MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'diary'. Sat, 03 Sep 2011 01:58:47 +0100 http://www.medworm.com/index.php?rid=5096849&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F08%2F04%2Fa-beginners-guide-to-bioruby-development%2F I’m the “biologist-turned-programmer” type of bioinformatician which makes me a hacker, not a developer. Most of the day-to-day coding that I do goes something like this: Colleague: Hey Neil, can you write me a script to read data from file X, do Y to it and output a table in file Z? Me: Sure… (clickety-click, hackety-hack…) …there you go. Colleague: Great! Thanks. I’m a big fan of the Bio* projects and have used them for many years, beginning with Bioperl and more recently, BioRuby. And I’ve always wanted to contribute some code to them, but have never got around to doing so. This week, two thoughts popped into my head: How hard can it be? There isn’t much introductory documentation for would-be Bio* developers The answer to the firs... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=5096849 Thu, 04 Aug 2011 13:31:35 +0100 5096849 http://www.medworm.com/index.php?rid=5028877&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F07%2F15%2Fi-give-up%2F It’s what – 10 years or more? – since we began to wonder when web technologies such as RSS, wikis and social bookmarking sites would be widely adopted by most working scientists, to further their productivity. The email that I received today which began “I’ve read 3 interesting papers” and included 1 .doc, 3 .docx and 4 .pdf files as attachments is indicative of the answer to this question, which is “not any time soon.” I’ve given up trying to educate colleagues in best practices. Clearly, I’m the one with the problem, since this is completely normal, acceptable behaviour for practically everyone that I’ve ever worked with. Instead, I’m just waiting for them to retire (or die). I reckon most senior scientists (and they... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=5028877 Fri, 15 Jul 2011 04:26:35 +0100 5028877 http://www.medworm.com/index.php?rid=5008521&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F07%2F07%2Fr-calculations-involving-months%2F Ask anyone how much time has elapsed since September last year and they’ll probably start counting on their fingers: “October, November…” and tell you “just over 9 months.” So, when faced as I was today with a data frame (named dates) like this: pmid1 year1 month1 pmid2 year2 month2 21355427 2010 Dec 21542215 2011 Mar 21323727 2011 Feb 21521365 2011 Jun 21297532 2011 Feb 21336080 2011 Mar 21291296 2011 Apr 21591868 2011 Jun ... How to add a 7th column, with the number of months between “year1/month1″ and “year2/month2″? R has lots of methods for date/time calculations, many of which seem notoriously difficult to get your head around. One answer for my problem came, as so often, from ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=5008521 Thu, 07 Jul 2011 13:32:38 +0100 5008521 http://www.medworm.com/index.php?rid=4934255&cid=t_96241_105_f&fid=39124&url=http%3A%2F%2Fwww.jeffreymlevinemd.com%2Fcity-diary-incident-on-the-brooklyn-bridge%2F I carry my camera around Manhattan, especially on weekends when my wife and I go adventuring around the City.  Sometimes when conditions line up correctly I might get some interesting shots.  This occurs when the light is right, my battery is charged, and I remember to insert the memory card.  The Sunday of Memorial Day weekend was beautiful and sunny, and we decided to walk ...Read More (Source: Jeffrey M. Levine MD | Geriatric Specialist | Wound Care | Pressure Ulcers) Jeffrey M. Levine MD | Geriatric Specialist | Wound Care | Pressure Ulcers blogs http://www.medworm.com/rss/comments.php?id=4934255 Tue, 14 Jun 2011 06:44:06 +0100 4934255 http://www.medworm.com/index.php?rid=4893458&cid=t_96241_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2F7xLwTeapZbs%2F This day...June 2nd 2011, marked the 6th running of the SKINS Cup...A classic 100m dash with staggered handicapped starts akin to the Stawell Gift (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4893458 Thu, 02 Jun 2011 22:21:44 +0100 4893458 http://www.medworm.com/index.php?rid=4841830&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F05%2F18%2Fhow-to-create-a-partial-ucsc-genome-mysql-database%2F File under: simple, but a useful reminder UCSC Genome Bioinformatics is one of the go-to locations for genomic data. They are also kind enough to provide access to their MySQL database server: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A However, users are given fair warning to “avoid excessive or heavy queries that may impact the server performance.” It’s not clear what constitutes excessive or heavy but if you’re in any doubt, it’s easy to create your own databases locally. It’s also easy to create only the tables that you require, as and when you need them. As an example, here’s how you could create only the ensGene table for the latest hg19 database. Here, USER and PASSWD represent a local MySQL user and password with full privileg... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4841830 Wed, 18 May 2011 04:54:10 +0100 4841830 http://www.medworm.com/index.php?rid=4631488&cid=t_96241_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2F8GZv3MMD9aI%2F Today, I had the honor and privilege to lead the emergency department ward round at GF Jooste Hospital in Manenberg (Cape Town), South Africa. It was an amazing experience, and one which I will never forget. (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4631488 Thu, 24 Mar 2011 21:28:51 +0100 4631488 http://www.medworm.com/index.php?rid=4610817&cid=t_96241_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2FN_s6ruYJNmc%2F Travelling with fit, well hydrated, socially capable, phototropic, extrovert athletes in a Westward direction (to South Africa) should, in theory, be a fairly straight forward exercise... (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4610817 Fri, 18 Mar 2011 07:45:46 +0100 4610817 http://www.medworm.com/index.php?rid=4605834&cid=t_96241_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2FEiYPOb8auHs%2F Travel is an integral part of a professional Rugby Union Players regime. Competition schedules require the crossing of time zones and the rapid re-setting of the body clock with minimal disruption to on-field performance. (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4605834 Thu, 17 Mar 2011 09:17:22 +0100 4605834 http://www.medworm.com/index.php?rid=4592610&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F03%2F15%2Fnew-publication-analysis-of-large-protein-assemblies-in-macrophage-cytoplasm%2F First for 2011: Proteomic and electron microscopy survey of large assemblies in macrophage cytoplasm. Maco, B., Ross I.L., Landsberg, M., Mouradov, D., Saunders, N.F.W., Hankamer, B. and Kobe, B. (2011) Molecular & Cellular Proteomics, in press, doi:10.1074/mcp.M111.008763 This is an in-press article which is freely-available just now (although strangely, the supplemental data are not). I’m pleased to note that we also made the raw data available in Proteome Commons. In fact, it was a condition of publication. Lots of hard work went into this one. My contribution was quite minor: some bioinformatic analysis and hacking away at PyMsXML to make it work with newer versions of vendor formats. I’d like to thank Brad Chapman with respect to PyMsXML, who provided invaluable advi... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4592610 Tue, 15 Mar 2011 04:07:58 +0100 4592610 http://www.medworm.com/index.php?rid=4455410&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F09%2Falgorithms-running-day-and-night%2F Warning: contains murky, somewhat unstructured thoughts on large-scale biological data analysis Picture this. It’s based on a true story: names and details altered. Alice, a biomedical researcher, performs an experiment to determine how gene expression in cells from a particular tissue is altered when the cells are exposed to an organic compound, substance Y. She collates a list of the most differentially-expressed genes and notes, in passing, that the expression of Gene X is much lower in the presence of substance Y. Bob, a bioinformatician in the same organisation but in a different city to Alice, is analysing a public dataset. This experiment looks at gene expression in the same tissue but under different conditions: normal compared with a disease state, Z Syndrome. He also notes ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4455410 Wed, 09 Feb 2011 03:41:21 +0100 4455410 http://www.medworm.com/index.php?rid=4450298&cid=t_96241_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2FPwZbVEdu5o4%2F I have taken on a new challenge as team doctor for the Emirates Western Force (EWF) Super XV Rugby Union Team in Perth, Western Australia (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4450298 Tue, 08 Feb 2011 09:37:26 +0100 4450298 http://www.medworm.com/index.php?rid=4405961&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F01%2F27%2Fapis-have-let-me-down-part-12-arrayexpress%2F The API – Application Programming Interface – is, in principle, a wonderful thing. You make a request to a server using a URL and back come lovely, structured data, ready to parse and analyse. We’ve begun to demand that all online data sources offer an API and lament the fact that so few online biological databases do so. Better though, to have no API at all than one which is poorly implemented and leads to frustration? I’m beginning to think so, after recent experiences on both a work project and one of my “fun side projects”. Let’s start with the work project, an attempt to mine a subset of the ArrayExpress microarray database. 1. Introduction ArrayExpress is an online database of microarray experiments, organised by both gene (the expression at... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4405961 Thu, 27 Jan 2011 09:04:11 +0100 4405961 http://www.medworm.com/index.php?rid=4142921&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F11%2F08%2Ffirst-publication-for-a-while-a-review-of-nuclear-localization%2F Thanks to my former colleagues at UQ for involving me with: Marfori, M., Mynott, A., Ellis, J.J., Mehdid, A.M., Saunders, N.F.W., Curmi, P.M., Forwood, J.K., Bodén, M. and Kobe, B. (2010) Molecular basis for specificity of nuclear import and prediction of nuclear localization. Biochimica et Biophysica Acta (BBA) – Molecular Cell Research: in press – uncorrected proof. A real group effort this one; I made a small contribution to Section 3 – Nuclear localization databases and computational tools to predict nuclear localization. Note that this version is an uncorrected proof and may change slightly before full publication. If nuclear localization is your thing, I think you’ll enjoy it; it’s a pretty comprehensive review. Filed under: bioinformatics, publicatio... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4142921 Mon, 08 Nov 2010 03:06:50 +0100 4142921 http://www.medworm.com/index.php?rid=4031304&cid=t_96241_109_f&fid=34750&url=http%3A%2F%2Fpsychcentral.com%2Fblog%2Farchives%2F2010%2F10%2F05%2Fbest-of-our-blogs-october-5-2010%2F It’s October and Mental Health Awareness Week! How are you celebrating? Yep, there’s no denying it’s fall. I went to the park this weekend and the crispy air and falling leaves were signs that this is indeed the end of the ease of summer and the beginning of a new season. Every ending has a new beginning and like New Year’s it is another opportunity for self-growth and change. It beckons us to ask the question, “Will I embrace the coming season or mourn the lost of the one before?” If you are courageous, brave and on a mission for change, then you’ll be tickled with this week’s top posts. Why? Do you remember the scene in Bridget Jones’s Diary where Bridget’s enemy Mark Darcy suddenly turns into the love of her life over night wi... World of Psychology blogs http://www.medworm.com/rss/comments.php?id=4031304 Tue, 05 Oct 2010 12:32:22 +0100 4031304 http://www.medworm.com/index.php?rid=3999181&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F09%2F24%2Fconnecting-to-a-mongodb-database-from-r-using-java%2F It would be nice if there were an R package, along the lines of RMySQL, for MongoDB. For now there is not – so, how best to get data from a MongoDB database into R? One option is to retrieve JSON via the MongoDB REST interface and parse it using the rjson package. Assuming, for example, that you have retrieved your CiteULike collection in JSON format from this URL: http://www.citeulike.org/json/user/neils - and saved it to a database named citeulike in a collection named articles, you can fetch the first 5 articles into R like so: library(RCurl) library(rjson) db <- "http://localhost:28017/citeulike/articles/?limit=5" articles <- fromJSON(getURL(db)) articles$rows[[1]]$title # [1] "A computational genomics pipeline for prokaryotic sequencing projects" ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3999181 Fri, 24 Sep 2010 07:15:00 +0100 3999181 http://www.medworm.com/index.php?rid=3718624&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F07%2F02%2Fhow-many-monotypic-genera%2F During all the recent discussion around Neandertals and modern humans, it’s often pointed out that Homo sapiens is the sole extant representative of the genus Homo. I began to wonder “how unusual is this?” in a FriendFeed comment thread. What resources exist that could help us to answer this question? Genera that contain only one species are termed monotypic. Wikipedia even has a category page for this topic but their lists are limited, since Wikipedia is not a comprehensive taxonomy resource. Taxonomy is not my specialty but once in a while, I enjoy challenging myself with unfamiliar resources and data types. I figured initially that we could get some way towards an answer using BioSQL and the NCBI taxonomy database. As it turned out I was completely wrong, but it was an... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3718624 Fri, 02 Jul 2010 02:56:59 +0100 3718624 http://www.medworm.com/index.php?rid=3552477&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F05%2F11%2Fbeware-of-rogue-header-files-bioconductor-installation%2F Just a short note concerning a “gotcha”. As I have many times before, I opened an R console on my newly-upgraded (to lucid 10.04) Ubuntu machine, typed source(“http://bioconductor.org/biocLite.R”) and began a Bioconductor install with biocLite(). Only this time, I saw this: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio/libs/affyio.so': /home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio/libs/affyio.so: undefined symbol: egzread ERROR: loading failed * removing ‘/home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio’ A quick email to the Bioconductor mailing list put me in touch with the very helpful Martin Morgan, who suggested that I check my zlib libraries. Sure enough, ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3552477 Tue, 11 May 2010 06:18:18 +0100 3552477 http://www.medworm.com/index.php?rid=3490802&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F04%2F21%2Fexperiments-with-igraph%2F Networks – social and biological – are all the rage, just now. Indeed, a recent entry at Duncan’s QOTD described the “hairball” network representation as the dominant cultural icon in molecular biology. I’ve not had occasion to explore networks “professionally”, but have always been fascinated by both networks and the tools used to analyse them. My grasp of graph theory, the mathematics behind networks, is more or less summarised by this Wikipedia page. I’ve also been exploring the igraph library and thought I’d share a few of my “experiments with igraph”. As I say, I’m learning myself as I go along, so none of this should be taken as professional advice. Let’s start with my favourite network – Friend... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3490802 Wed, 21 Apr 2010 06:21:36 +0100 3490802 http://www.medworm.com/index.php?rid=3483046&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F04%2F19%2Fgetting-your-web-application-and-rapache-to-talk-to-each-other%2F Here’s the situation. Web applications, built using a framework (e.g. Rails, Django) are great for fetching data from a database and rendering it. They’re not so great for crunching and charting the data. Conversely, R is great for crunching and charting, but doesn’t make for a great web application. Index view for values The idea then, is to let each do what it does best and enable the passing of data between them. There isn’t a whole lot of literature on this topic, but there are a couple of guides: In these seminar slides (PDF), Jeroen Ooms describes how data can be passed between a web browser and R. Briefly, he uses client-side javascript to format the data as a JSON string. Server-side R (RApache) then parses the POST variable using fromJSON() (in the rjson p... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3483046 Mon, 19 Apr 2010 13:44:08 +0100 3483046 http://www.medworm.com/index.php?rid=3471975&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F04%2F15%2Fid-be-more-than-happy-with-the-unlinked-data-web%2F Visit this URL and you’ll find a perfectly-formatted CSV file containing information about recent earthquakes. A nice feature of R is the ability to slurp such a URL straight into a data frame: quakes <- read.csv("http://neic.usgs.gov/neis/gis/qed.asc", header = T) colnames(quakes) # [1] "Date" "TimeUTC" "Latitude" "Longitude" "Magnitude" "Depth" # number of recent quakes nrow(quakes) # [1] 3135 # biggest recent quake subset(quakes, quakes$Magnitude == max(quakes$Magnitude, na.rm = T)) # Date TimeUTC Latitude Longitude Magnitude Depth # 2060 2010/02/27 06:34:14.0 -35.993 -72.828 8.8 35 I hear a lot about the “web of data” and the “linked data web” but honestly, I’ll ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3471975 Thu, 15 Apr 2010 05:02:15 +0100 3471975 http://www.medworm.com/index.php?rid=3408575&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F03%2F26%2Fbiomart-and-biomart%2F I’ve been vaguely aware of BioMart for a few years. Inexplicably, I’ve only recently started to use it. It’s one of the most useful applications I’ve ever used. The concept is simple. You have a set of identifiers that describe a biological object, such as a gene. These are called filters. They have values – for example, HGNC symbols. You want to retrieve other identifiers – attributes – for your objects. You can use BioMart as a web application called MartView. However, R users should check out the biomaRt package, part of the Bioconductor suite. Here’s a couple of examples. Example 1: fetch Ensembl gene identifiers given HGNC symbols Let’s start with a simple example. You have a CSV file in which one of the fields is a HGNC symbol (w... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3408575 Fri, 26 Mar 2010 07:23:18 +0100 3408575 http://www.medworm.com/index.php?rid=3395096&cid=t_96241_87_f&fid=36050&url=http%3A%2F%2Fblisstree.com%2Flive%2Fforget-me-not-put-me-online%2F Photo albums? So last year. A book? We’d rather read our Nook. If you missed the e-memo: Bound is out, digital is in. When you upgrade from paper to PDF, it’s time to toss your old journal. Thanks to new online diary services, you can use the Internet to unleash your inner Bridget Jones. Here are three of our fave places to soul-search on the World Wide Web: Penzu – Like the bound journals of yore, Penzu is a simple, straight-up diary platform. Its pages look like lined paper, and you can add digital photos through Flickr. You choose whether to keep your profile and journal private, or share entries with friends. (free) Cozi – This family journal blows your pen and paper off the table. It’s designed to be a collaborative journal, calendar, and communication service f... Breastfeeding 1-2-3 blogs http://www.medworm.com/rss/comments.php?id=3395096 Mon, 22 Mar 2010 17:41:37 +0100 3395096 http://www.medworm.com/index.php?rid=3212505&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F27%2Fclustering-geo-samples-by-title-briefly-revisited%2F So, we had a brief discussion regarding my previous post and clearly the statement: The longest key for which values exist classifies your titles does not hold true for all cases. Not that I ever said that it did! I remind you that this blog is a place for the half-formed ideas that spill out of my head, not an instruction manual. Let’s look, for example, at GSE19318. This GEO series comprises 2 platforms: one for dog (10 samples) and one for humans (1 sample), with these sample titles: ['Dog-tumor-81705', 'Dog-tumor-78709', 'Dog-tumor-88012', 'Dog-tumor-8888302', 'Dog-tumor-209439', 'Dog-tumor-212227', 'Dog-tumor-48', 'Dog-tumor-125', 'Dog-tumor-394', 'Dog-tumor-896', 'Human-tumor'] Run that through the Ruby code in my last post and we get: {"Dog-tumor-48"=>["... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3212505 Wed, 27 Jan 2010 01:29:56 +0100 3212505 http://www.medworm.com/index.php?rid=3201861&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F24%2Fthinking-algorithmically-clustering-geo-samples-by-title%2F Today’s challenge. Take a look at this array, which contains the “title” field for the 6 samples from GSE1323, a series in the GEO microarray database: ['SW-480-1','SW-480-2','SW-480-3','SW-620-1','SW-620-2','SW-620-3'] Humans are very good at classification. Almost instantly, you’ll see that there are 2 classes, “SW-480″ and “SW-620″, each with 3 samples. How can we write a program to do the same job? I’m sure that for those with formal training in computer science and algorithms, this is pretty trivial. The rest of us have to figure it out from first principles. Here’s what I did, in words: # Imagine that you have 2 titles: "abc1" and "abc2" # Take the first character - call it the key, call the remaining... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3201861 Sun, 24 Jan 2010 05:03:00 +0100 3201861 http://www.medworm.com/index.php?rid=3178941&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F15%2Fwhat-i-learned-this-week-about-productivity-mongodb-and-nginx%2F Productivity It was an excellent week. It was also a week in which I payed much less attention than usual to Twitter and FriendFeed. Something to think about… MongoDB I’m now using MongoDB so frequently that I’d like the database server to start up on boot and stay running. There are 2 init scripts for Debian/Ubuntu in this Google Groups thread. I followed the instructions in the second post, with minor modifications to the script: # I like to keep mongodb in /opt PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/mongodb/bin DAEMON=/opt/mongodb/bin/mongod # you don't need 'run' in these options DAEMON_OPTS='--dbpath /data/db' # I prefer lower-case name for the PID file NAME=mongodb # I think /data/db should be owned by the mongodb user sudo chown -R ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3178941 Fri, 15 Jan 2010 08:45:46 +0100 3178941 http://www.medworm.com/index.php?rid=3163976&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F12%2Fa-new-twist-on-the-identifier-mapping-problem%2F Yesterday, Deepak wrote about BridgeDB, a software package to deal with the “identifier mapping problem”. Put simply, biologists can name a biological entity in any way that they like, leading to multiple names for the same object. Easily solved, you might think, by choosing one identifier and sticking to it, but that’s apparently way too much of a challenge. However, there are times when this situation is forced upon us. Consider this code snippet, which uses the Bioconductor package GEOquery via the RSRuby library to retrieve a sample from the GEO database: require "rubygems" require "rsruby" if ENV['R_HOME'].nil? ENV['R_HOME'] = "/usr/lib/R" end r = RSRuby.instance r.library("GEOquery") sample = r.getGEO("GSM434143"... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3163976 Tue, 12 Jan 2010 03:57:02 +0100 3163976 http://www.medworm.com/index.php?rid=3048289&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F12%2F02%2Fhas-our-quest-for-completeness-made-things-too-complicated%2F In my opinion, yes. Let me elaborate. My current job is very much focused on “data integration”. What this means is that we have a large amount of diverse data from different “-omics” experiments: microarrays, protein mass spectrometry, DNA sequencing – really, whatever you like, but it’s all aimed at answering the same question. Namely: which of these biological entities (transcripts, proteins, metabolites) are markers for various human disease states? Somehow, we have to pull all of these data into a common framework so that it can be analysed using statistics. The problem: whilst a lot of effort has gone into designing schema and ontologies that describe the individual data types, less effort has been applied to the question: what do all these things... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3048289 Wed, 02 Dec 2009 02:38:06 +0100 3048289 http://www.medworm.com/index.php?rid=3039956&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F11%2F30%2Fa-brief-survey-of-r-web-interfaces%2F I’m looking at ways to provide access to R via a web application. First rule: see what’s available first, before you reinvent the wheel. It’s not pretty. From the R Web Interfaces FAQ: Software Brief notes Rweb Page last updated 1999. Of the 3 example links on the page one ran very slowly, the second not at all and the third is broken. R-Online Or rather, not online. Unless this CGI form is the same thing. I tried Example 1, it returned a server error. Rcgi Links to several CGI forms, none of which worked for me. CGI-based R access Link did not load. CGIwithR Package now maintained at Omegahat. Did not attempt installation. Last updated 2005. Rpad I could not connect to this URL. RApache The pick of the bunch. Provides server-side access to R through an Ap... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3039956 Mon, 30 Nov 2009 03:03:39 +0100 3039956 http://www.medworm.com/index.php?rid=2934767&cid=t_96241_109_f&fid=34750&url=http%3A%2F%2Fpsychcentral.com%2Fblog%2Farchives%2F2009%2F10%2F28%2Ftop-ten-bipolar-blogs-2009%2F Every year the entrants for the Best of the Web awards multiply. In 2009, veterans stood tough as new kids dazzled. It was difficult to narrow the list to just ten (and some more faves we want to mention), but here are our picks for the top blogs written by people who have been diagnosed with a bipolar disorder. 1. The Secret Life of a Manic Depressive Do’s and Don’ts for the Mentally Interesting was a BBC Radio play based on Seaneen’s blog produced last May and just nominated for a Mind Mental Health Media Award. Always a compelling and honest read, it was no fluke or sympathy vote that caused us to place this blog near the top of our list last year - it deserves many accolades. Well done. 2. The Trouble With Spikol Another great year for Liz Spikol, a stellar writer an... World of Psychology blogs http://www.medworm.com/rss/comments.php?id=2934767 Wed, 28 Oct 2009 12:58:05 +0100 2934767 http://www.medworm.com/index.php?rid=2851855&cid=t_96241_109_f&fid=38953&url=http%3A%2F%2Frileyjennifer.blogspot.com%2F2009%2F09%2Fi-have-already-posted-about-creativity.html I have already posted about creativity being associated with mental illnesses.If you are one of those people struggling with a psychiatric disorder, art therapy might be something you will want to try. You already have a statistical advantage of being able to creatively express yourself, and you have to do something in order to start feeling better, and mood diaries (as helpful as they are and you shouldn’t stop doing any other homework you are currently doing) and cleaning the cat box can get dull pretty quick. As well, as your condition improves, you will need to add more activities to your schedule in order to keep your mind healthy and active.The creation of an artistic piece of work can be emotionally difficult or it can be a relaxing process. It has been my experience that artists ... Psych Scamp blogs http://www.medworm.com/rss/comments.php?id=2851855 Wed, 30 Sep 2009 04:50:00 +0100 2851855 http://www.medworm.com/index.php?rid=2846435&cid=t_96241_109_f&fid=38953&url=http%3A%2F%2Frileyjennifer.blogspot.com%2F2009%2F09%2Fi-have-already-posted-about-creativity.html I have already posted about creativity being associated with mental illnesses.If you are one of those people struggling with a psychiatric disorder, art therapy might be something you will want to try. You already have a statistical advantage of being able to creatively express yourself, and you have to do something in order to start feeling better, and mood diaries (as helpful as they are and you shouldn’t stop doing any other homework you are currently doing) and cleaning the cat box can get dull pretty quick. As well, as your condition improves, you will need to add more activities to your schedule in order to keep your mind healthy and active.The creation of an artistic piece of work can be emotionally difficult or it can be a relaxing process. It has been my experience that artists ... Psych Scamp blogs http://www.medworm.com/rss/comments.php?id=2846435 Wed, 30 Sep 2009 04:50:00 +0100 2846435 http://www.medworm.com/index.php?rid=2699811&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F08%2F14%2Fimprovements-to-the-reference-management-workflow%2F I use Google Reader to subscribe to the RSS feeds from journals that interest me (see my public page). I’m also a big fan of CiteULike as a reference management system. For a long time I’ve thought: it would be great if GReader handled journal articles more efficiently. Rather than going from link in GReader -> article at journal -> CiteULike bookmark -> back to GReader, how about “post directly from GReader?” With Google Reader’s new send-to feature, you can do just that. See this forum post for the details. Also, take a look at this how-to for a quick way to post to CiteULike by entering a PubMed PMID, DOI or ISBN identifier in the address bar. Posted in bibliography, research diary, web resources (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2699811 Fri, 14 Aug 2009 00:30:22 +0100 2699811 http://www.medworm.com/index.php?rid=2561491&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F07%2F01%2Fhow-to-search-across-linked-tables-using-acts_as_ferret%2F I’m in the process of adding search to a Rails application, using acts_as_ferret and ran into this issue. How to search a table using a field from another table, supplied by a foreign key? Let’s say you created a table for a model named Feature: create_table "features", :force => true do |t| t.integer "feature_name_id" t.integer "chromosome_id" t.integer "start" t.integer "end" t.string "strand" t.datetime "created_at" t.datetime "updated_at" end This model, Feature, belongs_to two models, FeatureName and Chromosome, each with a field “name”: create_table "feature_names", :force => true do |t| t.string "name" t.datetime "created... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2561491 Wed, 01 Jul 2009 07:38:40 +0100 2561491 http://www.medworm.com/index.php?rid=2441169&cid=t_96241_87_f&fid=36438&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FCato-at-liberty%2F%7E3%2FDdyysKBdvUk%2F The Federal Diary column in the Washington Post is a curious piece of newspaper real estate. Most newspaper columns are aimed at the broad general public, but this column is aimed directly at the few hundred thousand government workers in the DC region. The result is that it takes a very government- and union-centric view of the world. The fact that the federal civilian workforce costs taxpayers an enormous $300 billion or so every year is beside the point for the column. In a briefing with reporters yesterday, the head of the Office of Personnel Management complained about a Lou Dobbs television bit that featured this data that I assembled from the Bureau of Economic Analysis. The Federal Diary columnist called me yesterday about the data, and I explained to him the shortcomings of ... Cato-at-liberty blogs http://www.medworm.com/rss/comments.php?id=2441169 Thu, 28 May 2009 20:46:14 +0100 2441169 http://www.medworm.com/index.php?rid=2100876&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F01%2F14%2Fwikification-thinking-in-public%2F Over the last 3 years, I’ve stored many small snippets of information in a set of Google Notebooks. Sample topics: notes for blog posts, programming skills that I’d like to learn and preliminary (or half-baked) ideas for research or software projects. I’ve learned that: Whilst Google Notebook is great for scraping information from web pages, it leaves a lot to be desired in terms of editing and presentation Ideas left in private notebooks quickly become dead ideas Yes you can publicise, tag and collaborate at a Google Notebook, but this doesn’t fit with my workflow - or that of many others, I suspect. So, I’ve taken as much of the material as I want to make public and dumped it on a wiki at Wikidot.com. By the way, if you’re looking for a free hosted w... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2100876 Wed, 14 Jan 2009 03:42:06 +0100 2100876 http://www.medworm.com/index.php?rid=2095831&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F01%2F11%2Feasy-visualisation-of-database-schemas-using-sqlfairy%2F BioSQL schema Here’s a common problem solved: how to generate a pretty picture of your database schema. A Google search throws up all manner of home-brewed solutions using graphviz, perl scripts and so on. Or you can make life easier and simply install SQLFairy. Under Ubuntu: as simple as “sudo apt-get install sqlfairy”. Next, dump your database tables, e.g. for MySQL: mysqldump -u username -p -d mydatabase > mydatabase.sql Finally, for a PNG image of your schema: sqlt-graph -f MySQL -o mydatabase.png -t png mydatabase.sql Too easy. Example shown is the BioSQL schema. update: if your schema lacks explicit foreign keys, try the –natural-join options (man sqlt-graph, man sqlt-diagram) Posted in bioinformatics, computing, linux, research diary  &nbsp... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2095831 Sun, 11 Jan 2009 08:45:44 +0100 2095831 http://www.medworm.com/index.php?rid=2083948&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F01%2F07%2Ftext-to-fasta-and-other-delights-of-the-shell%2F One thing I’ve learned in my current job is that some familiarity with Linux tools for processing text files: awk, sed, grep, head/tail, cut/paste and so on, often provides a speedier solution than writing a script in (insert scripting language of choice here). I know this stuff is trivial to shell gurus, but I still get a little buzz out of it. A couple of real-life examples. Delimited text to fasta Your collaborator has developed “peptides on a chip” and sends you a text file describing said chip where column 1 = spot number, column 2 = peptide sequence: 1 ELDQGSLATSF 2 VDLAATPTDVR 3 TTNEEYLDLSQ 4 SSLDVYDGRFL 5 ALVHSYMTGRR Your analysis requires that the peptide sequences be in fasta format. Easy, using awk: awk '{print ">peptide" $1 "\n&qu... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2083948 Wed, 07 Jan 2009 03:02:42 +0100 2083948 http://www.medworm.com/index.php?rid=2510246&cid=t_96241_87_f&fid=36516&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FAScannerBrightly%2F%7E3%2Frj02T93Pgpw%2Fid-blog-something-interesting.html But I'm too busy trying not to smoke.I've been a two pack a day guy for many years. I had a total of three cigs yesterday. This might be the year! (Source: A Scanner Brightly) A Scanner Brightly blogs http://www.medworm.com/rss/comments.php?id=2510246 Tue, 06 Jan 2009 17:52:00 +0100 2510246 http://www.medworm.com/index.php?rid=1883278&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F10%2F17%2Fthe-three-phases-of-mysql-usage%2F As Mike keeps reminding me, getting your data into database tables is A Good Thing. Like many people, my database of choice is MySQL - largely because it was the first one that I tried and it works for me. However, I’m far from being an expert MySQL user. In fact, I’ve identified 3 stages in my use of MySQL over the years; see if you recognise yourself in any of them. The single table database Early in your MySQL career, you discover either “LOAD DATA INFILE” or the command-line tool “mysqlimport”. You realise that this is a quick and easy way to get all of those delimited text files straight into a database. Off you go, merrily importing everything on your hard drive into tables. At some stage, you begin to wonder whether listing the same identifier (... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1883278 Fri, 17 Oct 2008 04:55:33 +0100 1883278 http://www.medworm.com/index.php?rid=1825493&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F09%2F25%2Fgenomic-analysis-of-pseudoalteromonas-tunicata%2F Some years ago, I provided advice and a little analysis for a group at UNSW studying marine bacteria. It’s nice to see that they remembered me: Thomas, T., Evans, F.F., Schleheck, D., Mai-Prochnow, A., Burke, C., Penesyan, A., Dalisay, D.S., Stelzer-Braid, S., Saunders, N., Johnson, J., Ferriera, S., Kjelleberg, S. and Egan, S. (2008). Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment. PLoS ONE 3:e3252. If correlating genomic features with microbial physiology is your thing, go and check it out. The article is open access, for your pleasure - as are five of my last six efforts, I just noticed. Posted in bioinformatics, genomics, publications, research diary   Tagged: plos one, pseudoalter... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1825493 Thu, 25 Sep 2008 06:31:41 +0100 1825493 http://www.medworm.com/index.php?rid=1802641&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F09%2F18%2Fnot-as-many-structures-as-you-might-think%2F In the midst of preparing a talk for next Monday. It occurred to me that perhaps we don’t see more protein structure-based prediction in bioinformatics because - there aren’t enough structures.pdbstatsSure, the PDB has grown a lot in the past 5 years or so and 53 103 structures (as of now) looks impressive. However, if you’re interested in protein-protein interaction, you want at least 2 chains: which more or less halves the dataset. If you want two different protein chains, you lose almost another 75%. Let’s specify a reasonable minimum resolution for X-ray diffraction data and there go ~ 3 000 entries. We probably don’t want multiple, similar proteins so let’s remove sequence identity at a redundancy of 90%. We’re left with about 2% of the origin... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1802641 Thu, 18 Sep 2008 05:14:26 +0100 1802641 http://www.medworm.com/index.php?rid=1763830&cid=t_96241_136_f&fid=35303&url=http%3A%2F%2Fwww.assertivepatient.com%2F2008%2F09%2F10-years-ago.html September is the anniversary of my cancer diagnosis, and this month is the 10-year anniversary. And while I celebrate this anniversary as a milestone--I've survived 10 years, after all, despite recurrences and metastases to my bones--it is also a difficult anniversary: The weeks following my mammogram were the most difficult of my life. I was afraid. I was angry. And the medical care I received was less than optimal--The attitudes of the doctor, nurses, and other staff who took care of me during this diagnosis period added to my distress, big time. That is one reason I always give priority to people who write to me who are newly diagnosed. I understand what they are feeling,  and I want to do whatever I can to help. Here's what I wrote in "Jeanne's Diar... The Assertive Cancer Patient blogs http://www.medworm.com/rss/comments.php?id=1763830 Thu, 04 Sep 2008 19:38:55 +0100 1763830 http://www.medworm.com/index.php?rid=1711726&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F08%2F18%2Fmysteries-of-ccp4%2F Since moving to a structural biology group, I’ve had to become somewhat familiar with CCP4, a suite of programs that do all manner of things using structural data, typically PDB files. Being a bioinformatician, I tend to ignore the GUI in favour of the input -> script -> output approach, as I’m mostly interested in batch processing. Documentation describing this operation for CCP4 programs is strangely lacking on the web. The best that I can find is the CCP4 wiki; if you know the package well, please contribute to it. I eventually dug up what I was looking for in: /opt/ccp4/ccp4-6.0.2/examples/unix/runnable/ or the equivalent on your system. Here, you’ll find a collection of shell scripts, confusingly named with the suffix “.exam”. As an example, here&... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1711726 Mon, 18 Aug 2008 07:30:45 +0100 1711726 http://www.medworm.com/index.php?rid=1677279&cid=t_96241_85_f&fid=36194&url=http%3A%2F%2Ftesstermulo.com%2F2008%2F08%2F03%2Fwhen-to-be-born-a-woman-is-a-curse-a-case-of-honor-killing%2F The atrocities of men and women around the world and the extent of which they commit such never fail to disgust and distress me.  Who has to believe in an afterlife of eternal torment and punishment when, here on earth, humans already bring it upon their fellowmen?  And the saddest thing is that in most of these crimes, the women receives the greater punishment. One of those horrific crimes of violence against women is the practice of “honor” killing. Honor killing is the revengeful murder of a female member of the family, carried out by any or all of the family member themselves, when it’s been perceived that she has brought dishonor upon the family name.  Refusing an arranged marriage, falling in love with another man that is not approved upon by the family for marri... Prudence and Madness blogs http://www.medworm.com/rss/comments.php?id=1677279 Sun, 03 Aug 2008 13:28:26 +0100 1677279 http://www.medworm.com/index.php?rid=1622074&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F07%2F15%2Foff-to-ismb-2008%2F ISMB 2008 posterThe last major international conference that I attended was ISMB 2003. It was - right here in Brisbane, although I was living in Sydney at the time. I have to admit that I haven’t always been proactive when it comes to seeking funds to attend meetings. I’ll admit too that I have mixed feelings about conferences. Many of my best friends are scientists, but there’s something about being in a confined space with several hundred intense, academic types that unsettles me. There’s also the prospect (for Australians) of travelling for 24 hours to reach N. America or Europe. Tomorrow, I’m jetting off to ISMB 2008 in Toronto. I’m sure that I’ll have a fine time once I get there and look forward to putting faces to those names that I’ve... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1622074 Tue, 15 Jul 2008 00:09:10 +0100 1622074 http://www.medworm.com/index.php?rid=1593770&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F07%2F08%2Fthoughts-on-other-programming-languages%2F With respect to their potential for bioinformatics web applications: Feature Python Ruby Modern, clean syntax, object-oriented Yes Yes Web framework Django Rails Bio library BioPython BioRuby Extensive Bio graphics library Not really - any more than this? Kind of - Bio::Graphics Use with App Engine Yes Not yet Well-regarded by scientific programmers Yes ?? To the novice, it looks like “much of a muchness”. Thoughts? (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1593770 Tue, 08 Jul 2008 01:53:38 +0100 1593770 http://www.medworm.com/index.php?rid=1593936&cid=t_96241_85_f&fid=36194&url=http%3A%2F%2Ftesstermulo.com%2F2008%2F07%2F08%2Fmy-top-10-emerging-influential-blogs-for-2008%2F Goodness!  It really did take me some time before I was able to decide which blogs to include in this list.  The problem I had in compiling the blogs was that most of the blogs I visit cannot qualify for the Top 10 anymore because their blogs started way before 2007.  I was keen on putting a vote for The Blog Rounds (TBR), a medical blog carnival started by Filipino doctors, as spearheaded by Bone MD.  But the problem is that the TBR isn’t hosted in its own blog, but rather is currently a section of Bone MD’s blog.  So I’m not sure if it would still qualify, though I’m more inclined to think that it wouldn’t.  So I’ve to review the other blogs I visit and came up with the following (listed in no particular order): Filipino Voices.com It is general... Prudence and Madness blogs http://www.medworm.com/rss/comments.php?id=1593936 Mon, 07 Jul 2008 16:13:13 +0100 1593936 http://www.medworm.com/index.php?rid=1488130&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F06%2F03%2Fnotes-from-the-day-job-published-3-4-2008%2F This year, I’ve experienced what bloggers call - um, not blogging very much. One reason is that much of our conversation has moved to other services - notably FriendFeed. However, the main reason is that I have a day job: develop bioinformatics applications, perform research, publish articles, present talks and keep the boss happy. Read on for some “notes from the day job” - especially if protein kinases and their substrates are your thing. When I arrived at UQ a couple of years ago, I inherited a project named Predikin. The goal of Predikin is to predict substrates for protein kinases, using structural features in the kinase catalytic domain. It’s a simple but effective idea: you look at the available structures of protein kinase-substrate peptide complexes and lo... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1488130 Tue, 03 Jun 2008 04:49:43 +0100 1488130 http://www.medworm.com/index.php?rid=1436793&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F05%2F12%2Fproteomics-discussion-from-the-science-streamosphere%2F We find ourselves wondering why codon adaptation index (CAI) is used as a measure of protein expression level in this article. One answer is that CAI does correlate well with protein expression in many proteomics studies; but surely these same studies contain raw data with protein expression level? On reflection, I bet the answer is that it’s too difficult and laborious to access this type of data. There are plenty of papers that describe large-scale analysis of protein expression using proteomics, but the data are locked up in the articles or as inappropriate supplementary files. Note to self: look into open-source software and standard data formats for proteomic data. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1436793 Mon, 12 May 2008 01:27:45 +0100 1436793 http://www.medworm.com/index.php?rid=1432379&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F05%2F09%2Fpublished-2-2008%2F It’s turned out to be a pretty good week. This one has been in press for ever, but finally hit the web: Frith, M.C., Saunders, N.F.W., Kobe, B. and Bailey, T.L. (2008). Discovering Sequence Motifs with Arbitrary Insertions and Deletions. PLoS Computational Biology 4(4):e1000071. [Open Access] | [PubMed] This paper describes GLAM2, a Gibbs sampler that finds and refines variable-width motifs, allowing insertion and deletion, in related but dissimilar sets of sequences. The work is very much Martin’s baby; my minor contribution was to try it out on some test datasets. It’s open-access, so you can all go and enjoy it. Two more (unrelated) in press to tell you about soon. See, I do have a day job outside of this blog. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1432379 Fri, 09 May 2008 13:42:36 +0100 1432379 http://www.medworm.com/index.php?rid=1292211&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F03%2F11%2Fpublished%2F It’s online, so I guess I can tell you about: Lonic, A. Barry, E.F., Quach, C., Kobe, B., Saunders, N.F.W. and Guthridge, M.A. (2008) FGFR2 phosphorylation on Serine 779 couples to 14-3-3 and regulates cell survival and proliferation. Mol. Cell. Biol. (ahead of print); DOI:10.1128/MCB.01837-07 [Abstract] | [Manuscript] A minor contribution from me: they asked which kinases might phosphorylate S779, I gave them a list (using a tool that may see the light of day eventually), they showed that activation of a candidate kinase leads to increased phosphorylation. That would rate an acknowledgement from some people, but these guys were kind enough to add our names to the paper. Just another scene from the life of the “go-to” bioinformatician. (Source: What You're Doing Is Rath... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1292211 Tue, 11 Mar 2008 01:42:00 +0100 1292211 http://www.medworm.com/index.php?rid=1259910&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F02%2F27%2Fhow-to-map-protein-sequence-onto-chromosomal-coordinates-using-bioperl%2F My coding challenge this week: given a protein sequence and its exons, how do you map single amino acid residues to a location on a DNA sequence? It’s trickier than you might think. Read on for my latest BioPerl how-to. Basic concepts Picture a hypothetical protein sequence, 7 amino acid residues long. Those residues are encoded by 7 x 3 = 21 codons. Therefore, to describe the location of an amino acid on a DNA sequence, we require 3 positions. In prokaryotes, the codons for our protein sequence are contiguous. If I tell you that the gene for our 7 amino acid protein begins at position 1000 on the chromosome, you can tell me that amino acid #1 maps to (1000, 1001, 1002), amino acid #2 maps to (1003, 1004, 1005) and so on, up to amino acid #7 at (1018, 1019, 1020). In general, the co... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1259910 Wed, 27 Feb 2008 07:41:10 +0100 1259910 http://www.medworm.com/index.php?rid=1246583&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F02%2F21%2Fopenwetware%2F This post from the OpenWetWare blog (discovered via Pedro’s shared items) has inspired me to sign up to OWW - should have done so much earlier. Here’s my user page and the beginnings of a wiki for our lab. Read the OWW mission statement if you’re not familiar with their goals. I think the OWW site provides an excellent space for collaborative projects. Note to self: aim to set up at least one in the next couple of months or so. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1246583 Thu, 21 Feb 2008 00:04:42 +0100 1246583 http://www.medworm.com/index.php?rid=1243608&cid=t_96241_87_f&fid=36516&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FAScannerBrightly%2F%7E3%2F237955795%2Fhospital-bill-appendix-ultimatum.html I have finally squared away my various hospital bills from last August's appendectomy, so what follows is a discussion of the hospital charges versus what everyone involved finally got paid. Excitement! Suspense! Thrills! Chills! Horror! It's hospital claims data!Episode OneFirst things first. A hospital visit includes a bunch of stuff, so I'm going to give you the full price for the entire episode of care, but I'll also break it down so we can see the component parts. And special thanks to CIGNA, who upgraded their Web site and now allow me to get claim records from more than a year ago. I'm now with Aetna as of January, and I haven't dealt with their Web site yet...Episode of Care:Total Charges: $28,089.62Total Paid: $8,324.25 (real cost)29.6% of charges paid. In other words, my bill was... A Scanner Brightly blogs http://www.medworm.com/rss/comments.php?id=1243608 Wed, 20 Feb 2008 01:07:00 +0100 1243608 http://www.medworm.com/index.php?rid=1183223&cid=t_96241_87_f&fid=36516&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FAScannerBrightly%2F%7E3%2F224709698%2Fchiropractor-scans.html I finally got around to getting my electro-magnetic scans from my first chiropractor visit online.If it's not readable I'll post it somewhere else, in fact I'll upload this to Flickr once I'm done. I'm not used to uploading pictures on Blogger. Thanks to Ronnie for scanning them in. (Source: A Scanner Brightly) A Scanner Brightly blogs http://www.medworm.com/rss/comments.php?id=1183223 Mon, 28 Jan 2008 17:55:00 +0100 1183223 http://www.medworm.com/index.php?rid=1174873&cid=t_96241_87_f&fid=34595&url=http%3A%2F%2Fnhsblogdoc.blogspot.com%2F2008%2F01%2Fcrippen-diary-2008-january-3.html What do you want to do when you grow up...January 2008 (3)Mr Green is a new patient. He lives in the posh part of town. According to the notes, he is a quantity surveyor. I was running about twenty minutes late when he came in. I smiled, and said I was sorry to have kept him waiting. He did not smile. He sat down and said, "I want to see a dermatologist.""Is there anything I can help with?""No, I have tried everything I can think of, and it has not helped so I need to see a dermatologist.""OK, right, er... have you ruled out the possibility that anyone here can help you?""I have had this rash for nearly a year, and I want to see a dermatologist" he said, firmly.Not winning here. "OK, I will refer you today.""How long will it take?" he asked."Several weeks" I said.Mr Green was not happy. I ... NHS Blog Doctor blogs http://www.medworm.com/rss/comments.php?id=1174873 Thu, 24 Jan 2008 14:46:00 +0100 1174873 http://www.medworm.com/index.php?rid=1162004&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F01%2F19%2Fwhen-scripts-fail-check-databases%2F Note to self: how many biological databases provide their release notes as an RSS feed? One of my database mining scripts failed today; on reading the SwissProt What’s New page, I discovered why: Changes concerning keywords (KW line) Modified keywords: * Phosphorylation -> Phosphoprotein Perhaps there’s a better way than looking for keywords? Then again, they changed the MOD_RES line a few months ago too. Scripts are bound to fail eventually if providers can change their format whenever they see fit. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1162004 Sat, 19 Jan 2008 08:04:43 +0100 1162004 http://www.medworm.com/index.php?rid=1148143&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F01%2F14%2Frapid-command-line-access-to-the-pdb%2F This is hardly earth-shattering stuff, but just for reference. There are multiple ways to grab PDB files from the RCSB PDB servers. If you know the accession code of a structure, the simplest way is wget (or similar) straight off the FTP server: wget ftp://ftp.wwpdb.org:/pub/pdb/data/structures/all/pdb/pdbXXXX.ent.gz where XXXX is the 4-character PDB accession code. Note the recent change of URL for the PDB archive: ftp://ftp.wwpdb.org. Note also the confusing 2, not 3 “w” in the URL. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1148143 Mon, 14 Jan 2008 05:56:07 +0100 1148143 http://www.medworm.com/index.php?rid=1132679&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F01%2F07%2Fprokaryotes-not-so-simple-after-all%2F One of my research challenges for 2008 is to marry my previous work (and my “true interest”), microbial genomics, with my current project which focuses on protein kinase substrate prediction. It should prove to be fascinating and fun, provided that publications such as this one keep appearing: Schneiker, S. et al. (2007) Complete genome sequence of the myxobacterium Sorangium cellulosum. Nature Biotech. 25: 1281-1289 doi:10.1038/nbt1354 | Abstract | Full Text (subscription) | PubMed It’s years since I read a textbook but I imagine that many of them will tell you that cell signalling via serine/threonine/tyrosine phosphorylation is “eukaryotic”, whereas Bacteria and Archaea use two-component sensor/histidine kinase systems. Some far-sighted individuals have b... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1132679 Mon, 07 Jan 2008 04:29:26 +0100 1132679 http://www.medworm.com/index.php?rid=1119427&cid=t_96241_87_f&fid=36516&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FAScannerBrightly%2F%7E3%2F207172736%2Fi-am-deformed.html I've been having some annoying shoulder and neck pain lately which I've been attributing to rugby and like all good Welsh rugby idiots, I've figured if I ignored it it would go away eventually. Ah well.After a month of wincing I finally decided to see someone about it, but really didn't want to go the whole doctor/surgeon route. So I went to a chiropractor.I will document my experience over the next few months, which I'll start here by talking about the first visit.My first note on arrival was that it was pretty much like a doctor's office, girls behind the desk, a bunch of chairs, some magazines. Everything was more naturopathic though, the magazines were all granola types.After my insurance card was inspected, I was taken to a back room with a massage table device and a computer. A tech ... A Scanner Brightly blogs http://www.medworm.com/rss/comments.php?id=1119427 Thu, 27 Dec 2007 19:33:00 +0100 1119427 http://www.medworm.com/index.php?rid=1085551&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F12%2F11%2Ftiehandlecsv%2F Bioinformaticians like tabular data; plain ASCII text delimited by tabs, commas or whatever. In the past, I’ve written an awful lot of scripts that begin something like this: open IN, $file; while(<IN>) { chomp; my @line = split("\t", $_); ## count fields in a line and check for header if($#line == 6 && $line[0] ne "ID") { ## do something with fields } } close IN; Bad programmer! Why not use one of the many Perl modules for handling CSV files, such as Tie::Handle::CSV? Read the rest… (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1085551 Tue, 11 Dec 2007 06:21:34 +0100 1085551 http://www.medworm.com/index.php?rid=1034609&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F11%2F18%2Fhandy-perl-variables-and%2F Regular expression matching is one of the key features that makes Perl a widely used language in bioinformatics. For example, we can match a peptide to a longer protein sequence like this: my $seq = "MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPG"; my $pep = "MAGTAM"; while($seq =~/$pep/g) { print "Found a match\n"; } Perl also uses a bunch of “special variables”, that are automatically assigned values when you perform certain operations. Two of these, @- and @+, contain indices representing the start and end of a regular expression match. Very handy for when you want to know the matching positions in the longer sequence. Note that you need to add one to the start position since indices start at 0, whereas sequences start at 1: while($seq =~/$pep/g) { pr... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1034609 Sun, 18 Nov 2007 04:01:07 +0100 1034609 http://www.medworm.com/index.php?rid=996486&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F11%2F01%2Fa-small-achievement%2F Moving to a new group and a new project is always difficult. However, one of the better aspects of being a bioinformatician is that you can often contribute to other projects - which can be a bonus when your own are not progressing so well. I’m happy to announce: Thakur, A.S., Robin, G., Guncar, G., Saunders, N.F.W., Newman, J., Martin, J.L. and Kobe, B. (2007). Improved Success of Protein Crystallization Sparse Matrix Screening with Heterogeneous Nucleating Agents. PLoS ONE 2:e1091. Open Access My contribution was very minor; some writing and a little statistical evaluation (although the method that I had in mind didn’t make it to the final version). The take-home message is: if your protein won’t crystallise, try throwing some dried seaweed into the mix! It’s no... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=996486 Thu, 01 Nov 2007 03:59:54 +0100 996486 http://www.medworm.com/index.php?rid=949486&cid=t_96241_87_f&fid=36516&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FAScannerBrightly%2F%7E3%2F159477550%2Fappendix-ultimatum.html So, the old appendix flared up again, as of course it should. Same symptoms as before, it was evident what was coming. I left work, drove home, and prepared for my first hospital stay.(Quick reminder for the uninitiated: I visited Hospital A in February with symptoms of appendicitis, waited six and a half hours in the E.R. until giving up and going home. I then visited Hospital B the next day and had the most awful day I've had in quite some time, culminating in me being seated on a gurney two corridors away from the E.R. outside the isolation room where a guy with full-blown tuberculosis and his wife were wandering in and out of isolation back and forth in front of me complaining of the heat. I've had a dodgy appendix for quite some time. Read the full story in all it's glory here.)I gath... A Scanner Brightly blogs http://www.medworm.com/rss/comments.php?id=949486 Fri, 21 Sep 2007 13:51:00 +0100 949486 http://www.medworm.com/index.php?rid=883647&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F09%2F19%2Fwhere-n-is-an-arbitrarily-large-fraction-approaching-one%2F What’s N? It’s the fraction of time that bioinformaticians spend obtaining, formatting and getting raw data ready to use, as opposed to analysing it. There’ll be a longer post on this topic soon. Suffice to say, I’ve spent the last month evaluating the performance of 5 predictive tools that are available on the web. To do this, a test dataset of 200 or so sequences had to be submitted to each one. Each tool generates a score for particular residues in the sequence. The final output, which is what I require to do some statistical analysis, looks something like this: P08153 114 method 61.74 0 P08153 522 method 82.10 1 where we have a sequence UniProt accession number, a sequence position, the name of the tool used (method), a score and either 1 (a positi... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=883647 Wed, 19 Sep 2007 03:06:00 +0100 883647 http://www.medworm.com/index.php?rid=844777&cid=t_96241_158_f&fid=36018&url=http%3A%2F%2Fcaregiversbeacon.blogspot.com%2F2007%2F09%2Fcaregivers-daily-care-diary-or-journal.html Updates on diet, meals, medication, exercise, activities, household management, and schedules can be kept in a caregiver's daily logbook. If blood pressure is being taken, or blood suger is being monitored this can be included in the notes. The daily diary notes are useful because family caregivers, paid caregivers, and medical personnel can refer to the notes for updates and to track conditions.At the website for osspublishing.com you can see what a typical care diary looks like and order a published one or make your own version. You can get a notebook, paper, and dividers with labels for sections such as Daily Notes, Medications, Phone Numbers, Care Plan and so on.For example, if a caregiver is preparing meals for a senior who is a diabetic, then writing down the foods and amounts as wel... The Caregiver's Beacon - Resources, Links, Ideas, News blogs http://www.medworm.com/rss/comments.php?id=844777 Wed, 05 Sep 2007 13:25:00 +0100 844777 http://www.medworm.com/index.php?rid=837467&cid=t_96241_133_f&fid=35096&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FAutismVox%2F%7E3%2F151477846%2F “Hollie puts me into situations where I end up learning something about myself and about her.” Says Trisha Kayden about her 7-year-old autistic daughter in a profile in the September 2nd Midland Daily News (Michigan). Kayden also notes that “‘If I couldn’t find a reason to laugh, I’d probably be crying a lot……You get rewards that other people take for granted.’” Kayden’s story, “McBuns” (about a trip with Hollie to McDonalds) will be included in Chicken Soup for the Soul: Children with Special Needs, which is due out today. The Midland Daily News notes that Kayden has been “writing in a journal for as long as she can remember” and that keeping the journal “helped her better understand and subseq... Autism Vox blogs http://www.medworm.com/rss/comments.php?id=837467 Mon, 03 Sep 2007 04:30:49 +0100 837467 http://www.medworm.com/index.php?rid=825370&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F08%2F28%2Fr-tip-for-the-day%2F The ROCR package is very useful - and a bit tricky to install. The documentation says: You will also need gplots from the R package bundle gregmisc To avoid packages complaining that they can’t find other packages, install the packages in this order: sudo R install.packages("gtools","gdata","gplots","ROCR") Reading in data is easiest using read.table if you can hack an input file with column 1 = scores, column 2 = true/false, like this: 6.17 1 5.98 0 5.97 0 5.92 0 5.87 1 data <- read.table("myfile.dat") pred <- prediction(data[,1], data[,2]) ## ROC curve plot(performance(pred, measure = "tpr", x.measure = "fpr")) (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=825370 Tue, 28 Aug 2007 09:07:42 +0100 825370 http://www.medworm.com/index.php?rid=808595&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F08%2F20%2Fzotero-word-processor-integration%2F Zotero have quietly released plugins for integration with OpenOffice and NeoOffice (oh, and the other commonly-used word processor). There’s not much documentation yet. Here’s what I did for OpenOffice, Ubuntu/Feisty: Download and unzip the extension In OpenOffice go to Tools->Extension Manager->Add Locate the Zotero.oxt file and install Restart OpenOffice You should now see a new menu like this: Clicking on “insert citation” brings up your Zotero database. It’s a bit rough and ready just now with limited options, but definitely an exciting development. Technorati Tags: zotero, bibliography (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=808595 Sun, 19 Aug 2007 22:49:33 +0100 808595 http://www.medworm.com/index.php?rid=786656&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F08%2F08%2Frejection-and-acceptance%2F From Schmap: I am delighted to let you know that your submitted photo has been selected for inclusion in the newly released third edition of our Schmap Brisbane Guide: Mt Coot-tha Lookout And from an unnamed journal: I am sorry to say that we cannot consider the manuscript for publication… …If at some stage you are able to fully address the referees’ concerns, we are happy to consider a new manuscript… The first email made me happy, at least. I don’t think there’s a way to blog about manuscript rejection that won’t turn into an angry rant, so I’ll leave it. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=786656 Wed, 08 Aug 2007 07:16:30 +0100 786656 http://www.medworm.com/index.php?rid=782903&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F08%2F07%2Fbrief-note-on-mgltools%2F MGLTools provides a GUI and python scripts for use with AutoDock. Installation on Ubuntu 7.04 is easy enough with the binary installer. However, none of the GUIs want to run: TclError: Togl: couldn't get visual hit enter to continue We at least get to a window by appending “DISPLAY=:0″ to the front of the command. Seems to be an Xgl issue. Why am I running Xgl? Take a guess. Oh, how I hate the ATI fglrx driver for Linux. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=782903 Mon, 06 Aug 2007 23:20:31 +0100 782903 http://www.medworm.com/index.php?rid=781273&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F08%2F06%2Fautodock-40-now-with-added-gpl%2F It’s been a year or two since I investigated AutoDock, a software suite for docking small molecules to receptors. I was pleased to discover today that the latest version, 4.0.1, is freely available for academic use under a GPL license. Oddly, version 3 still requires the incredibly old-fashioned “fax a signed agreement” procedure, for some reason. Looks like it’s going to be a learning curve. I’ve made it through the configure, make, make install cycle giving me the autodock and autogrid binaries, but that’s about it for now. There’s an installation of MGLTools to figure out, then some combing through the website in search of documentation. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=781273 Mon, 06 Aug 2007 11:42:20 +0100 781273 http://www.medworm.com/index.php?rid=761441&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F07%2F27%2Fa-nasty-mod_res-surprise%2F A lot of bioinformatics consists of fetching files in various formats from databases and writing parsers to extract features. What to do when one of your trusty parsers unexpectedly fails? Don’t panic Make sure that you haven’t done something silly: did you inadvertently alter the code recently? did you run a different version of the code by mistake? did you use the correct file(s) as input? does the machine that you’re using have the required libraries and software used by the parser? If your code or machine setup hasn’t changed, then the culprit must be the input file Take a look at the file - use something like grep if possible to examine specific lines and see if their format has altered. One of my more robust perl scripts is designed to examine the MOD_RES ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=761441 Fri, 27 Jul 2007 03:42:53 +0100 761441 http://www.medworm.com/index.php?rid=756658&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F07%2F25%2Fhowto-generate-random-sequences-using-emboss-and-perl%2F Once in a while, you need a “random” sequence.  For instance, you might perform a simple statistical analysis on a bunch of sequences from a database and decide that it looks interesting.  However, if the analysis looks the same when performed on a set of completely random sequences, it’s a fair bet that it isn’t interesting at all. Read the rest. . . (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=756658 Wed, 25 Jul 2007 08:01:19 +0100 756658 http://www.medworm.com/index.php?rid=752764&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F07%2F24%2Ffinally-ati-fglrx-xgl-beryl-for-ubuntu-feisty%2F I’ve had harsh words to say about ATI Linux video drivers in the past - and I’m not withdrawing them. My advice is still do yourself a favour and buy NVIDIA. That said, I did an Ubuntu install on a work machine today (we get little choice with the specs) and finally got the proprietary fglrx driver working with Xgl and beryl, for a fancy desktop. All thanks to this very clear post; I’ve read many and this is the best. The key points are: The open-source radeon driver has composite (for beryl/compiz), but no TV-out and doesn’t support newer cards The closed fglrx driver has TV-out but no composite. However, you can get beryl/compiz to run by combining it with Xgl, which is as simple as installing xserver-xgl and editing a small start-up script. Here’s the key:... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=752764 Tue, 24 Jul 2007 09:34:34 +0100 752764 http://www.medworm.com/index.php?rid=743283&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F07%2F19%2Fparse-the-pdb-using-bioperl%2F I think it’s time for a quick Perl tutorial. This week: how to extract PDB entries based on 3 factors: a domain that interests you, the number of chains and their length. Read the rest. . . (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=743283 Thu, 19 Jul 2007 12:51:54 +0100 743283 http://www.medworm.com/index.php?rid=733534&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F07%2F13%2Fopen-science-discussion%2F Question: does the open research world need a single access point? You do open research. You write about it in your blog. Feedback comes in the form of blog comments. Great, but undoubtedly others can learn from the discussion - if they can find it. Do people find it? If a blogger has research questions and you have the answers, consider creating an article on the Nodalpoint open research discussion wiki page. I’m not suggesting that this become the place to go for answers (although that would be nice), but it’s a place. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=733534 Fri, 13 Jul 2007 05:27:24 +0100 733534 http://www.medworm.com/index.php?rid=949489&cid=t_96241_87_f&fid=36516&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FAScannerBrightly%2F%7E3%2F125839910%2Fnote-to-pharmacists.html Stop pressing my buttons! It's my question, I'll answer it!The last three prescriptions I filled I encountered the same complete lack of customer service that is really beginning to peeve me off.During checkout, here in NYC at least, after the money has changed hands the little screen pops up a screen that allows you to respond "No I do not need advice" or "Yes I received advice on my medication" or something to that effect.Each of the last three times, the person handling the transaction leaned over and clicked the "no I don't need advice" button for me.Un-flippin'-believable.The first time was an independent pharmacy where I was getting my son's first ever dose of penicillin and yes, actually, I had some questions. I was worried about an allergic reaction as this would be the first time ... A Scanner Brightly blogs http://www.medworm.com/rss/comments.php?id=949489 Mon, 18 Jun 2007 16:22:00 +0100 949489 http://www.medworm.com/index.php?rid=674623&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F06%2F15%2Fexplaining-the-resistance-to-sharing-data%2F I have a theory. My theory is that many scientists are prone to doublethink. They believe that they are acting in a certain way when in fact, they’re doing the exact opposite. Take data sharing. Read the rest. . . (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=674623 Fri, 15 Jun 2007 06:17:57 +0100 674623 http://www.medworm.com/index.php?rid=674629&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F06%2F07%2Fgetting-biologists-to-think-about-software%2F Every few months, my colleagues decide that electronic laboratory notebooks (ELNs) are a good idea. I go through the ritual of searching the web, bookmarking some resources and where possible downloading, installing, configuring and running packages to see how well they work. I know in advance that I’m wasting my time, because I’ve tried them all and there isn’t one free/open-source ELN that works for me. Read the rest. . . (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=674629 Thu, 07 Jun 2007 04:52:37 +0100 674629 http://www.medworm.com/index.php?rid=644666&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F05%2F29%2Fhow-to-create-bioinformatics-code-from-a-published-article%2F It’s been a while since I posted a “how to” article - and now is a good time, as Bio::Blogs #11 is going to feature a special tips and tricks section. So today, I’d like to illustrate how to create some useful code for bioinformatics analysis by reading a scientific paper. Read the rest. . . (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=644666 Tue, 29 May 2007 00:06:13 +0100 644666 http://www.medworm.com/index.php?rid=644667&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F05%2F28%2Fa-welcome-surprise%2F I attended a departmental seminar today, entitled “drug discovery in tropical diseases” and given by Matthew Todd. Much of the talk focused on the synthesis of praziquantel, a drug used to treat schistosomiasis. Interesting, though organic chemistry isn’t my strong point. However, it turns out that Matthew is one of the faces behind The Synaptic Leap and he devoted a few slides to TSL, Jean-Claude Bradley’s Useful Chemistry blog and the concept of open science. This might be the first time in 7 years that I’ve heard anyone in Australia talk about open science in a university seminar. Note this day and may there be many more. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=644667 Mon, 28 May 2007 04:36:37 +0100 644667 http://www.medworm.com/index.php?rid=611376&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F05%2F16%2Fcitation-clouds%2F I’m preparing a presentation in which one slide is a survey of published methods for predicting the substrates of protein kinases. Just for fun, I made a note of the number of citations for each method, as judged by Google Scholar. Next, I tried out a couple of Perl modules from CPAN: TagCloud and WWW::CloudCreator. Result: the “citation cloud”. I’m sure that this is not an original idea. I’m not convinced that it’s any more informative than the raw numbers, but it is at least an instant visual impression. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=611376 Wed, 16 May 2007 04:21:40 +0100 611376 http://www.medworm.com/index.php?rid=578654&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F04%2F30%2Fannouncing-joomlalims-formerly-mambolims%2F A couple of years ago, I threw together a basic LIMS for my lab using a CMS called Mambo and a component called FacileForms. I made it publicly available and there was a little interest. Time passed, Mambo forked into the Joomla project, FacileForms went through several upgrades and my LIMS broke and fell into disuse. Recently I resurrected the project as JoomlaLIMS. It uses the latest Joomla (1.0.12), the latest FacileForms (1.4.7), PHP 5 and MySQL 5. I’ve got it working to the point where I’m comfortable letting it loose in the world. So I give you JoomlaLIMS at Google Groups. You can download the tarball from there, unpack it in your web root, create the appropriate database, tables and user and hopefully, you’ll be ready to go. If you’re looking for a simple lab... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=578654 Mon, 30 Apr 2007 14:01:43 +0100 578654 http://www.medworm.com/index.php?rid=578655&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F04%2F30%2Fremoving-a-mysql-user%2F Many of us have installed a MySQL database as part of a PHP/MySQL-based web application. Normally this procedure includes adding a specific user and password for the database: mysql> grant all on mynewdb.* to idiot@localhost identified by 'guessme' What the setup guide never tells you is how to remove that user should you decide to remove the application. You need to see what grants they have, revoke them, then remove the user from the user table: mysql> show grants for idiot@localhost; mysql> revoke all privileges, grant option from idiot@localhost; mysql> drop user idiot@localhost; (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=578655 Mon, 30 Apr 2007 01:10:23 +0100 578655 http://www.medworm.com/index.php?rid=554309&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F04%2F19%2Fhow-many-protein-kinases-in-the-pdb%2F I often find that the most satisfying problems in bioinformatics are not related to a specific research project. They arise when someone has a query and you have a neat way to send them an answer, quickly. Take this email that I received yesterday: I’m compiling a table of serine-threonine protein kinase structures. Can you take a look and see if anything is missing? Strangely, I don’t carry a list of current PDB accessions for every protein kinase in my head. On the other hand if you ask me “can I extract all structures that are protein kinases from the PDB?”, the answer is yes, you can. So here’s what I did. Read the rest. . . (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=554309 Thu, 19 Apr 2007 11:16:52 +0100 554309 http://www.medworm.com/index.php?rid=545513&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F04%2F16%2Foutlets-for-hypotheses%2F The tale of the blog post that led to the journal article set me thinking about forums for publishing our hypotheses. We all have ideas, some of them wild, but many based on good science, that we’ve never been able to develop as we’d like. By develop I mean validate experimentally. A chance observation in a genome sequence perhaps, or some data from an old project that was left unfinished when we changed jobs. Often we know just what needs to be done in order to confirm our idea but are unable, for whatever reason, to do so. It would be great if these types of observation could be written up and published somewhere - perhaps it would spur someone else in the field to do the key experiment. My lazy query - as I don’t have time to survey every life sciences journal is this:... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=545513 Mon, 16 Apr 2007 09:55:55 +0100 545513 http://www.medworm.com/index.php?rid=508866&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F03%2F29%2Fzen-of-latex%2F Zen moments are common if you use a lot of open-source software. Sometimes you download software, work your way through some tutorials and how-tos and scan mailing lists, but you don’t quite see what all the fuss is about. Then one day you have your zen moment - “Aaah!” - when you get it. It’s taken way too many years but this week, I finally had my LaTeX zen moment. Read the rest… (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=508866 Thu, 29 Mar 2007 12:25:40 +0100 508866 http://www.medworm.com/index.php?rid=949503&cid=t_96241_87_f&fid=36516&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FAScannerBrightly%2F%7E3%2F104401125%2Fhospital-bill-appendix-addendum.html Well, my weekend got away from me, so I'll settle for blogging the hospital bill I just received regarding my recent day trip to the local Emergency Room, as chronicled in Appendix Addendum.In case you missed the first post, I went to one ER, bailed, and went to a second one the next day. In all fairness, I haven't seen a claim made on my first, failed visit, which I'd be cool with if they billed for the labs they more than likely ordered before I left.So, Hospital B.In short summary, I had a blood and urine workup, one CAT scan, and was seen by an ER doc and a surgeon.The bill goes like this:Eight, count them, eight lab charges.$101.00, $125.00, $28.20, $89.00, $89.00 again, $96.00, $50.00 and $62.00Total lab charges: $640.20Total amount covered by my insurance company? $62.41All lab char... A Scanner Brightly blogs http://www.medworm.com/rss/comments.php?id=949503 Mon, 26 Mar 2007 02:09:00 +0100 949503 http://www.medworm.com/index.php?rid=949507&cid=t_96241_87_f&fid=36516&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FAScannerBrightly%2F%7E3%2F102217074%2Fappendix-addendum.html This is a personal account of my recent brush with appendicitis and the fun I had getting hospital care...I had appendicitis, but it took me a week and a half to figure it out. Couple that with my built-in fear of all things medicinal and by the time I had a CAT scan I'd actually beaten the inflammation back from whence it came.As it turns out, I now know what that funny stomach ache that lasted a week back when I lived in France actually was. That's right. I've had appendicitis TWICE.So seeing as how I'm this health care report card guy, I decided to put my money where my mouth is and chose a hospital based on the report card I built. Due to the nature of my work I have a better knowledge than most of the hospitals in my area, and I chose Hospital A, high scores for quality and surgical i... A Scanner Brightly blogs http://www.medworm.com/rss/comments.php?id=949507 Fri, 16 Mar 2007 16:38:00 +0100 949507 http://www.medworm.com/index.php?rid=484829&cid=t_96241_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F03%2F13%2Fcalling-all-pssm-experts%2F I’ve been employing an equation in one of my Perl modules. It’s used to convert a matrix of frequencies at positions in a sequence to a matrix of weights; you see this called a position-weight matrix (PWM) or position site-specific matrix (PSSM). The equation looks like this (behold, the WordPress LaTeX plugin): where f(b,i) is frequency of base at position i, N is the sum of frequencies for a column and p(b) is the prior probability of the base in the sequence. Those terms with N are a statistical fudge called a pseudocount. The thing is - I’ve been using it somewhat empirically - which means that it seems to do what I want, but I’m not confident that my usage is justifiable in terms of the theory. So if you’re a PSSM expert, here are 3 questions for you: I... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=484829 Tue, 13 Mar 2007 06:50:18 +0100 484829