails to identify what it is trying to predict. (Short molecular recognition features in this case.) Still, imagine yourself in a lab meeting, trying to tell your supervisor which prediction tool you were using from memory!</p>
<p>MFSPSSMpred does have one thing going for it, though, and that’s Google-friendliness. Providing you spell it right, that is!</p>
<p><em>P.S. Whilst Googling MFSPSSMpred, I discovered that <a href="http://orcacronyms.blogspot.co.uk/2013/08/jabba-just-another-bogus-bioinformatics.html">OCTAGON-winning Keith Bradnam</a> got there first and <a href="http://keithbradnam.com/blog/2013/10/8/new-recipient-of-the-just-another-bogus-bioinformatics-acron.html">MFSPSSMpred is a JABBA Award winner</a>!</em></p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-91240598559999159602014-05-21T20:12:00.001+10:002014-05-21T20:12:40.799+10:00ARENA - Australian Renewable ENergy Agency<p><strong>ARENA</strong> is the <a href="http://arena.gov.au/"><strong>A</strong>ustralian <strong>R</strong>enewable <strong>En</strong>ergy <strong>A</strong>gency</a>,</p>
<blockquote>
<p>an independent agency established by the Australian Government on 1 July 2012. We have two objectives: to improve the competitiveness of renewable energy technologies, and to increase the supply of renewable energy in Australia.</p>
</blockquote>
<p>Unfortunately, ARENA was one of the losers from the recent Australian budget and might not be around much longer.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-19192532383571885172014-05-07T20:59:00.000+10:002014-05-07T20:59:01.989+10:00HOTAIR - HOX Transcript Antisense RNA<p>According to <a href="http://en.wikipedia.org/wiki/HOTAIR">Wikipedia</a>:</p>
<blockquote>
<p>HOTAIR (for HOX antisense intergenic RNA) is a human gene located on chromosome 12. It is the first example of an RNA expressed on one chromosome that has been found to influence transcription on another chromosome.</p>
</blockquote>
<p>However, Wikipedia itself cites <a href="http://www.genecards.org/cgi-bin/carddisp.pl?gene=HOTAIR">Genecards</a>, which has a slightly different metanym expansion (without any missing letters) for <strong>HOTAIR</strong>: <strong>HO</strong>X <strong>T</strong>ranscript <strong>A</strong>nt<strong>i</strong>sense <strong>R</strong>NA. Either way, a very interesting gene and, though <em>ad hoc</em> intranym, certainly contrived enough for ORCA!</p>
<p>(HOTAIR possibly needs a new <a href="http://orcacronyms.blogspot.com.au/p/acronym-classification-acronyms-in-orca.html">ORCA classification</a> because both “metanym” sub-acronyms - HOX (<strong>H</strong>omeob<em><em>ox</em><em>) and RNA (<strong>R</strong>ibo</em><em>n</em></em>ucleic <strong>a</strong>cid) are themselves “itranyms”, as is HOTAIR.) </p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-24185105707981882042014-04-27T17:42:00.000+10:002014-04-27T17:42:27.358+10:00MODULUS - Methods Of Determining and Understanding Light elements from Unequivocal Stable isotope compositions<p><a href="http://orcacronyms.blogspot.com.au/2014/04/sesame-surface-electric-sounding-and.html">Another one</a> from <a href="http://en.wikipedia.org/wiki/Rosetta_(spacecraft)">Rosetta</a>, <strong>MODULUS</strong> - <strong>M</strong>ethods <strong>O</strong>f <strong>D</strong>etermining and <strong>U</strong>nderstanding <strong>L</strong>ight elements from <strong>U</strong>nequivocal <strong>S</strong>table isotope compositions - is described in <a href="http://beta.cosmosmagazine.com/space/all-set-our-first-comet-landing?utm_source=This+Week+in+Cosmos&utm_campaign=c6a721ef3f-This_week_in_Cosmos_7_April_20144_7_2014&utm_medium=email&utm_term=0_1df827744a-c6a721ef3f-112042229">Cosmos</a> as part of the <a href="http://www.esa.int/Our_Activities/Space_Science/Rosetta/MODULUS_PTOLEMY">PTOLEMY</a> instrumentation "to understand the geochemistry of light elements, such as hydrogen, carbon, nitrogen and oxygen".</p>
<p>That’s a lot of words and definitely an ORCA level of commitment to contrive a word out of it, even if they were not able to use them all!</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-39849842035326641942014-04-26T22:51:00.000+10:002014-04-26T22:51:08.428+10:00miRCat - miRNA Categoriser<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi0yEGhLer9RWiM9_cGCsZkqTPBygt9sim28r7El4LaSPYfbroyAM8I74eBzxWd9wLLlmxEK0kvVZNHbqlhnVM1ioza-f6vZxby-FBaIW0TE64Muo7fVMuYQCEeB7h1_ILYy0STGAyjj3A/s1600/meerkat_big.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi0yEGhLer9RWiM9_cGCsZkqTPBygt9sim28r7El4LaSPYfbroyAM8I74eBzxWd9wLLlmxEK0kvVZNHbqlhnVM1ioza-f6vZxby-FBaIW0TE64Muo7fVMuYQCEeB7h1_ILYy0STGAyjj3A/s320/meerkat_big.jpg" align="right" style="margin-left:10px"/></a>I am currently writing some lectures on RNA biology and came across the charmingly named <strong>miRCat</strong>: <strong>miR</strong>NA <strong>C</strong>ategoriser.</p>
<p>This is a meta-acronym, with miRNA being short for <a href="http://en.wikipedia.org/wiki/MicroRNA"><strong>mi</strong>cro<strong>RNA</strong> </a> (often abbreviated further to "miR" and pronounced “meer”, hence the logo) and RNA itself an acronym for <strong>R</strong>ibo<b>n</b>ucleic <strong>A</strong>cid).</p>
<blockquote>
<p>miRCat is a tool to identify miRNAs in high-throughput small RNA sequence data… miRCat takes a FASTA file of small RNA reads as input and will map them to a reference genome… The tool then looks at genomic hit distribution patterns and secondary structure of genomic regions corresponding to sRNA hits and will predict miRNAs and their precursor structures. </p>
</blockquote>
<p>Given the homophonic aspect of the acronym, I reckon this counts as <em>pre hoc</em>. As far as I am aware, “Categoriser” is not even a real (English) word, so this is definitely acronym contrivance worth of ORCA.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-78518470494147275192014-04-25T13:47:00.000+10:002014-04-25T13:47:18.317+10:00New ORCA acronym listings page<p>Just for a bit of extra organisation, there is now an <a href="http://orcacronyms.blogspot.com.au/p/acronyms.html">alphabetical listing of acronyms</a> featured in ORCA.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-61097579852905411602014-04-24T23:02:00.000+10:002014-04-24T23:02:37.778+10:00TARDIS - TARDigrades In Space<p>Yesterday’s <a href="http://orcacronyms.blogspot.com.au/2014/04/tardis-time-and-relative-dimension-in.html">TARDIS</a> post was preamble for another <strong>TARDIS</strong>: <a href="http://tardigradesinspace.blogspot.com.au/"><strong>Tard</strong>igrades <strong>i</strong>n <strong>S</strong>pace</a>. This TARDIS is science rather than science fiction and you can read about it at the Tardigrades In Space <a href="http://tardigradesinspace.blogspot.com.au/">blog.</a></p>
<blockquote>
<p>Tardigrades In Space or “TARDIS” is the first research project to evaluate the ability of tardigrades to survive under open space conditions. TARDIS is one of the projects within the Biopan-6 research platform provided by European Space Agency (ESA), and will be sent into space with the russian FOTON-M3 mission.</p>
</blockquote>
<p>Apparently, <a href="http://en.wikipedia.org/wiki/Tardigrade">Tardigrades</a> (a.k.a. “waterbears” or "moss piglets") can survive the vacuum and cosmic radiation of space.</p>
<p>h/t: This one is a <a href="http://orcacronyms.blogspot.com.au/p/submissions-to-orca-if-you-think-you-or.html">submission</a> from reader <a href="http://www.blogger.com/profile/10032370997576003348">vardis</a>.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-15304357141335906092014-04-23T22:13:00.000+10:002014-04-23T22:26:55.124+10:00TARDIS - Time And Relative Dimension In Space<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjtCpJ0r5aPjVie3yYAx3S8rid02Nri6ElDAG7UM43GeHWUsHLgRR9nf2vEVSFk8MK6doNmOCkzekGdBoNS2GVftSj9hStu5de_XbhZpuUZt09VUrwESEwaIvQC_dvWG96XVLFbOviI6lI/s1600/photo-756552.JPG"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjtCpJ0r5aPjVie3yYAx3S8rid02Nri6ElDAG7UM43GeHWUsHLgRR9nf2vEVSFk8MK6doNmOCkzekGdBoNS2GVftSj9hStu5de_XbhZpuUZt09VUrwESEwaIvQC_dvWG96XVLFbOviI6lI/s400/photo-756552.JPG" border="0" alt="" id="BLOGGER_PHOTO_ID_6005026814427225042" align="left" style="margin-right:20px"/></a>Like many geeks, I am a fan of the rebooted <a href="http://en.wikipedia.org/wiki/Doctor_Who">Dr Who</a> science fiction series.</p>
<p>As I suspect everyone with internet access knows, the Doctor’s spaceship-come-time-machine is the (or a) <a href="http://en.wikipedia.org/wiki/TARDIS"><strong>TARDIS</strong></a>: <strong>T</strong>ime <strong>A</strong>nd <strong>R</strong>elative <strong>D</strong>imension <strong>I</strong>n <strong>S</strong>pace.</p>
<p>It’s not my favourite acronym, I must admit, but it certainly is contrived. It is also a good excuse to share the photo on the left of the TARDIS in beautiful knitted form from the recent <a href="http://cabbagesofdoom.blogspot.co.uk/2014/04/the-royal-easter-show.html">Royal Easter Show</a> in Sydney. (Bravo, Andrew Galagher!) Mostly, though, it is a primer for the next ORCA post.</p>
<p>(NB. I always thought that the “Dimension” was plural but apparently not. I don’t really think that it makes sense in the singular but what do I know?)</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-51674524806872064132014-04-12T21:52:00.002+10:002014-04-23T22:20:32.566+10:00SESAME - Surface Electric Sounding and Acoustic Monitoring Experiment<p>As well as providing several years of geeky suspense from its launch in 2004 until its <a href="http://beta.cosmosmagazine.com/space/all-set-our-first-comet-landing?utm_source=This+Week+in+Cosmos&utm_campaign=c6a721ef3f-This_week_in_Cosmos_7_April_20144_7_2014&utm_medium=email&utm_term=0_1df827744a-c6a721ef3f-112042229">comet landing later this year</a>, the <a href="http://en.wikipedia.org/wiki/Rosetta_(spacecraft)">Rosetta mission</a> is replete with acronyms. One of the most ORCA-worthy of these is <strong>SESAME</strong>, the <a href="http://www.esa.int/Our_Activities/Space_Science/Rosetta/SESAME"><strong>S</strong>urface <strong>E</strong>lectric <strong>S</strong>ounding and <strong>A</strong>coustic <strong>M</strong>onitoring <strong>E</strong>xperiments</a>.</p>
<blockquote>
<p>Three instruments measure properties of the comet’s outer layers. The Cometary Acoustic Sounding Surface Experiment (CASSE) measures the way in which sound travels through the surface. The Permittivity Probe (PP) investigates its electrical characteristics, and the Dust Impact Monitor (DIM) measures dust falling back to the surface.</p>
</blockquote>
<p>Not a space-related word but still a good <em>ad hoc</em> algorithm.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-1018704634964348424.post-58186917255232625562014-04-01T22:09:00.000+11:002014-04-23T22:22:17.143+10:00TrIPE - T. rex International Paleontonomics Experiment (TrIPE)<a href="http://en.wikipedia.org/wiki/File:Tyrannoskull.jpg" ><img border="0" style="margin-right:10px" src="http://upload.wikimedia.org/wikipedia/commons/thumb/e/e4/Tyrannoskull.jpg/320px-Tyrannoskull.jpg" align="left"/></a><p>The <em><strong>T</strong>. <strong>r</strong>ex</em> <strong>I</strong>nternational <strong>P</strong>aleontonomics <strong>E</strong>xperiment (<strong>TrIPE</strong>) was responsible for the <a href="http://www.genomeweb.com/sanger-institute-releases-draft-sequence-tyrannosaurus-rex-genome"> <em>Tyrannosaurus rex</em> draft genome</a>, released on 1st April 2003 and described as “the genetic blueprint for the most important of the dinosaurs used in genetics today”. Unfortunately, it is no longer available on the <a href="http://www.ensembl.org/index.html">Ensembl genome database</a>, having been withdrawn for being totally fabricated. <big>☺</big></p>
<p><em>[Image from <a href="http://en.wikipedia.org/wiki/File:Tyrannoskull.jpg">Wikimedia Commons</a>]</em></p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0