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 'data management'. Sat, 03 Sep 2011 02:17:32 +0100 http://www.medworm.com/index.php?rid=4433149&cid=t_104654_113_f&fid=34625&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FNeilVerselsHealthcareItBlog%2F%7E3%2FQYTLUG33_IE%2Fi-havent-done-much-with-my-youtube-page.html I haven't done much with my YouTube page since I launched it last month, but here's some new video of me, courtesy of Nuesoft Technologies. Nuesoft hosts a podcast series, and they recently invited me, along with Health Data Management Editor-in-Chief Greg Gillespie to discuss mobile healthcare technologies. We all had webcams, so the result is this YouTube video.In a bit of serendipity, Gillespie happened to be looking for freelance help with HDM's HIMSS Microsite, a collection of articles previewing HIMSS11. My first story should be up within the next hour. (Source: Neil Versel's Healthcare IT Blog) Neil Versel's Healthcare IT Blog blogs http://www.medworm.com/rss/comments.php?id=4433149 Thu, 03 Feb 2011 21:59:29 +0100 4433149 http://www.medworm.com/index.php?rid=4304954&cid=t_104654_113_f&fid=34634&url=http%3A%2F%2Fwww.emrandhipaa.com%2Femr-and-hipaa%2F2010%2F12%2F30%2Fsurescripts-becomes-onc-atcb-ehr-certification-body%2F In the weirdest news I’ve seen in a while, SureScripts has become an ONC-ATCB. Here’s the details from Health Data Management: In a Dec. 23 announcement, the Office for the National Coordinator for Health IT said that Arlington, Va.-based Surescripts can verify that e-prescribing, privacy and security modules meet the standards laid out in the meaningful use requirements. Surescripts is the sixth authorizer to be approved by ONCHIT, but it’s the only one with limited certification abilities—the five others have ONCHIT’s blessing to certify Complete EHRs and EHR modules. Doesn’t this scream conflict of interest? They run a nationwide e-Prescribing network, and yet they can certify ePrescribing for ONC. I guess you could make the argument that they know ePrescribing w... EMR and HIPAA blogs http://www.medworm.com/rss/comments.php?id=4304954 Fri, 31 Dec 2010 05:59:44 +0100 4304954 http://www.medworm.com/index.php?rid=4298689&cid=t_104654_113_f&fid=34634&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FEmrAndHipaa%2F%7E3%2FEaXwhFuiM7w%2F I’m excited to announce the beginning of Meaningful Use Monday on EMR and HIPAA. I first came up with the idea when Lynn Scheps from SRSsoft commented on one of my previous meaningful use posts. Lynn provided such valuable information, I asked her if she’d be interested in becoming a regular guest blogger on EMR and HIPAA. As they say, the rest is history. Each Monday, Lynn (and sometimes myself) will be covering some topic related to the EMR Stimulus money and meaningful use. We hope you enjoy Meaningful Use Monday. -John With the impending start of the EHR incentive program on January 1, the results of a recent Health Data Management poll are troublesome. 72% of respondents feel that the meaningful use guidance provided by the government to-date has been either “inadequate ... EMR and HIPAA blogs http://www.medworm.com/rss/comments.php?id=4298689 Mon, 27 Dec 2010 19:18:40 +0100 4298689 http://www.medworm.com/index.php?rid=4139480&cid=t_104654_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FQQmWLy0WjS4%2F Hired someone new and exciting? Promoted a rising star? Finally solved that hard-to-fill spot? Share the news with us and we’ll share with it others. That’s right. Send us your announcements and we’ll find a home for them. Don’t be shy. Everyone wants to know who is coming and going, especially with all the layoffs. Despite the downsizing, there is movement. Here are some of the latest changes. Recognize anyone? And here is our regular feature. Send us a photo and we will spotlight a different person each week. This time around, we note that Weill Cornell Medical College hired Steve Paul to head the Appel Institute for Alzheimer’s Research. Before joining the institution, Paul was vp of science and technology and president of at Eli Lilly Research Labs and was the scientific ... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4139480 Fri, 05 Nov 2010 12:32:57 +0100 4139480 http://www.medworm.com/index.php?rid=3592356&cid=t_104654_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F05%2F24%2Fif-you-must-send-me-an-excel-spreadsheet%2F …please, try to follow these simple guidelines. 1. Don’t bother to format the cells Where possible, I will not open your spreadsheet in a spreadsheet application. If I do, it will be only to marvel at the horror, then export it as rapidly as possible to a delimited text file. I do not care about the font, the font size or the font weight. I do not care whether there are grid lines around the cells. I especially do not care about cells which you have highlighted using some arbitrary (and unexplained) colour scheme. 2. No multiple tables If you include multiple “tables” on one sheet, separated by blank rows, there is a good chance that I will not notice them. If you include multiple tables on multiple “sheets”, there is an excellent chance that I will not ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3592356 Mon, 24 May 2010 06:33:57 +0100 3592356 http://www.medworm.com/index.php?rid=3573865&cid=t_104654_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F05%2F18%2Fdata-management-its-funny-because-its-true%2F Please read My Data Management Plan – a satire Have a good giggle Ask yourself if anything sounds familiar If you answered yes to (3), do something about it That is all. Filed under: bioinformatics, blogroll, computing, programming Tagged: best practice, data management, humour, satire (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3573865 Tue, 18 May 2010 01:52:43 +0100 3573865 http://www.medworm.com/index.php?rid=2902915&cid=t_104654_132_f&fid=35001&url=http%3A%2F%2Farchive.nodalpoint.org%2F2008%2F12%2F09%2Fdrupal_and_pubmed If you are interested in running a Drupal site with PubMed content you should check the screencast below. It explains how it can be done with existing Drupal modules. I'm working with a student from the University of Szeged on a PubMed module for Drupal. So in the future this should become a bit more straightforward ;) read more (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=2902915 Tue, 09 Dec 2008 19:32:50 +0100 2902915 http://www.medworm.com/index.php?rid=1432528&cid=t_104654_132_f&fid=35001&url=http%3A%2F%2Fwww.nodalpoint.org%2F2008%2F05%2F09%2Fi_still_havent_found_what_im_googling_for Twenty one years ago this month, in May 1987, Irish rockers U2 released their classic Joshua Tree single, I Still Haven't Found What I'm Looking For. Those twenty one years have seen incredible technological change: the adoption of desktop computers, mobile phones, the birth of the Web and the widespread use of search engines like Google. So with sincere apologies to Bono, The Edge, Adam and Larry, it's time we updated the lyrics for the 21st century. So, I give you "I Still Haven't Found What I'm Googling For" (21st anniversary, 2008 webby edition)... read more (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=1432528 Fri, 09 May 2008 09:48:48 +0100 1432528 http://www.medworm.com/index.php?rid=1420473&cid=t_104654_132_f&fid=35001&url=http%3A%2F%2Fwww.nodalpoint.org%2F2008%2F05%2F03%2Fintroducing_the_eyelims_project Scientists usually share information with collaborators from all around the world. For that purpose, eyeOS (www.eyeos.org) provides an unvaluable system to access and share documents, create and save data files or store crucial personal and professional information. To see eyeOS widely used by scientists all around the world, we initiated the eyeLIMS project ! eyeLIMS is a community-driven project which aims at providing a Free, web-based, Open Source Laboratory Information Management System (LIMS) powered by eyeOS. read more (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=1420473 Sat, 03 May 2008 15:22:57 +0100 1420473 http://www.medworm.com/index.php?rid=1182840&cid=t_104654_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2008%2F01%2Fthree-stories-about-science-and-the-web-the-movie%2F In a previous post I wrote about how great new web tools are making it easier for scientists to collaborate, find information, and share information. This light-hearted introduction was rather popular, so heres’s a tongue-in-cheek video version. (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=1182840 Mon, 21 Jan 2008 14:03:45 +0100 1182840 http://www.medworm.com/index.php?rid=1161036&cid=t_104654_132_f&fid=35001&url=http%3A%2F%2Fwww.nodalpoint.org%2F2008%2F01%2F18%2Fone_thousand_databases_high_and_rising Well it's that time of year again. The 15th annual stamp collecting edition of Nucleic Acids Research, also known as the 2008 Database issue [1], was published earlier this week. This year there are 1078 databases listed in the collection, 110 more than the previous one (see Figure 1). As we pass the one thousand databases mark (1kDB) I wonder, what proportion of the data in these databases will never be used? read more (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=1161036 Fri, 18 Jan 2008 13:08:37 +0100 1161036 http://www.medworm.com/index.php?rid=1182841&cid=t_104654_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2008%2F01%2Fdecouple-the-data-format-from-the-analysis%2F A common task in bioinformatics is to read data from a set of files, arrange into the required format, then run an analysis to verify or falsify your expectation. An example would be reading in the yeast interaction network, and protein evolution rates, then correlating the two sets of data to see if there is a trend. Using Perl, you would specify how each file gets read in, arrange the sets of data by gene name, then correlate the two. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=1182841 Mon, 07 Jan 2008 19:27:10 +0100 1182841 http://www.medworm.com/index.php?rid=1030156&cid=t_104654_132_f&fid=35001&url=http%3A%2F%2Fwww.nodalpoint.org%2F2007%2F11%2F15%2Fdata_integration_in_the_life_sciences_2008 Mon dieu! Doesn't time fly? Data Integration in the Life Sciences (DILS) is here again, see the Call For Papers. This time, DILS will be in Evry near Paris. The conference is on June 25-27, 2008 but if you're thinking of doing a paper, you've got until February 20th 2008 to submit. (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=1030156 Thu, 15 Nov 2007 20:38:53 +0100 1030156 http://www.medworm.com/index.php?rid=1028220&cid=t_104654_132_f&fid=35001&url=http%3A%2F%2Fwww.nodalpoint.org%2F2007%2F11%2F13%2Fjournal_article_search_via_rss_mashup I've been trying to come up with a nice way to mashup and process RSS feeds, mostly for the reason to be able to track articles from Journals that publish content that interests me. The best solution seems to be the workflows that can be constructed at Yahoo Pipes. read more (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=1028220 Tue, 13 Nov 2007 18:58:26 +0100 1028220 http://www.medworm.com/index.php?rid=1182844&cid=t_104654_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F11%2Fhow-to-avoid-errors-when-processing-csv-files%2F A lot of bioinformatics involves reading data from files to manipulate them for our analysis. For example, I spend a lot of time importing data from CSV files into my database. Doing this involves creating a script to iterate over each line of the file, then referencing each token in the row by its column number. However this is bad for two reasons. The first reason is because it introduces a dependency on the column number, which may feasibly change. You can fix this by changing the script though, so this is not too bad. The second reason is much more worse, because it could introduce a silent error. If the column number was wrong, then the wrong entry would be referenced. If correct and wrong entry where both of the same type, e.g. floats, then there is a chance you would miss the mistak... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=1182844 Thu, 01 Nov 2007 18:44:49 +0100 1182844 http://www.medworm.com/index.php?rid=795126&cid=t_104654_132_f&fid=35001&url=http%3A%2F%2Fwww.nodalpoint.org%2F2007%2F08%2F13%2Fa_most_ugly_hack_translating_from_charmm_to_amber_trajectories Ever wondered how you might translate trajectories from one Molecular Dynamics package to another? It's a thorny little problem that's afflicted quite a few structural biologists. Here's one ugly solution that I am rather proud of. (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=795126 Mon, 13 Aug 2007 05:48:49 +0100 795126 http://www.medworm.com/index.php?rid=841725&cid=t_104654_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F07%2Fjournals-the-open-science-question%2F I think journal policies towards preprint servers are covered by the data from the Romeo database, outlined previously. For the next stage of the open science edition of tips and tricks I think I need to include clarification of journal positions towards publication and discussion of data on blogs, wikis, and such like. I spent a while trying to come up with a suitably clever letter, but this is the best I could do. Dear Sirs, I’m compiling, with the bioinformatics blogging community, a guide to open science. I believe one of the one of most important points on in this issue are journal editorial polices towards sharing and discussing research, prior to publication. The use of preprint servers is becoming accepted, however the position of journals towards the use of blogs and wikis t... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841725 Wed, 04 Jul 2007 16:43:33 +0100 841725 http://www.medworm.com/index.php?rid=692348&cid=t_104654_87_f&fid=34867&url=http%3A%2F%2Fwww.thediabetesblog.com%2F2007%2F06%2F23%2Fmedtronic-software-designed-to-help-docs-juggle-patient-records%2F Filed under: Type 1, Type 2, SupportA major player in the world of diabetes management, Medtronic Inc., has just released a new product: CareLink Pro Software. The product is part of Medtronic's CareLink line for diabetes management. Designed for use by physicians, CareLink Pro Software is intended to help docs - specifically, endocrinologists - with what seems to be an increasingly impossible task: juggling all the information on diabetic patients without dropping any balls - that is, without losing anything, without making mistakes, and just generally making it more likely patients will get optimal care. So, your doctor can store and retrieve patient info from the Internet, and can store data from a patient's continuous glucose monitoring device, among other things. All this info is loca... The Diabetes Blog blogs http://www.medworm.com/rss/comments.php?id=692348 Sat, 23 Jun 2007 04:00:00 +0100 692348 http://www.medworm.com/index.php?rid=841729&cid=t_104654_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F06%2Fthe-case-for-open-science%2F Traditional science is carried out by experimentation, interpreting the results in respect to the hypothesis, and repeating this until publication. Publication is everything, and as such it’s important to keep your research secret, lest anyone publish something similar which undermines the opportunity to publish in a high impact journal. An open science philosophy says that this closed approach slows scientific advancement. Results should be made available as soon as possible, then everyone in the field can benefit from them sooner. There is no delay for peer review and publication. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841729 Sun, 17 Jun 2007 19:43:39 +0100 841729 http://www.medworm.com/index.php?rid=579748&cid=t_104654_132_f&fid=35001&url=http%3A%2F%2Fwww.nodalpoint.org%2F2007%2F04%2F29%2Fpublish_or_perish_software_now_for_linux Publish or Perish is an interesting (and free) piece of software, that obtains citations using Google Scholar and then analyses them in various ways. In particular it makes use of h-indices, which have been proposed as a "fairer" citation metric. I've been in correspondence with the developers over the past couple of months and they kindly let me know that a native Linux version, built using GTK+ 2.x is now available. If citation analysis is your thing, give it a try and let the authors know what you think. read more (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=579748 Mon, 30 Apr 2007 03:48:29 +0100 579748 http://www.medworm.com/index.php?rid=841741&cid=t_104654_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F04%2Fuse-a-hyperlinked-document-as-a-bioinformatics-lab-book%2F I wrote previously about using the file system to organise your scripts and data. I use this method and it does help my organisation, but it doesn’t replace a lab book. I want a system that explains the relationships between the different set of results, and shows the outline of my work. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841741 Fri, 13 Apr 2007 15:34:11 +0100 841741 http://www.medworm.com/index.php?rid=841742&cid=t_104654_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F03%2Fthree-libraries-and-a-tool-to-enhance-your-bioinformatics-coding%2F Coding is fact of life for bioinformatics. If you work in bioinformatics you probably enjoy coding to some extent. It’s our equivalent to PCR, western blots and sequencing. So whether your weapon of choice is Java, Perl, Python or C++, here’s three packages and a tool worth a look. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841742 Fri, 30 Mar 2007 12:32:21 +0100 841742 http://www.medworm.com/index.php?rid=486209&cid=t_104654_132_f&fid=35001&url=http%3A%2F%2Fwww.nodalpoint.org%2F2007%2F03%2F18%2Fa_pipeline_is_a_makefile What is a pipeline? For me, it' s series of steps that munch DNA/protein data, combines it with other data using various small scripts and outputs the results as diagrams or HTML. Do we want to code this kind of software as a script? If you think "makefile!" now, then you're much more clever than I was. But personally, until recently, I've glued my scripts together using other scripts. And used makefiles only for compiling my programs. That was a bad idea. (it's a quite detailed post, click on "read more" for the full article) read more (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=486209 Sun, 18 Mar 2007 19:16:10 +0100 486209 http://www.medworm.com/index.php?rid=841745&cid=t_104654_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F03%2Fbioinformatics-which-programming-language-to-use%2F Two recent posts on using programming languages in bioinformatics. One at biowhat and the other at Omics! Omics!. Both discuss what type of language to use. Heavy weight languages such as C++ and Java versus lighter scripting languages such as Perl, Ruby and Python. I think this depends on what what your research goals are. If your aim is to build a tool for biologists, then you probably need an application building language such as C or Java. On the other hand if you want to find an answer to a biological question then it’s a lot easier to create a short Perl script than manipulates the data to produce the desired result. Heavy weight My background is biology rather than computing science, but I find languages like Java encourage a better coding style. Which if you’re working ... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841745 Wed, 14 Mar 2007 20:42:02 +0100 841745 http://www.medworm.com/index.php?rid=841752&cid=t_104654_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F02%2Fbioinformatics-use-a-database-for-data%2F Previously, I wrote about organising your file system to make the relationships between files that produce data, and files containing data more descriptive. One of the best tips I’ve been given, is to store all my data in a database. Regardless of what the data is, or how “mission critical”. Here are some reasons to use a database, rather than files, to store your data. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841752 Mon, 26 Feb 2007 15:21:11 +0100 841752