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 'best practice'. Sat, 03 Sep 2011 02:21:48 +0100 http://www.medworm.com/index.php?rid=5028877&cid=t_145162_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=4489812&cid=t_145162_118_f&fid=39279&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffoxepractice%2F%7E3%2FfVzBFpO3VkI%2F Want to take your medical practice Facebook Page to the next level? To stand out from all the other healthcare organizations, adding a simple Facebook App can increase the functionality for your patients and make a difference.Keep it simple for your patientsRemember to keep it simple. There is nothing that turns away people more than a bloated Facebook Page. We are very wary of recommending customization of a Facebook Page to our medical practice clients. Facebook has a tendency to change their core code frequently, which often breaks the functionality of poorly maintained Facebook Apps.Use Facebook’s Standard AppsBefore going to a third party to extend the functionality of your healthcare Facebook page, make sure you are using the standard functionality to its fullest.Automatically ... Fox ePractice blogs http://www.medworm.com/rss/comments.php?id=4489812 Wed, 16 Feb 2011 18:20:34 +0100 4489812 http://www.medworm.com/index.php?rid=4489813&cid=t_145162_118_f&fid=39279&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffoxepractice%2F%7E3%2FsnlnBCWA5Ew%2Fbest-practices-healthcare-facebook-page In its initial stage, healthcare social media was perceived by some as “free advertising”. That was a grave misunderstanding.Such a perception might have come about because there were no direct cash outlays for using this communication channel in healthcare organizations. Brochures, print, TV, and phone communication all have a usage price tag on them, but social media has a different kind price tag–time, creativity, openness, and a love for the services you provide.In short, there is nothing free in healthcare social media. As with everything else in life, a successful healthcare social media presence takes work. But that being said, following some basic principles will get you going and keep you on track. As an example, below are some best practices for management of yo... Fox ePractice blogs http://www.medworm.com/rss/comments.php?id=4489813 Tue, 08 Feb 2011 17:59:01 +0100 4489813 http://www.medworm.com/index.php?rid=4265735&cid=t_145162_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fleading-healthcare-systems-collaborate-on-best-practices-for-common-conditions%2F2010.12.17 Six of the nation’s leading healthcare systems will collaborate on outcomes, quality, and costs across eight common conditions or procedures in an effort to share best practices and reduce costs with the entire healthcare system. Cleveland Clinic, Dartmouth-Hitchcock, Denver Health, Geisinger Health System, Intermountain Healthcare, and Mayo Clinic will to share data among their 10 million patients with The Dartmouth Institute, which will analyze the data and report back to the collaborative and the rest of the country, according to a press release. The collaborative will focus on eight conditions and treatments for which costs have been increasing rapidly and for which there are wide variations in quality and outcomes across the country. The first three conditions to be studies are ... Better Health blogs http://www.medworm.com/rss/comments.php?id=4265735 Fri, 17 Dec 2010 22:00:00 +0100 4265735 http://www.medworm.com/index.php?rid=3890501&cid=t_145162_109_f&fid=34750&url=http%3A%2F%2Fpsychcentral.com%2Fblog%2Farchives%2F2010%2F08%2F21%2Fethical-best-practice-in-an-evidence-based-age%2F There were 2 presentations at this year’s annual American Psychological Association convention, which were important to psychotherapists in particular. With the ever-growing challenge to prove efficacy of each and every treatment, healthcare providers and consumers alike face some confusion as to how much information is enough, or too much. Does every therapists need to give a long presentation about the relative proven efficacy of low-dose medication combined with verbal therapy — and 2 hours gardening per week? (I made up the last part, but hiking and fresh air were a popular cure for quite a long time in 19th Century Europe.) Physicians are acutely aware of the need to know the research, and most ethical codes demand informed consent. Both health and mental health professionals ... World of Psychology blogs http://www.medworm.com/rss/comments.php?id=3890501 Sat, 21 Aug 2010 14:20:35 +0100 3890501 http://www.medworm.com/index.php?rid=4018280&cid=t_145162_118_f&fid=39279&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffoxepractice%2F%7E3%2FG_yMdBR7kvc%2Fhcsm-scoop-week30 At Fox ePractice we’re committed to providing you with everything you need to understand, position yourself, and to take advantage of the fundamental shift that is taking place in marketing a medical practice. To that end, each week this page will highlight some of the best content that we have come across on the web in order to further your knowledge of the opportunities before you. We will showcase both Healthcare Social Media experts who speak out on the subject, as well as those sites that demonstrate what we feel are healthy examples of how to put the concept of Web 2.0 to work for their healthcare businesses. So read on … and “get the scoop”: An Introduction to Media Psychology for Bloggers and Tweeters This great indepht article “focuses on the former unders... Fox ePractice blogs http://www.medworm.com/rss/comments.php?id=4018280 Fri, 30 Jul 2010 22:16:02 +0100 4018280 http://www.medworm.com/index.php?rid=3757865&cid=t_145162_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Funease-about-blogging-and-social-media-in-medicine%2F2010.07.15 Although it happened a few weeks ago, I only recently learned of the “retirement” of the blog called “Medic999” by EMS social media superstar Mark Glencourse who works in the United Kingdom. I only learned of Mark and his blog (which was recognized as the 2009 Fire/EMS Blog of the Year) in the past few months in association with the hugely popular Chronicles of EMS project (see the first episode on video here). In stating why he was stopping his blog, unfortunately, I find similar thoughts being shared by the medical colleagues I know about why people either stop blogging or don’t ever start in the first place: I find it a shame that the reason for this blog ending is the general lack of understanding of blogging and social media. I feel that I have promote... Better Health blogs http://www.medworm.com/rss/comments.php?id=3757865 Thu, 15 Jul 2010 14:00:00 +0100 3757865 http://www.medworm.com/index.php?rid=3753759&cid=t_145162_86_f&fid=36669&url=http%3A%2F%2Ffadelibrary.wordpress.com%2F2010%2F07%2F14%2Finvolving-users-in-commissioning-local-services%2F Title: Involving users in commissioning local services Skinny: Study by Age Concern London brought commissioners and diverse service users together to discuss how service users can be involved in shaping local services. The project reflected on what is actually happening and provided pointers to how user involvement in commissioning could work in practice. Publisher: Joseph Rowntree Foundation Size of Publication: 58p Published: 18/05/2010 Filed under: Community Services, Grey Literature, Practice Based Commissioning Tagged: Best Practice, Commisioning, Cost Effectiveness, Joseph Rowntree Foundation, Service Users, Social Care, World Class Commissioning (Source: Fade Library) Fade Library blogs http://www.medworm.com/rss/comments.php?id=3753759 Wed, 14 Jul 2010 13:41:52 +0100 3753759 http://www.medworm.com/index.php?rid=3592356&cid=t_145162_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=3573635&cid=t_145162_86_f&fid=36669&url=http%3A%2F%2Ffadelibrary.wordpress.com%2F2010%2F05%2F18%2Fnursing-times-2010-vol-106-no-18%2F Fade Fave: How do we deliver best practice? Fade Skinny: Using evidence to improve productivity and efficiency is not as straighforward as may first appear. The article reports on the discussions by a panel of experts on the difficulties of adopting and delivering best practice. Contact the library for a copy of this article Filed under: Ooops Missed Category! Tagged: Best Practice, Commissioning, Evidence Based Practice, NHS Evidence, Quality (Source: Fade Library) Fade Library blogs http://www.medworm.com/rss/comments.php?id=3573635 Tue, 18 May 2010 07:30:11 +0100 3573635 http://www.medworm.com/index.php?rid=3573865&cid=t_145162_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=3089226&cid=t_145162_86_f&fid=36669&url=http%3A%2F%2Ffadelibrary.wordpress.com%2F2009%2F12%2F14%2Fnhs-stop-smoking-services-service-and-monitoring-guidance-201011%2F Title: NHS Stop Smoking Services: service and monitoring guidance 2010/11 Skinny: Provides best practice guidance relevant to the provision of all NHS stop smoking interventions and sets out fundamental quality principles for the delivery of services which can be used to inform the development of local commissioning arrangements. It also includes full details of the data reporting requirements for NHS Stop Smoking Services Publisher: DH Size of Publication: 112p. Published: 04/12/2009 Posted in Commissioning, Grey Literature, NHS, Primary Care, Smoking, Smoking Cessation Tagged: Best Practice, Commissioning, Grey Literature, Primary Care, Quality, Smoking Cessation, Standards (Source: Fade Library) Fade Library blogs http://www.medworm.com/rss/comments.php?id=3089226 Mon, 14 Dec 2009 18:30:06 +0100 3089226 http://www.medworm.com/index.php?rid=2774571&cid=t_145162_86_f&fid=36669&url=http%3A%2F%2Ffadelibrary.wordpress.com%2F2009%2F09%2F08%2Faiming-high-for-disabled-children%2F Title: Aiming high for disabled children: delivering improved health services The Skinny: Report for Primary Care Trusts to aid them achieve the following outcomes by providing case studies of best practice. Short breaks: ensure that disabled children with complex healthcare needs and their families can enjoy the same opportunities for short breaks as other children. Community equipment: the NHS to work with partners to ensure there is timely and comprehensive assessment of the complete needs of the disabled child, taking account of clinical, social and education needs, and the needs of the family and carers; and to improve the timely provision of equipment. Wheelchairs: to improve access to powered wheelchairs for children who need them, and reduce waiting times for assessment and provis... Fade Library blogs http://www.medworm.com/rss/comments.php?id=2774571 Tue, 08 Sep 2009 08:38:01 +0100 2774571 http://www.medworm.com/index.php?rid=1981284&cid=t_145162_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F461204934%2F Two days after lashing into Fred Goodwin, who hosts “The Infinite Mind” on National Public Radio, US Senator Chuck Grassley is now investigating Best Practice, a pharmaceutical consulting firm that Goodwin helped establish in the late ’90’s. Among the many services that have been offered by the firm - marketing consultations to drugmakers and the “dissemination of new off-label information.” Doctors can prescribe a drug to treat an illness even if the FDA has not approved that use, but promotion of off-label activity is a big no-no. So in a letter sent today to Roger Meyer, who heads the firm (pictured right), Grassley wants to know more about Best Practice’s questionable practices. The Senator notes that the claims can be found on older versions o... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1981284 Fri, 21 Nov 2008 21:38:48 +0100 1981284 http://www.medworm.com/index.php?rid=1622038&cid=t_145162_86_f&fid=36669&url=http%3A%2F%2Ffadelibrary.wordpress.com%2F2008%2F07%2F15%2Fjournal-of-management-marketing-in-healthcare-14%2F This study examines how technological innovation is encouraged, and discouraged, in Canada and other selected Organisation for Economic Cooperation and Development (OECD) countries, including the UK, France and the USA. The research uses The Conference Board of Canada’s Innovation Framework as an analytical tool in benchmarking the performance of Canada and other OECD countries in several areas of health innovation, including the innovation environment, and the creation, diffusion, transformation and use of knowledge. The results of this study are discouraging for Canada as it scores poorly in many important areas of technological health innovation. Substantial efforts are needed, and needed now, to revitalise health innovation systems and to refuel the capacity to commercialise heal... Fade Library blogs http://www.medworm.com/rss/comments.php?id=1622038 Tue, 15 Jul 2008 06:27:58 +0100 1622038 http://www.medworm.com/index.php?rid=1602934&cid=t_145162_86_f&fid=36669&url=http%3A%2F%2Ffadelibrary.wordpress.com%2F2008%2F07%2F08%2Fmaking-the-difference-the-pacesetters-beginners-guide-to-service-improvement-for-equality-and-diversity-in-the-nhs%2F Making the difference: The Pacesetters beginner’s guide to service improvement for equality and diversity in the NHS considers service improvement approaches for those working within the Pacesetters programme. Service improvement is concerned with testing ideas, sustaining and sharing best practice to make a tangible difference in outcomes and experience for staff and service users. It is primarily intended for NHS organisations who are part of the Pacesetters programme; however, will also be useful for other organisations. (Source: Fade Library) Fade Library blogs http://www.medworm.com/rss/comments.php?id=1602934 Tue, 08 Jul 2008 03:40:38 +0100 1602934 http://www.medworm.com/index.php?rid=1546726&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2008%2F05%2Forganised-bioinformatics-experiments%2F One of the things I’ve found in two years of doing bioinformatics, is that directories quickly fill up with files, usually data, scripts, and results. Working out the contents of each file is difficult as the only identifier is the name, which with lots of similarly named files, is confusing. Using lots of scripts gets more complicated when there are dependencies. For example scripts need the data from one file, or are dependent on an intermediate set of results from the output of another script. These dependencies mean that when a set of results needs updating, usually many times when producing a manuscript, scripts need to be re-run in the correct order. The requirement of manually re-running scripts in a specific order is cumbersome, and easily generates errors. A previous post I wro... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=1546726 Sat, 24 May 2008 18:43:04 +0100 1546726 http://www.medworm.com/index.php?rid=1436755&cid=t_145162_86_f&fid=36669&url=http%3A%2F%2Ffadelibrary.wordpress.com%2F2008%2F05%2F12%2Fwhen-to-share-information%2F has been developed as a cross-governmental initiative on behalf of Department of Health, Department for Children, Schools and Families, the Youth Justice Board and the Prison Service. It is set out in a pathway approach, with best practice case studies used to identify when, what, where and how information needs to be shared to ensure improved outcomes for children and young people, as outlined in Every Child Matters: Change for Children. (Source: Fade Library) Fade Library blogs http://www.medworm.com/rss/comments.php?id=1436755 Mon, 12 May 2008 14:28:46 +0100 1436755 http://www.medworm.com/index.php?rid=1198651&cid=t_145162_86_f&fid=36669&url=http%3A%2F%2Ffadelibrary.wordpress.com%2F2008%2F02%2F03%2Fbest-practice-guidance-on-joint-working-between-the-nhs-and-pharmaceutical-industry%2F In February 2007, the Ministerial Industry Strategy Group published its Long-Term Leadership Strategy for medicines. To encourage joint working between the NHS and pharmaceutical industry it recommended that the Department would publish guidance to support this to: Encourage NHS organisations and staff to consider joint working as a realistic option for the delivery of high-quality healthcare Inform and advise NHS staff of their main responsibilities when entering into consider joint working arrangements with the pharmaceutical industry Best Practice Guidance on joint working between the NHS and pharmaceutical industry (Source: Fade Library) Fade Library blogs http://www.medworm.com/rss/comments.php?id=1198651 Sun, 03 Feb 2008 22:58:20 +0100 1198651 http://www.medworm.com/index.php?rid=1182841&cid=t_145162_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=1182842&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F12%2Fwhy-data-testing-is-important-in-computational-research%2F I wrote in a previous post about the importance of testing in computational research. If you’re developing a piece of software, functional testing is essential. However, we bioinformaticians don’t just develop software, we also have to develop conclusions and hypothesis, based on data, as well as code we’ve written. Here is an example of why I think data testing is as equally important as functional testing in research. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=1182842 Mon, 31 Dec 2007 19:33:08 +0100 1182842 http://www.medworm.com/index.php?rid=1182843&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F11%2Fgood-programming-versus-biological-intuition%2F As I write my first paper, my biggest worry is that my results are wrong. In particular, that my code, which I think does one thing, has a bug and does something different. This, in turn, produces inaccurate results and leads me to incorrect conclusions. I then produce a paper where the story I am telling is wrong. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=1182843 Tue, 20 Nov 2007 18:38:52 +0100 1182843 http://www.medworm.com/index.php?rid=1182844&cid=t_145162_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=841718&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F08%2Fbe-more-productive-throw-away-your-mouse%2F The mouse, or two dimensional motion pointing device, is undoubtedly useful, especially when you’re new to computers. It lets you open windows, click around, and explore. However the more time you spend using a computer, and the more proficient you become, the more the mouse becomes a hindrance to how fast you can work. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841718 Wed, 22 Aug 2007 17:24:07 +0100 841718 http://www.medworm.com/index.php?rid=841724&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F07%2Fhow-to-save-the-world-and-make-everyone-happy-one-powerpoint-presentation-at-a-time%2F Computers and the Internet have made things great for scientists, particularly for us, since our jobs are sitting in front of them analysing data all day. Imagine being a bioinformatician without a computer, multivariate statistics is more of a pain than usual, genome sequence alignments need large pieces of paper. There would however be an upside to this analog dystopia - no more powerpoint presentations. Computers have arguably had a detrimental effect on the presentation of research, they allow the easy creation of big, text heavy slide sets. The emphasis of a talk leans towards the slides, and not the speaker. Being asked to give a talk is viewed as a dull task: time taken away from research plus the discomfort of public speaking. If you’ve already decided beforehand that it&#821... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841724 Mon, 09 Jul 2007 21:39:05 +0100 841724 http://www.medworm.com/index.php?rid=841731&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F06%2Fbioblogs-11-special-edition%2F Short and to the point - the tips & tricks supplement to this month’s bio::blogs edition has been compiled. The link to the pdf is at the end of this post. But first I want to thank those who contributed. Thanks to Dan Swan, Pierre Lindenbaum and Konrad Forstner, who contributed particularly large articles covering every aspect of being a bioinformatian. Euan Adie (Stew) wrote about revision control, creating applications and blogging. Bertalan Meskó sent in a list of genetic disorder databases. Roland Krause offers tips on managing and searching data sets. Ryan Castillo wrote about his experiences in bioinformatics. Paras Chopra offers advice for undergraduates on how to use their summers. Pedro Beltrao, editor of bio::blogs, discusses the importance of keeping up to date on t... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841731 Fri, 01 Jun 2007 18:29:39 +0100 841731 http://www.medworm.com/index.php?rid=841732&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F05%2Femail-is-your-friend-email-is-your-enemy%2F How often do you check your email? Once or twice a day? Obviously it’s not really necessary to check email more regularly than this. Well, speaking from experience, this is a bit of a fantasy world. Hands up everybody who I checks their email at least twenty times a day? (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841732 Tue, 29 May 2007 21:49:59 +0100 841732 http://www.medworm.com/index.php?rid=841734&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F05%2Fbioblogs-call-for-submissions%2F Bio::Blogs is a monthly round up of what’s being discussed on bioinformatics blogs. In addition, to next month’s edition at NodalPoint, there will also be a special edition here at Bioinformatics Zen. The aim, a community generated article of tips for computational biologists. I hope that the text of the article will be generated by submissions from the bioinformatics community. That’s means you reading this now. What would be your best piece of advice you would offer someone starting out in bioinformatics? Databases, coding, organisation? Send your suggestions, with your website if you have one, to the Bioinformatics Zen email address. Everything will be compiled and posted with the next edition of Bio::Blogs, on June 1. (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841734 Sun, 20 May 2007 20:15:50 +0100 841734 http://www.medworm.com/index.php?rid=841741&cid=t_145162_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_145162_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=841744&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F03%2Ftwelve-reasons-to-favour-simplicity-over-complexity%2F I think simple is better. Statistics says so too. Statistics says that you’ll probably read the first two paragraphs of this post, look at the pictures then go elsewhere. So I’d simply better get to my point. In terms of attention spans, computer code and (statistical) explanations, and possibly everything in general, I think it’s always better to favour simplicity over complexity. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841744 Tue, 20 Mar 2007 10:14:38 +0100 841744 http://www.medworm.com/index.php?rid=841747&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F03%2Fthree-ways-to-keep-your-work-focused-in-bioinformatics%2F Computational biology moves fast in comparison with traditional biology. All it takes is a few lines of code to produce results. Contrast this with the wet lab, where every step usually requires a full working day, or more. Difficulties with direction, often arise from having too much data, rather than not enough. As such, in bioinformatics, it’s important to keep focused on what you are trying to achieve. Do you need to add the extra search feature to your tool? What does it add? Can the question be answered with what you’ve built already? I threw away 10,000 words from my masters thesis because I lost direction. Here’s three practical ideas that I use to keep focused. Talk about your work Talk to someone about what you’re up to. Go for a coffee and have a chat abo... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841747 Mon, 12 Mar 2007 00:06:28 +0100 841747 http://www.medworm.com/index.php?rid=841748&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F03%2Fyour-ideas-are-valuable%2F Scientists have to be left brained, rational and analytical. But at the same time very right brained, inventive and holistic. We produce ideas, and often make a creative leaps to connect previous work and new concepts. Your ideas are part of you as a scientist. If like me, you’re a touch obsessed with your work, you probably think about it everywhere. Maybe you talk abut it with your partner over dinner? How about standing in the shower running things through your head? But how often have you come up with an idea that you’ve quickly forgotten? For me, writing down every idea I have has been one of my most worthwhile habits. I find that writing down ideas is an activity that gets better with practice. By giving my creative side the attention it deserves, I find that I become mor... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841748 Wed, 07 Mar 2007 00:45:19 +0100 841748 http://www.medworm.com/index.php?rid=841750&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F03%2Fbioinformatics-sometimes-you-have-to-write-and-not-computer-code%2F You love making programs that reveal yourself as a programming god. You produce results that demonstrate you are, quite obviously, the greatest scientist of our generation. You show these to everyone in your office/corridor/family, they all appreciate your magnificence. After a few talks at conferences comes the bit you’ve been avoiding - writing everything up. I think I’m fair in saying that you went into bioinformatics for something other than writing reports and papers. At some point though, you have to. Set a daily goal When I have to write, I set a goal of 500 words a day. Even if they are complete nonsense, which they usually are. Writing, like everything else, gets better with practice. My writing usually becomes more coherent, the more I do. Once you’ve got everyt... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841750 Fri, 02 Mar 2007 15:49:47 +0100 841750 http://www.medworm.com/index.php?rid=841751&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F02%2Fthe-right-graph-at-the-right-time%2F I think everyone would agree that the most important thing in science is results. The best scientists produce the most relevant and important results. Of course, the best results won’t matter if no one knows about them. Which is why we publish and give presentations. Sometimes I see results in papers and presentations illustrated poorly. Graphs that don’t demostrate the point to the reader/audience in the best possible way. Here I give examples of how data can be presented in different contexts, based on two of my favorite resources. The first is the R language for statistics, the other is Garr Reynolds‘ Presentation Zen ideology. A bad example Here’s an extreme case, but not completely uncommon in presentations. Two continuous variables - the oxidation of ammonia ... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841751 Wed, 28 Feb 2007 01:13:55 +0100 841751 http://www.medworm.com/index.php?rid=841752&cid=t_145162_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 http://www.medworm.com/index.php?rid=841753&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F02%2Freinventing-the-wheel%2F I spent several hours today implementing a sequence analysis method taken from a paper I had read earlier. I created a database, downloaded yeast coding sequences, then coded the whole method up in java. Shortly after doing this, a google search showed that not only had a tool been published to perform this analysis, but that the original method I implemented was flawed. I think the lesson here is to always check what the goal is of the research. Before touching the keyboard. Do you sometimes find that it’s easy to get bogged down in the individual details of implementation, such as coding, rather than the higher scientific question. Coding is enjoyable and is one of the reasons why I like bioinformatics. But what I have to keep telling myself is that in the end it’s about the ... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841753 Mon, 19 Feb 2007 22:10:07 +0100 841753 http://www.medworm.com/index.php?rid=841754&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F02%2Fgetting-your-point-across%2F A great post at creating passionate users, I think really applicable to science too. I know this is horribly overgeneralized, but as a high-level rule, we believe: If you’re using formal language in a lecture, learning book […], you’re worrying about how people perceive YOU. If you’re thinking only about the USERS, on the other hand, you’re probably using more conversational language. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841754 Sat, 17 Feb 2007 18:30:33 +0100 841754 http://www.medworm.com/index.php?rid=841755&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F02%2Forganising-yourself-as-a-dry-lab-scientist%2F Browsing wikiomics, I found this small section on keeping organised as a practising bioinformatician. In particular these lines contain gems of information. Use text files/plain e-mail whenever possible Give meaningful names to your files Create separate folders/directories for each project with meaningful names I find keeping my work organised one of the most frustrating but necessary tasks of being a bioinformatician. Also this subject seems to recieve little attention in the bioinformatics community. Wet scientists are expected to keep laboratory books. Where not doing so considered very bad practice. I am jealous when I see these books filled with pictures of gels and printed tables of results. I’ve tried using a lab book, but I didn’t find it applicable for the many ... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841755 Fri, 16 Feb 2007 18:17:38 +0100 841755 http://www.medworm.com/index.php?rid=841756&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F02%2F10-simple-rules-for-getting-published%2F A post at Nodal point discusses a PLoS Computional Biology article on the problems of being a post doc. The post also contains another interesting PLoS reference - 10 simple rules for getting published. The main points of the article are reading papers regularly, and being objective about research, especially your own. UPDATE : There’s also a discussion of this at Biocurious (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841756 Wed, 14 Feb 2007 19:27:45 +0100 841756 http://www.medworm.com/index.php?rid=841757&cid=t_145162_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F02%2Fthe-dark-side-of-bioinformatics-data-mining%2F An anti-post to my previous post on data mining. The point, to illustrate how data mining can quickly become unrewarding, and worse demotivating. I spend much of my day analysing yeast high throughput data, recently produced in the laboratory. On one hand I’m very lucky to have access to fresh data at many cellular levels. On the other hand, with all this information, I’m easily swept away by the amount of variables I have access to - the dark side of data mining. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841757 Tue, 13 Feb 2007 21:26:00 +0100 841757