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• Third-party open-source projects in .NET and Ruby and NIH syndrome

  - by Anton Gogolev

  The title might seem to be inflammatory, but it's here to catch your eye after all. I'm a professional .NET developer, but I try to follow other platforms as well. With Ruby being all hyped up (mostly due to Rails, I guess) I cannot help but compare the situation in open-source projects in Ruby and .NET. What I personally find interesting is that .NET developers are for the most part severely suffering from the NIH syndrome and are very hesitant to use someone else's code in pretty much any shape or form. Comparing it with Ruby, I see a striking difference. Folks out there have gems literally for every little piece of functionality imaginable. New projects are popping out left and right and generally are heartily welcomed. On the .NET side we have CodePlex which I personally find to be a place where abandoned projects grow old and eventually get abandoned. Now, there certainly are several well-known and maintained projects, but the number of those pales in comparison with that of Ruby. Granted, NIH on the .NET devs part comes mostly from the fact that there are very few quality .NET projects out there, let alone projects that solve their specific needs, but even if there is such a project, it's often frowned upon and is reinvented in-house. So my question is multi-fold: Do you find my observations anywhere near being correct? If so, what are your thoughts on quality and quantitiy of OSS projects in .NET? Again, if you do agree with my thoughts on "NIH in .NET", what do you think is causing it? And finally, is it Ruby's feature set & community standpoint (dynamic language, strong focus on testing) that allows for such easy integration of third-party code?

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• How can I tackle 'profoundly found elsewhere' syndrome (inverse of NIH)?

  - by Alistair Knock

  How can I encourage colleagues to embrace small-scale innovation within our team(s), in order to get things done quicker and to encourage skills development? (the term 'profoundly found elsewhere' comes from Wikipedia, although it is scarcely used anywhere else apart from a reference to Proctor & Gamble) I've worked in both environments where there is a strong opposition to software which hasn't been developed in-house (usually because there's a large community of developers), and more recently (with far fewer central developers) where off-the-shelf products are far more favoured for the usual reasons: maintenance, total cost over product lifecycle, risk management and so on. I think the off the shelf argument works in the majority of cases for the majority of users, even though as a developer the product never quite does what I'd like it to do. However, in some cases there are clear gaps where the market isn't able to provide specifically what we would need, or at least it isn't able to without charging astronomical consultancy rates for a bespoke solution. These can be small web applications which provide a short-term solution to a particular need in one specific department, or could be larger developments that have the potential to serve a wider audience, both across the organisation and into external markets. The problem is that while development of these applications would be incredibly cheap in terms of developer hours, and delivered very quickly without the need for glacial consultation, the proposal usually falls flat because of risk: 'Who'll maintain the project tracker that hasn't had any maintenance for the past 7 years while you're on holiday for 2 weeks?' 'What if one of our systems changes and the connector breaks?' 'How can you guarantee it's secure/better/faster/cheaper/holier than Company X's?' With one developer behind these little projects, the answers are invariably: 'Nobody, but...' 'It will break, just like any other application would...' 'I, uh...' How can I better answer these questions and encourage people to take a little risk in order to stimulate creativity and fast-paced, short-lifecycle development instead of using that 6 months to consult about what tender process we might use?

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• PeopleSoft Grants & the Federal Agency Letter of Credit Draw Changes

  - by Mark Rosenberg

  For decades, most, if not all, US Federal agencies that sponsor research allowed grant recipients to request and receive payments using pooled accounts, commonly known as pooled letter of credit (LOC) draws. This enabled organizations, such as universities and hospitals, fast and efficient access to reimbursement of the expenditures they incurred conducting research across a portfolio of grants. To support this business practice, the PeopleSoft Grants solution has delivered an LOC Draw report to provide the total request amount along with all of the supporting invoice details for reconciliation and audit purposes. Now, in an attempt to provide greater transparency, eliminate fraud, strengthen accountability for grant-related financial transactions, and simplify grant award closeout, many US Federal sponsors are transitioning from the “pooling” letter of credit draw method to requesting on a “grant-by-grant” basis. The National Science Foundation, the second largest issuer of Federal awards, already transitioned to detailed grant draws in 2013. And, in response to the U.S. Department of Health and Human Services (HHS) directive to HHS-supported Agencies, the largest Federal awards sponsor, the National Institutes of Health (NIH), will fully transition to the new HHS subaccount draw method. This will require NIH award recipients to request payments based on actual expenses incurred on an award-by-award basis. NIH is expected to fully transition to this new draw method by the end of Federal fiscal year 2015.  (The NIH had planned to fully transition to this new method by the end of fiscal 2014; however, the impact to institutions was deemed to be significant enough that a reprieve was recently granted.) In light of these new Federal draw requirements, we have recently released these new features to aid our customers on both PeopleSoft Grants releases 9.1 and 9.2:1. Federal Award Identification Number on the Proposal and Award Profile 2. Letter of credit fields on contract lines to support award basis draws and comply with Federal close out mandates3. Process to produce both pro forma and final LOC Draw Reports in BI Publisher report format4. Subacccount ID field on the LOC Summary and a new BI Publisher version of the LOC Summary report 5. Added Subaccount Field and contract info to be displayed on the LOC summary page6. Ability to generate by a variety of dimensions pro forma and invoiced draw listings 7. Queries for generation and manipulation of data to upload into sponsor payment request systems and perform payment matching8. Contracts LOC Close Out query to quickly review final balances prior to initiating final draws and preparing Federal Financial Reports prior to close The PeopleSoft Development team actively monitors this and other major Federal changes and continues working closely with the Grants Product Advisory Group of the Higher Education User Group to ensure a clear understanding of what our customers need in order to transition to new approaches for doing business with the Federal government. For more information regarding the enhancements to the PeopleSoft Grants solution, existing customers can login to My Oracle Support and review the Enhancements to Letter of Credit Process (Doc ID 1912692.1) associated with resolution ID 904830. This enhanced LOC functionality is available in both PeopleSoft FSCM 9.1 Bundle #31 and PeopleSoft FSCM 9.2 Update Image 8.

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• Python finding index in a array

  - by NIH

  I am trying to see if a company from a list of companies is in a line in a file. If it is I utilize the index of that company to increment a variable in another array. The following is my python code. I keep getting the following error: AttributeError: 'set' object has no attribute 'index'. I cannot figure out what is going wrong and think the error is the line that is surrounded by **. companies={'white house black market', 'macy','nordstrom','filene','walmart'} positives=[0 for x in xrange(len(companies))] negatives=[0 for x in xrange(len(companies))] for line in f: for company in companies: if company in line.lower(): words=tokenize.word_tokenize(line) bag=bag_of_words(words) classif=classifier.classify(bag) if classif=='pos': **indice =companies.index(company)** positives[indice]+=1 elif classif=='neg': **indice =companies.index(company)** negatives[indice]+=1

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• How can I use Qt to get html code of the redirected page??

  - by Claire Huang

  I'm trying to use Qt to download the html code from the following url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=AB100362 this url will re-direct to www.ncbi.nlm.nih.gov/nuccore/27884304 I try to do it by following way, but I cannot get anything. it works for some webpage such as www.google.com, but not for this NCBI page. is there any way to get this page?? QNetworkReply::NetworkError downloadURL(const QUrl &url, QByteArray &data) { QNetworkAccessManager manager; QNetworkRequest request(url); QNetworkReply *reply = manager.get(request); QEventLoop loop; QObject::connect(reply, SIGNAL(finished()), &loop, SLOT(quit())); loop.exec(); if (reply->error() != QNetworkReply::NoError) { return reply->error(); } data = reply->readAll(); delete reply; return QNetworkReply::NoError; } void GetGi() { int pos; QString sGetFromURL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"; QUrl url(sGetFromURL); url.addQueryItem("db", "nucleotide"); url.addQueryItem("cmd", "search"); url.addQueryItem("term", "AB100362"); QByteArray InfoNCBI; int errorCode = downloadURL(url, InfoNCBI); if (errorCode != 0 ) { QMessageBox::about(0,tr("Internet Error "), tr("Internet Error %1: Failed to connect to NCBI.\t\nPlease check your internect connection.").arg(errorCode)); return "ERROR"; } }

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• How can I use Qt to get html code of this NCBI page??

  - by user308503

  I'm trying to use Qt to download the html code from the following url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=AB100362 this url will re-direct to www.ncbi.nlm.nih.gov/nuccore/27884304 I try to do it by following way, but I cannot get anything. it works for some webpage such as www.google.com, but not for this NCBI page. is there any way to get this page?? QNetworkReply::NetworkError downloadURL(const QUrl &url, QByteArray &data) { QNetworkAccessManager manager; QNetworkRequest request(url); QNetworkReply *reply = manager.get(request); QEventLoop loop; QObject::connect(reply, SIGNAL(finished()), &loop, SLOT(quit())); loop.exec(); if (reply->error() != QNetworkReply::NoError) { return reply->error(); } data = reply->readAll(); delete reply; return QNetworkReply::NoError; } void GetGi() { int pos; QString sGetFromURL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"; QUrl url(sGetFromURL); url.addQueryItem("db", "nucleotide"); url.addQueryItem("cmd", "search"); url.addQueryItem("term", "AB100362"); QByteArray InfoNCBI; int errorCode = downloadURL(url, InfoNCBI); if (errorCode != 0 ) { QMessageBox::about(0,tr("Internet Error "), tr("Internet Error %1: Failed to connect to NCBI.\t\nPlease check your internect connection.").arg(errorCode)); return "ERROR"; } }

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• "fopen: No such file or directory" error

  - by Akshay Bhat

  I am getting following cryptic error: akshay@akshay-VirtualBox:/mnt/mmpp$ ./bin/metamap10 /mnt/mmpp/bin/SKRrun.10 -L 2010 /mnt/mmpp/bin/metamap10.BINARY.Linux -Z 10 --debug input.txt fopen: No such file or directory does this error implies that it cannot fopen cannot find a required file or fopen itself is nonexistent, note that both SKRrun.10 and metamap10.BINARY.Linux are present at the correct location I am using this software http://metamap.nlm.nih.gov/ on Ubuntu.

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• How can I extract paragaphs and selected lines with Perl?

  - by neversaint

  I have a text where I need to: to extract the whole paragraph under the section "Aceview summary" until the line that starts with "Please quote" (not to be included). to extract the line that starts with "The closest human gene". to store them into array with two elements. The text looks like this (also on pastebin): AceView: gene:1700049G17Rik, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView. <META NAME="title" CONTENT=" AceView: gene:1700049G17Rik a comprehensive annotation of human, mouse and worm genes with mRNAs or EST"> <META NAME="keywords" CONTENT=" AceView, genes, Acembly, AceDB, Homo sapiens, Human, nematode, Worm, Caenorhabditis elegans , WormGenes, WormBase, mouse, mammal, Arabidopsis, gene, alternative splicing variant, structure, sequence, DNA, EST, mRNA, cDNA clone, transcript, transcription, genome, transcriptome, proteome, peptide, GenBank accession, dbest, RefSeq, LocusLink, non-coding, coding, exon, intron, boundary, exon-intron junction, donor, acceptor, 3'UTR, 5'UTR, uORF, poly A, poly-A site, molecular function, protein annotation, isoform, gene family, Pfam, motif ,Blast, Psort, GO, taxonomy, homolog, cellular compartment, disease, illness, phenotype, RNA interference, RNAi, knock out mutant expression, regulation, protein interaction, genetic, map, antisense, trans-splicing, operon, chromosome, domain, selenocysteine, Start, Met, Stop, U12, RNA editing, bibliography"> <META NAME="Description" CONTENT= " AceView offers a comprehensive annotation of human, mouse and nematode genes reconstructed by co-alignment and clustering of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes, their functions, alternative variants, expression, regulation and interactions, in the hope to stimulate further validating experiments at the bench "> <meta name="author" content="Danielle Thierry-Mieg and Jean Thierry-Mieg, NCBI/NLM/NIH, [email protected].nih.gov"> <!-- var myurl="av.cgi?db=mouse" ; var db="mouse" ; var doSwf="s" ; var classe="gene" ; //--> However I am stuck with the following script logic. What's the right way to achieve that? #!/usr/bin/perl -w my $INFILE_file_name = $file; # input file name open ( INFILE, '<', $INFILE_file_name ) or croak "$0 : failed to open input file $INFILE_file_name : $!\n"; my @allsum; while ( <INFILE> ) { chomp; my $line = $_; my @temp1 = (); if ( $line =~ /^ AceView summary/ ) { print "$line\n"; push @temp1, $line; } elsif( $line =~ /Please quote/) { push @allsum, [@temp1]; @temp1 = (); } elsif ($line =~ /The closest human gene/) { push @allsum, $line; } } close ( INFILE ); # close input file # Do something with @allsum There are many files like that I need to process.

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• Please recommend PDU SMS format code or library for .NET or C++

  - by Pavel Radzivilovsky

  I have been searching a lot for a chunk of code, or a library to format SMS messages in PDU format and had little luck. They were either huge monsters with terrific dependencies on everything way above my requirements and a very obscure interface, totally not justifying the straight-forward, although rather complex encoding. Being on the edge of creating a NIH, my question is - have encountered the same problem and how have you solved it?

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• How to access members of an rdf list with rdflib (or plain sparql)

  - by tjb

  What is the best way to access the members of an rdf list? I'm using rdflib (python) but an answer given in plain SPARQL is also ok (this type of answer can be used through rdfextras, a rdflib helper library). I'm trying to access the authors of a particular journal article in rdf produced by Zotero (some fields have been removed for brevity): <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:z="http://www.zotero.org/namespaces/export#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bib="http://purl.org/net/biblio#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:prism="http://prismstandard.org/namespaces/1.2/basic/" xmlns:link="http://purl.org/rss/1.0/modules/link/"> <bib:Article rdf:about="http://www.ncbi.nlm.nih.gov/pubmed/18273724"> <z:itemType>journalArticle</z:itemType> <dcterms:isPartOf rdf:resource="urn:issn:0954-6634"/> <bib:authors> <rdf:Seq> <rdf:li> <foaf:Person> <foaf:surname>Lee</foaf:surname> <foaf:givenname>Hyoun Seung</foaf:givenname> </foaf:Person> </rdf:li> <rdf:li> <foaf:Person> <foaf:surname>Lee</foaf:surname> <foaf:givenname>Jong Hee</foaf:givenname> </foaf:Person> </rdf:li> <rdf:li> <foaf:Person> <foaf:surname>Ahn</foaf:surname> <foaf:givenname>Gun Young</foaf:givenname> </foaf:Person> </rdf:li> <rdf:li> <foaf:Person> <foaf:surname>Lee</foaf:surname> <foaf:givenname>Dong Hun</foaf:givenname> </foaf:Person> </rdf:li> <rdf:li> <foaf:Person> <foaf:surname>Shin</foaf:surname> <foaf:givenname>Jung Won</foaf:givenname> </foaf:Person> </rdf:li> <rdf:li> <foaf:Person> <foaf:surname>Kim</foaf:surname> <foaf:givenname>Dong Hyun</foaf:givenname> </foaf:Person> </rdf:li> <rdf:li> <foaf:Person> <foaf:surname>Chung</foaf:surname> <foaf:givenname>Jin Ho</foaf:givenname> </foaf:Person> </rdf:li> </rdf:Seq> </bib:authors> <dc:title>Fractional photothermolysis for the treatment of acne scars: a report of 27 Korean patients</dc:title> <dcterms:abstract>OBJECTIVES: Atrophic post-acne scarring remains a therapeutically challe *CUT*, erythema and edema. CONCLUSIONS: The 1550-nm erbium-doped FP is associated with significant patient-reported improvement in the appearance of acne scars, with minimal downtime.</dcterms:abstract> <bib:pages>45-49</bib:pages> <dc:date>2008</dc:date> <z:shortTitle>Fractional photothermolysis for the treatment of acne scars</z:shortTitle> <dc:identifier> <dcterms:URI> <rdf:value>http://www.ncbi.nlm.nih.gov/pubmed/18273724</rdf:value> </dcterms:URI> </dc:identifier> <dcterms:dateSubmitted>2010-12-06 11:36:52</dcterms:dateSubmitted> <z:libraryCatalog>NCBI PubMed</z:libraryCatalog> <dc:description>PMID: 18273724</dc:description> </bib:Article> <bib:Journal rdf:about="urn:issn:0954-6634"> <dc:title>The Journal of Dermatological Treatment</dc:title> <prism:volume>19</prism:volume> <prism:number>1</prism:number> <dcterms:alternative>J Dermatolog Treat</dcterms:alternative> <dc:identifier>DOI 10.1080/09546630701691244</dc:identifier> <dc:identifier>ISSN 0954-6634</dc:identifier> </bib:Journal>

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• Saving html page from MATLAB web browser

  - by yuk

  Following this question I get a message on the retrieved page that "Your browser does not support JavaScript so some functionality may be missing!" If I open this page with web(url) in MATLAB web browser and accept certificate (once per session), the page opens properly. How can I save the page source from the browser with a script? Or from system browser? Or may be there is a way to get that page even without browser? url='https://cgwb.nci.nih.gov/cgi-bin/hgTracks?position=chr7:55054218-55242525';

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• How to enable 'wget' to download the whole content of HTML with Javascript

  - by neversaint

  I have a site which I want to download using Unix wget. If you look at the source code and content of the file it contain section called SUMMARY. However after issuing a wget command like this: wget -O downdloadedtext.txt http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=mouse&c=gene&a=fiche&l=2610008E11Rik The content of the downdloadedtext.txt is incomplete and different with the source code of that site. For example it doesn't contain SUMMARY section. Is there a correct way to obtain the full content correctly? The reason I ask this because I want to automate the download from different values in that HTML.

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• Getting data into MATLAB from HTTPS

  - by yuk

  Anybody know if it's possible? I'm trying to get the data by using the following code url = 'https://cgwb.nci.nih.gov/cgi-bin/hgTracks'; params = {'org','Human','db','hg18','position','EGFR'}; urltxt = urlread(url,'get',params); but get the error ??? Error using ==> urlread at 111 Error downloading URL. Your network connection may be down or your proxy settings improperly configured. If I substitute https to http, it works, but I get "301 Moved Permanently" page with the above https-link. The link in browser works properly in both cases (redirecting http request). The site does not require any authentication. May be there are other ways than urlread?

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• Career Change Need Advice: Professional Web Developer

  - by bikedorkseattle

  I'm hoping to get some advice here on the steps I should take to make a career change into professional web development. I've been working in cancer research the last 14 years and I need a change. The job market is terrible, the pay is worse, and despite what one would think the atmosphere is generally un-collegial, even in your own group. Venture funding never returned after the dot com burst and with 3 to 5 wars our country is now in, NIH funding is only going to get worse. I know things are not going to get better for my field, sadly, and I know I need to move on. For probably just as long I have fiddled around with web development, I even run a fairly popular site with close to 1 million/month pageviews that pulls a decent income, but not stable enough to live off of right now. My skills are ok for being self taught. I enjoy the fast paced nature of the web and the tools the community creates and how eager people are to help and share knowledge; it's what science should be. I have been trying to find an entry level developer job doing standard HTML/CSS/PHP/MySQL/JS/jQuery type work. A good 50%+ of the jobs want someone with a CS degree, and most want 5 years experience. Having no professional experience and no formal education, I know I'm at a huge disadvantage. I am now considering my options on how to move forward professionally. The way I see it I have basically 3 options. Build up my portfolio of work as much as I can and continue to learn as much as I can on my own. Try to contribute on some open source project when time allows. Network like crazy and go to meetups. Be confident and pray a lot in private. OR While doing above, do some certification programs in PHP and Java, possibly others. Get a Zend Certification. OR Spend a few years getting a CS degree while doing 1. I've already done the work fulltime go to school thing and it doesn't excite me one bit. I didn't have the greatest college experience and am not too eager to return, but I have a family to feed. Is the degree really necessary or is it more of a right of passage type thing in most instances? I appreciate everyones input. Thanks for taking the time to respond.

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• How can I do batch image processing with ImageJ in Java or clojure?

  - by Robert McIntyre

  I want to use ImageJ to do some processing of several thousand images. Is there a way to take any general imageJ plugin and apply it to hundreds of images automatically? For example, say I want to take my thousand images and apply a polar transformation to each--- A polar transformation plugin for ImageJ can be found here: http://rsbweb.nih.gov/ij/plugins/polar-transformer.html Great! Let's use it. From: [http://albert.rierol.net/imagej_programming_tutorials.html#How%20to%20automate%20an%20ImageJ%20dialog] I find that I can apply a plugin using the following: (defn x-polar [imageP] (let [thread (Thread/currentThread) options ""] (.setName thread "Run$_polar-transform") (Macro/setOptions thread options) (IJ/runPlugIn imageP "Polar_Transformer" ""))) This is good because it suppresses the dialog which would otherwise pop up for every image. But running this always brings up a window containing the transformed image, when what I want is to simply return the transformed image. The stupidest way to do what I want is to just close the window that comes up and return the image which it was displaying. Does what I want but is absolutely retarded: (defn x-polar [imageP] (let [thread (Thread/currentThread) options ""] (.setName thread "Run$_polar-transform") (Macro/setOptions thread options) (IJ/runPlugIn imageP "Polar_Transformer" "") (let [return-image (IJ/getImage)] (.hide return-image) return-image))) I'm obviously missing something about how to use imageJ plugins in a programming context. Does anyone know the right way to do this? Thanks, --Robert McIntyre

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• How to set QNetworkReply properties to get correct NCBI pages?

  - by Claire Huang

  I try to get this following url using the downloadURL function: http://www.ncbi.nlm.nih.gov/nuccore/27884304 But the data is not as what we can see through the browser. Now I know it's because that I need to give the correct information such as browser, how can I know what kind of information I need to set, and how can I set it? (By setHeader function??) In VC++, we can use CInternetSession and CHttpConnection Object to get the correct information without setting any other detail information, is there any similar way in Qt or other cross-platform C++ network lib?? (Yes, I need the the cross-platform property.) QNetworkReply::NetworkError downloadURL(const QUrl &url, QByteArray &data) { QNetworkAccessManager manager; QNetworkRequest request(url); request.setHeader(QNetworkRequest::ContentTypeHeader ,"Mozilla/5.0 (Windows; U; Windows NT 6.0; en-US; rv:1.9.1.7) Gecko/20091221 Firefox/3.5.7 (.NET CLR 3.5.30729)"); QNetworkReply *reply = manager.get(request); QEventLoop loop; QObject::connect(reply, SIGNAL(finished()), &loop, SLOT(quit())); loop.exec(); QVariant statusCodeV = reply->attribute(QNetworkRequest::RedirectionTargetAttribute); QUrl redirectTo = statusCodeV.toUrl(); if (!redirectTo.isEmpty()) { if (redirectTo.host().isEmpty()) { const QByteArray newaddr = ("http://"+url.host()+redirectTo.encodedPath()).toAscii(); redirectTo.setEncodedUrl(newaddr); redirectTo.setHost(url.host()); } return (downloadURL(redirectTo, data)); } if (reply->error() != QNetworkReply::NoError) { return reply->error(); } data = reply->readAll(); delete reply; return QNetworkReply::NoError; }

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• How can I do batch image processing with ImageJ in clojure?

  - by Robert McIntyre

  I want to use ImageJ to do some processing of several thousand images. Is there a way to take any general imageJ plugin and apply it to hundreds of images automatically? For example, say I want to take my thousand images and apply a polar transformation to each--- A polar transformation plugin for ImageJ can be found here: http://rsbweb.nih.gov/ij/plugins/polar-transformer.html Great! Let's use it. From: [http://albert.rierol.net/imagej_programming_tutorials.html#How%20to%20automate%20an%20ImageJ%20dialog] I find that I can apply a plugin using the following: (defn x-polar [imageP] (let [thread (Thread/currentThread) options ""] (.setName thread "Run$_polar-transform") (Macro/setOptions thread options) (IJ/runPlugIn imageP "Polar_Transformer" ""))) This is good because it suppresses the dialog which would otherwise pop up for every image. But running this always brings up a window containing the transformed image, when what I want is to simply return the transformed image. The stupidest way to do what I want is to just close the window that comes up and return the image which it was displaying. Does what I want but is absolutely retarded: (defn x-polar [imageP] (let [thread (Thread/currentThread) options ""] (.setName thread "Run$_polar-transform") (Macro/setOptions thread options) (IJ/runPlugIn imageP "Polar_Transformer" "") (let [return-image (IJ/getImage)] (.hide return-image) return-image))) I'm obviously missing something about how to use imageJ plugins in a programming context. Does anyone know the right way to do this? Thanks, --Robert McIntyre

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• How can I set QNetworkReply properties to get correct NCBI pages?

  - by Claire Huang

  I try to get this following url using the downloadURL function: http://www.ncbi.nlm.nih.gov/nuccore/27884304 But the data is not as what we can see through the browser. Now I know it's because that I need to give the correct information such as browser, how can I know what kind of information I need to set, and how can I set it? (By setHeader function??) In VC++, we can use CInternetSession and CHttpConnection Object to get the correct information without setting any other detail information, is there any similar way in Qt or other cross-platform C++ network lib?? (Yes, I need the the cross-platform property.) QNetworkReply::NetworkError downloadURL(const QUrl &url, QByteArray &data) { QNetworkAccessManager manager; QNetworkRequest request(url); request.setHeader(QNetworkRequest::ContentTypeHeader ,"Mozilla/5.0 (Windows; U; Windows NT 6.0; en-US; rv:1.9.1.7) Gecko/20091221 Firefox/3.5.7 (.NET CLR 3.5.30729)"); QNetworkReply *reply = manager.get(request); QEventLoop loop; QObject::connect(reply, SIGNAL(finished()), &loop, SLOT(quit())); loop.exec(); int direction; QVariant statusCodeV = reply->attribute(QNetworkRequest::RedirectionTargetAttribute); QUrl redirectTo = statusCodeV.toUrl(); if (!redirectTo.isEmpty()) { if (redirectTo.host().isEmpty()) { const QByteArray newaddr = ("http://"+url.host()+redirectTo.encodedPath()).toAscii(); redirectTo.setEncodedUrl(newaddr); redirectTo.setHost(url.host()); } return (downloadURL(redirectTo, data)); } if (reply->error() != QNetworkReply::NoError) { return reply->error(); } data = reply->readAll(); delete reply; return QNetworkReply::NoError; }

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• R: Why does read.table stop reading a file?

  - by Mike Dewar

  I have a file, called genes.txt, which I'd like to become a data.frame. It's got a lot of lines, each line has three, tab delimited fields: mike$ wc -l genes.txt 42476 genes.txt I'd like to read this file into a data.frame in R. I use the command read.table, like this: genes = read.table( genes_file, sep="\t", na.strings="-", fill=TRUE, col.names=c("GeneSymbol","synonyms","description") ) Which seems to work fine, where genes_file points at genes.txt. However, the number of lines in my data.frame is significantly less than the number of lines in my text file: > nrow(genes) [1] 27896 and things I can find in the text file: mike$ grep "SELL" genes.txt SELL CD62L|LAM1|LECAM1|LEU8|LNHR|LSEL|LYAM1|PLNHR|TQ1 selectin L don't seem to be in the data.frame > grep("SELL",genes$GeneSymbol) integer(0) it turns out that genes = read.delim( genes_file, header=FALSE, na.strings="-", fill=TRUE, col.names=c("GeneSymbol","synonyms","description"), ) works just fine. Why does read.delim work when read.table not? If it's of use, you can recreate genes.txt using the following commands which you should run from a command line curl -O ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz gzip -cd gene_info.gz | awk -Ft '$1==9606{print $3 "\t" $5 "\t" $9}' > genes.txt be warned, though, that gene_info.gz is 101MBish.

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• ASP.NET CacheDependency out of ThreadPool

  - by Stephen

  In an async http handler, we add items to the ASP.NET cache, with dependencies on some files. If the async method executes on a thread from the ThreadPool, all is fine: AsyncResult result = new AsyncResult(context, cb, extraData); ThreadPool.QueueUserWorkItem(new WaitCallBack(DoProcessRequest), result); But as soon as we try to execute on a thread out of the ThreadPool: AsyncResult result = new AsyncResult(context, cb, extraData); Runner runner = new Runner(result); Thread thread = new Thread(new ThreadStart(runner.Run()); ... where Runner.Run just invokes DoProcessRequest, The dependencies do trigger right after the thread exits. I.e. the items are immediately removed from the cache, the reason being the dependencies. We want to use an out-of-pool thread because the processing might take a long time. So obviously something's missing when we create the thread. We might need to propagate the call context, the http context... Has anybody already encountered that issue? Note: off-the-shelf custom threadpools probably solve this. Writing our own threadpool is probably a bad idea (think NIH syndrom). Yet I'd like to understand this in details, though.

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• Why can't I run a Perl program from TextMate?

  - by JZ

  I'm following a bioinformatics text, and this represents one of my first Perl scripts. While in TextMate, this does not produce any result. Is it functioning? I added "hello world" at the bottom and I don't see that when I run the script in TextMate. What have I done wrong? #!/usr/local/bin/perl -w use lib "/Users/fogonthedowns/myperllib"; use LWP::Simple; use strict; #Set base URL for all eutils my $utils = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils"; my $db = "Pubmed"; my $query ="Cancer+Prostate"; my $retmax = 10; my $esearch = "$utils/esearch.fcgi?" . "db=$db&retmax=$retmax&term="; my $esearch_result = get($esearch.$query); print "ESEARCH RESULT: $esearch_result\n"; print "Using Query: \n$esearch$query\n"; print "hello world\n";

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• Can RPM packages be installed into Cygwin?

  - by Dejian Zhao

  I noticed that there is a command - rpm - under Cygwin 1.7. Does that mean RPM packages can be installed into Cygwin? I tried to install ncbi-blast-2.2.26+-3.i686.rpm (see: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ ) into Cygwin 1.7.13 with the command "install -i ncbi-blast-2.2.26+-3.i686.rpm". However, error message appeared as below. I tried to search for the missing libs using the setup.exe of Cygwin. It seems that some of them were not present, such as libc.so.6, libdl.so.2, libm.so.6, libnsl.so.1, and libz.so.1. Where can I get these libs? Thanks! $ rpm -i ncbi-blast-2.2.26+-3.i686.rpm error: Failed dependencies: /usr/bin/perl is needed by ncbi-blast-2.2.26+-3 libbz2.so.1 is needed by ncbi-blast-2.2.26+-3 libc.so.6 is needed by ncbi-blast-2.2.26+-3 libc.so.6(GLIBC_2.0) is needed by ncbi-blast-2.2.26+-3 libc.so.6(GLIBC_2.1) is needed by ncbi-blast-2.2.26+-3 libc.so.6(GLIBC_2.1.2) is needed by ncbi-blast-2.2.26+-3 libc.so.6(GLIBC_2.1.3) is needed by ncbi-blast-2.2.26+-3 libc.so.6(GLIBC_2.2) is needed by ncbi-blast-2.2.26+-3 libc.so.6(GLIBC_2.3) is needed by ncbi-blast-2.2.26+-3 libdl.so.2 is needed by ncbi-blast-2.2.26+-3 libdl.so.2(GLIBC_2.0) is needed by ncbi-blast-2.2.26+-3 libdl.so.2(GLIBC_2.1) is needed by ncbi-blast-2.2.26+-3 libgcc_s.so.1 is needed by ncbi-blast-2.2.26+-3 libgcc_s.so.1(GCC_3.0) is needed by ncbi-blast-2.2.26+-3 libgcc_s.so.1(GLIBC_2.0) is needed by ncbi-blast-2.2.26+-3 libm.so.6 is needed by ncbi-blast-2.2.26+-3 libnsl.so.1 is needed by ncbi-blast-2.2.26+-3 libpthread.so.0 is needed by ncbi-blast-2.2.26+-3 libpthread.so.0(GLIBC_2.0) is needed by ncbi-blast-2.2.26+-3 libpthread.so.0(GLIBC_2.1) is needed by ncbi-blast-2.2.26+-3 libpthread.so.0(GLIBC_2.2) is needed by ncbi-blast-2.2.26+-3 libpthread.so.0(GLIBC_2.3.2) is needed by ncbi-blast-2.2.26+-3 librt.so.1 is needed by ncbi-blast-2.2.26+-3 libstdc++.so.6 is needed by ncbi-blast-2.2.26+-3 libstdc++.so.6(CXXABI_1.3) is needed by ncbi-blast-2.2.26+-3 libstdc++.so.6(GLIBCXX_3.4) is needed by ncbi-blast-2.2.26+-3 libstdc++.so.6(GLIBCXX_3.4.5) is needed by ncbi-blast-2.2.26+-3 libz.so.1 is needed by ncbi-blast-2.2.26+-3 perl(Archive::Tar) is needed by ncbi-blast-2.2.26+-3 perl(Digest::MD5) is needed by ncbi-blast-2.2.26+-3 perl(File::Temp) is needed by ncbi-blast-2.2.26+-3 perl(File::stat) is needed by ncbi-blast-2.2.26+-3 perl(Getopt::Long) is needed by ncbi-blast-2.2.26+-3 perl(Net::FTP) is needed by ncbi-blast-2.2.26+-3 perl(Pod::Usage) is needed by ncbi-blast-2.2.26+-3 perl(constant) is needed by ncbi-blast-2.2.26+-3 perl(strict) is needed by ncbi-blast-2.2.26+-3 perl(warnings) is needed by ncbi-blast-2.2.26+-3

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• Daylight saving time and Timezone best practices

  - by Oded

  I am hoping to make this question and the answers to it the definitive guide to dealing with daylight saving time, in particular for dealing with the actual change overs. If you have anything to add, please do Many systems are dependent on keeping accurate time, the problem is with changes to time due to daylight savings - moving the clock forward or backwards. For instance, one has business rules in an order taking system that depend on the time of the order - if the clock changes, the rules might not be as clear. How should the time of the order be persisted? There is of course an endless number of scenarios - this one is simply an illustrative one. How have you dealt with the daylight saving issue? What assumptions are part of your solution? (looking for context here) As important, if not more so: What did you try that did not work? Why did it not work? I would be interested in programming, OS, data persistence and other pertinent aspects of the issue. General answers are great, but I would also like to see details especially if they are only available on one platform. Summary of answers and other data: (please add yours) Do: Always persist time according to a unified standard that is not affected by daylight savings. GMT and UTC have been mentioned by different people. Include the local time offset (including DST offset) in stored timestamps. Remember that DST offsets are not always an integer number of hours (e.g. Indian Standard Time is UTC+05:30). If using Java, use JodaTime. - http://joda-time.sourceforge.net/ Create a table TZOffsets with three columns: RegionClassId, StartDateTime, and OffsetMinutes (int, in minutes). See answer Check if your DBMS needs to be shutdown during transition. Business rules should always work on civil time. Internally, keep timestamps in something like civil-time-seconds-from-epoch. See answer Only convert to local times at the last possible moment. Don't: Do not use javascript date and time calculations in web apps unless you ABSOLUTELY have to. Testing: When testing make sure you test countries in the Western and Eastern hemispheres, with both DST in progress and not and a country that does not use DST (6 in total). Reference: Olson database, aka Tz_database - ftp://elsie.nci.nih.gov/pub Sources for Time Zone and DST - http://www.twinsun.com/tz/tz-link.htm ISO format (ISO 8601) - http://en.wikipedia.org/wiki/ISO_8601 Mapping between Olson database and Windows TimeZone Ids, from the Unicode Consortium - http://unicode.org/repos/cldr-tmp/trunk/diff/supplemental/windows_tzid.html TimeZone page on WikiPedia - http://en.wikipedia.org/wiki/Tz_database StackOverflow questions tagged dst - http://stackoverflow.com/questions/tagged/dst StackOverflow questions tagged timezone - http://stackoverflow.com/questions/tagged/timezone Other: Lobby your representative to end the abomination that is DST. We can always hope...

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• replaceAll() method using parameter from text file

  - by Herman Plani Ginting

  i have a collection of raw text in a table in database, i need to replace some words in this collection using a set of words. i put all the term to be replace and its substitutes in a text file as below min=admin lelet=lambat lemot=lambat nii=nih ntu=itu and so on. i have successfully initiate a variabel of File and Scanner to read the collection of the term and its substitutes. i loop all the dataset and save the raw text in a string in the same loop i loop all the term collection and save its row to a string name 'pattern', and split the pattern into two string named 'term' and 'replacer' in this loop i initiate a new string which its value is the string from the dataset modified by replaceAll(term,replacer) end loop for term collection then i insert the new string to another table in database end loop for dataset i do it manualy as below replaceAll("min","admin") and its works but its really something to code it manually for almost 2000 terms to be replace it. anyone ever face this kind of really something.. i really need a help now desperate :( package sentimenrepo; import javax.swing.*; import java.sql.*; import java.io.*; //import java.util.HashMap; import java.util.Scanner; //import java.util.Map; /** * * @author herman */ public class synonimReplaceV2 extends SwingWorker { protected Object doInBackground() throws Exception { new skripsisentimen.sentimenttwitter().setVisible(true); Integer row = 0; File synonimV2 = new File("synV2/catatan_kata_sinonim.txt"); String newTweet = ""; DB db = new DB(); Connection conn = db.dbConnect("jdbc:mysql://localhost:3306/tweet", "root", ""); try{ Statement select = conn.createStatement(); select.executeQuery("select * from synonimtweet"); ResultSet RS = select.getResultSet(); Scanner scSynV2 = new Scanner(synonimV2); while(RS.next()){ row++; String no = RS.getString("no"); String tweet = " "+ RS.getString("tweet"); String published = RS.getString("published"); String label = RS.getString("label"); clean2 cleanv2 = new clean2(); newTweet = cleanv2.cleanTweet(tweet); try{ Statement insert = conn.createStatement(); insert.executeUpdate("INSERT INTO synonimtweet_v2(no,tweet,published,label) values('" +no+"','"+newTweet+"','"+published+"','"+label+"')"); String current = skripsisentimen.sentimenttwitter.txtAreaResult.getText(); skripsisentimen.sentimenttwitter.txtAreaResult.setText(current+"\n"+row+"original : "+tweet+"\n"+newTweet+"\n______________________\n"); skripsisentimen.sentimenttwitter.lblStat.setText(row+" tweet read"); skripsisentimen.sentimenttwitter.txtAreaResult.setCaretPosition(skripsisentimen.sentimenttwitter.txtAreaResult.getText().length() - 1); }catch(Exception e){ skripsisentimen.sentimenttwitter.lblStat.setText(e.getMessage()); } skripsisentimen.sentimenttwitter.lblStat.setText(e.getMessage()); } }catch(Exception e){ skripsisentimen.sentimenttwitter.lblStat.setText(e.getMessage()); } return row; } class clean2{ public clean2(){} public String cleanTweet(String tweet){ File synonimV2 = new File("synV2/catatan_kata_sinonim.txt"); String pattern = ""; String term = ""; String replacer = ""; String newTweet=""; try{ Scanner scSynV2 = new Scanner(synonimV2); while(scSynV2.hasNext()){ pattern = scSynV2.next(); term = pattern.split("=")[0]; replacer = pattern.split("=")[1]; newTweet = tweet.replace(term, replacer); } }catch(Exception e){ e.printStackTrace(); } System.out.println(newTweet+"\n"+tweet); return newTweet; } } }

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