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National Coalition Building Institute staff were getting things ready at Camp Watanopa phentermine n

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National Coalition Building Institute staff were getting things ready at Camp Watanopa phentermine near Georgetown Lake for their 7th annual high school Train-the-Trainer phentermine event. The event lasts all weekend and teaches students about how to lead antibullying, violence prevention and prejudice-reduction phentermine workshops. Two buses pulled into Camp Watanopa to drop off Missoula County Public School students. Big Sky High School student Mckayla Hansen was the first one off. "This is my second year," phentermine she said. But this isn't your average summer camp, it's the National Coalition Building Institute's annual Train-the-Trainer event. phentermine Students participate phentermine in workshops, do skits and share stories about their experiences. "It's a lot of just getting to know people, trying to create a safe environment for everyone," said Hansen. Ekoo Beck trains students to teach other students about social issues. She said students tend to listen more to people their own age. "It creates these amazing phentermine people who go on to do great things both within the community phentermine and thoughout the U.S.," said Beck. Big Sky teachers said they have seen the event change the way students view themselves and others. "This gives them confidence to step out," said Big Sky teacher Amy Miller. "And actually phentermine try out the new role as a leader, but more than anything I think what I see it do the most for students is have compassion for each other." "Seeing phentermine the kids change and look for conflict resolution and trying to avoid certain situations has been essential; it's just been really really eye-opening," said Big Sky teacher Mike Marcinkowski. It's not all about the workshops -- students have free time to play on the campground, have campfires phentermine or swim. Hansen said she leaves camp with a whole new level of confidence. "Going to something, anything I do with NCBI," said Hansen, "I feel like I walk away with a lot of empowerment and I feel like that really helps me with my leadership skills."
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Like many of the other NCBI resources, Retroviruses could be viewed as a bit long in the tooth these

Many people will have seen the NCBI Bookshelf , but it’s always a surprise to me that a resource of this quality has existed, for free, for so long. It’s also a reminder adn of how long I’ve been in this microbiology game and how much has changed.
Like many of the other NCBI resources, Retroviruses could be viewed as a bit long in the tooth these days. Certainly everything in it needs to be checked for currency by following citation trails to later knowledge (you do have the information skills that allow you to do that, don’t you?) but as an authorative resource it’s second to none.
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This entry was posted on Friday, July 25th, 2014 at 10:17 am and is filed under Events , Resources .

Two Upcoming NCBI Webinars on July 30 and Aug. 13 « Louise M. Darling Biomedical Library Blog
NLM s National Center for Biotechnology Information (NCBI) is hosting two upcoming webinars. On July 30, 12:00-1:30 PM PDT, is the session BLAST in the Cloud, which will showcase the experimental NCBI-BLAST Amazon Machine Image (AMI) to configure hardware for BLAST searches using the Amazon Elastic Compute Cloud (EC2). Further rutracker details and registration information are available here . On August 13, 10-11:00 AM PDT, is the session Using the New NCBI Variation Viewer to Explore Human Genetic Variation. Details are available here .
This entry was posted on Friday, July 25th, 2014 at 10:17 am and is filed under Events , Resources . You can follow any responses rutracker to this entry through the RSS 2.0 feed. You can leave a response , or trackback from your own site.
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All of this might make you wonder, are there any decent PubMed puns left? Here

Punning with the Pub in PubMed: Are there any decent NCBI puns left? #PubMedPuns | O'Really?
Filed under: data mining , Googleology , paperware , publishing , Science , technology hepatitis b — Duncan Hull @ 10:31 am Tags: Casey Bergman hepatitis b , defrosting , Elizabeth Gibney , gastropub , google scholar , Johanna McEntyre , Karsten Hokamp , Ken Wolfe , Leo Chalupa , Mark Gerstein , Phil Bourne , portmanteau , pubbit , Pubble , PubBrawl , pubby , PubCast , pubchase , pubclean , PubCrawl , pubcrawler , pubfetch , PubFig , PubFight , pubgames , publican , PubLick , publunch , Publy , PubManteau , PubMatch , pubmed , PubMedication , PubMine , pubnet , pubpeer , PubQuiz , PubSCIENCE , pubsearch , PubSnacks , PubSnax , PubSoft , PubSort , Pubsy , Richard van Noorden , RSS , text mining , twitter , twitterbot
Many people claim they get all their best ideas in the pub, but for lots of scientists their best ideas probably come from PubMed.gov – the NCBI’s monster database of biomedical literature. Consequently, the database has spawned a whole slew of tools that riff off the PubMed name, with many puns and portmanteaus (aka PubManteaus ), and the pub-based wordplays are very common. [1,2]
All of this might make you wonder, are there any decent PubMed puns left? Here’s an incomplete collection: PubCrawler pubcrawler.ie goes to the library while you go to the pub… [3,4] PubChase pubchase.com is a life sciences and medical literature recommendations engine. Search smarter, organize, and discover the articles most important to you. [5] PubCast scivee.tv/pubcasts allow users to enliven articles and help drive more views (to PubMed) [6] PubFig nothing to do with PubMed, but research done on face and image recognition that happens to be indexed by PubMed. [7] PubGet pubget.com is a comprehensive source for science PDFs, including everything you’d find in Medline. [8] PubMine supports intelligent knowledge discovery [9] PubNet pubnet.gersteinlab.org is a web-based tool that extracts several types of relationships returned hepatitis b by PubMed queries and maps them into networks aka a publication network graph utility. [10] GastroPub repackages and re-sells ordinary PubMed content disguised as high-end luxury data at a higher premium, similar to a Gastropub . PubQuiz is either the new name for NCBI database search www.ncbi.nlm.nih.gov/gquery or a quiz where you’re only allowed to use PubMed hepatitis b to answer questions. PubSearch & PubFetch allows hepatitis b users to store literature, keyword, and gene information in a relational hepatitis b database, index the literature with keywords and gene names, and provide hepatitis b a Web user interface for annotating the genes from experimental data found in the associated literature [11] PubScience is either “peer-reviewed drinking” courtesy of pubsci.co.uk or an ambitious publishing project tragically axed by the U.S. Department of Energy (DoE). [12,13] PubSub is anything that makes use of the publish subscribe hepatitis b pattern , such as NCBI feeds . [14] PubLick as far as I can see, hasn’t been used yet, unless you count this @publick on twitter . If anyone was launching a startup, working in the area of licking the tastiest data out of PubMed, that could be a great name for their data-mining business. Alternatively, it could be a catchy new nickname hepatitis b for PubMedCentral (PMC) or Europe PubMedCentral (EuropePMC) [15] – names which don’t exactly trip off the tongue. Since PMC is a free digital archive of publicly accessible full-text scholarly articles, PubLick seems like a appropriate moniker.
There’s probably lots more PubMed puns and portmanteaus out there just waiting hepatitis b to be used. Pubby, Pubsy, PubLican, Pubble, Pubbit, hepatitis b Publy, PubSoft, PubSort, PubBrawl, hepatitis b PubMatch, PubGames, PubGuide, PubWisdom, PubTalk, PubChat, PubShare, PubGrub, PubSnacks and PubLunch could all work. If you’ve know of any other decent (or dodgy) PubMed puns, leave them in the comments below and go and build a scientific twitterbot or cool tool using the same name if you haven’t already. References Lu Z. (2011). PubMed and beyond: a survey of web tools for searching biomedical literature., Database: The Journal of Biological Databases hepatitis b and Curation, hepatitis b http://pubmed.gov/21245076 Hull D., Pettifer S.R. & Kell D.B. (2008). Defrosting the digital hepatitis b library: bibliographic tools for the next generation web., PLOS Computational Biology, PMID: http://pubmed.gov/18974831 Hokamp K. & Wolfe K.H. (2004) PubCrawler: keeping up comfortably with PubMed hepatitis b and GenBank., Nucleic acids research, http://pubmed.gov/15215341 Hokamp K. & Wolfe K. (1999) What’s new in the library? What’s hepatitis b new in GenBank? let PubCrawler tell you., Trends in Genetics, http://pubmed.gov/10529811 Gibney E. (2014). How to tame the flood of literature., Nature, 513 (7516) http://pubmed.gov/25186906 Bourne P. & Chalupa L. (2008). A new approach to scientific dissemination, Materials

We plan to consistently support the approach of having a full set of RNA products represented in our

You probably haven t spent much time thinking about how we represent genes in a genomic cna reference sequence context. And by genes, I really mean transcripts since genes are just a collection of transcripts that produce the same product.
But in fact, there is more complexity here than you ever really wanted to know about. cna Andrew Jesaitis covered some of this in detail as he dove deep in the analysis of variant cna annotation against transcripts in his recent post The State of Variant Annotation: A Comparison of AnnoVar, snpEff and VEP .
The databases that catalog and provide labels for transcripts are really cna cataloging transcribed RNA, like you might identify from a RNA-Seq experiment, cna as well as the spliced and translated protein products. To represent these RNA sequences in genomic space we must actually take a step backward. In fact, it takes a special type of alignment algorithm (see my webcast on alignment algorithms , the same family of algorithms are applied to this problem).
First cna we have our new RefSeq Genes track that I will be discussing in this post. This is built off of a GFF file that is part of the NCBI Human Annotation Release 105 using NCBI s Splign algorithm. The second track is the latest Ensembl release cna on GRCh37, which uses the Ensembl genebuild algorithm, and finally cna the UCSC alignments of the same RNA using their BLAT algorithm.
You can see they disagree on how to handle a gap between the NM_006331 transcript s RNA sequence and the human genomic sequence. The Ensembl alignments most correctly preserve the actual protein sequence of NP_006322.4 in this case by introducing a 2bp intron (which has no real biological reality). Note that given this is in the first exon, this disagreement extends for the rest of the protein sequence.
Of course, they are trying to do the best with a bad situation where the reference sequence is not ideal. In fact, this is a great example of the real improvements of the latest GRCh38 reference sequence. It incorporated a patch that changes the local sequence at this region. You can see the same gene with all three algorithms agreeing on simple alignment with the GRCh38 genomic reference:
In our latest release of Golden Helix SVS 8.2.0 and GenomeBrowse 2.0.4, we shipped by default the RefSeq Genes from NCBI Human Annotation 105 as the default gene track. Going forward we will curate RefSeq genes from NCBI directly and no longer from UCSC.
There are a few of reasons we believe this to be the right path going forward: NCBI provides mitochondrial gene mappings to NC_012920.1; the MT referenced used in GRCh37_g1k and GRCh38 that nearly all NGS alignment is done with. NCBI has official releases of annotations for species, compared cna to UCSC more continuously changing approach. NCBI provides extremely good cross references for their transcripts with other resources, providing great hyperlinks and summary information for analysis. The NCBI set of alignments includes more non-coding transcripts such as microRNA, tRNA as well as various annotations of transcripts such as pseudo cna and predicted .
The UCSC provided RefSeq genes does not actually provide any mitochondrial gene annotations. As inherieted mitochondrial gene disorders are testable with NGS gene panels, it s important to provide as much annotation support for Dx tests based on variant data.
The Revised Cambridge Reference Sequence ( rCRS ) has been adopted by the community (and now by GRCh in 38) as the standard reference to use, and probably would have been used by UCSC if it was available when they defined their hg19 reference (and decided not to update hg19 when it was clear that rCRS was the way forward).
We plan to consistently support the approach of having a full set of RNA products represented in our gene track with predicted mRNA, pseudo (incomplete) RNAs and non-coding RNAs all intermixed. To achieve this, we took great care to provide extra fields to the track that allow for easy identification and filtering of the type of transcript you are interested in.
In this way, we updated our Variant Classification algorithm in SVS 8.2.0 to by default only annotate non-predicted, protein coding transcripts (that will have NM_ transcript identifiers). This brings RefSeq cna in line with the Ensembl gene track which similarly has been inclusive of incomplete and predicted transcripts.
Here are the stats of the RefSeq Genes 105 transcript set by type: Transcript Type Count mRNA (NM_*) 34,663 mRNA Predicted (XM_*) 30,077 microRNA 1,501 ncRNA (rRNA, tRNA, other) 7,090 Puedo, incomplete cna 11,619 Total 84,950
While I could write many posts on the difficulties of dealing cna with the GFF file NCBI produced, it was worth the effort to handle the many edge cases which demanded cna special parsing to produce our latest default gene track. The extra annotations cna provided by NCBI have been cleaned up and hyperlinked to provide a platform for exploring a gene and its

Minister Fitzgerald signs of pregnancy said:

with Aoibhinn Breslin & her mum Caitriona Local TD Frances Fitzgerald paid a visit to the National Council for the Blind (NCBI) Solas Early Learning Centre, Clondalkin on Friday 19th September, signs of pregnancy meeting students, staff, parents and NCBI management to discuss the “great work being done to support the educational needs of children with sight loss and visual impairment”. The Solas Early Learning Centre has been open since 2003. What started out as an activity room and a computer room now includes a state-of-the-art multi-sensory room and a garden with a sensory area and climbing apparatus. The programmes provided by NCBI at the centre, signs of pregnancy and through its work with children nationally, facilitate each child’s individual needs, focusing on daily living, learning and play, all designed to encourage independence.
Minister Fitzgerald signs of pregnancy said: “I was most favourably impressed by the range of activities, supports and equipment available to students at the Solas Centre. Meeting with the Centre staff and NCBI officials gave a thorough overview signs of pregnancy of the education on offer and how their programmes signs of pregnancy have been designed, while a wide-ranging discussion signs of pregnancy with parents really emphasised how valuable signs of pregnancy this has been for their children’s development. “I commend Margaret and her colleagues for the vital service they provide, and will work with them to ensure that their efforts are supported wherever possible.
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