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 'api'. Sat, 03 Sep 2011 02:00:32 +0100 http://www.medworm.com/index.php?rid=5008662&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2Fjg8EpAu81jA%2F And so, another working week will soon draw to a close. As always, this is the signal to daydream about weekend plans. Our agenda calls for a dip in the pool, a little yardwork, hanging with assorted short people and catching up on some interesting R&D. What about you? Is a day at the beach in order? Or a drive in the country? Maybe catching up on some sleep or thinking big thoughts? Whatever you do, have a good time and be safe. Meanwhile, here are some tidbits. See you soon… Bayer Loses European Patent For Yasmin (Reuters) PETA Proposes Procter & Gamble Stop Animal Testing (Dayton Business Journal) Republicans Complain FDA Review Procedures Slow Innovation (Bloomberg News) Bydureon Diabetes Med Passed The Test In Heart Trial (Reuters) FDA Bans Imports From Dr. Reddy&#8217... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=5008662 Fri, 08 Jul 2011 12:04:58 +0100 5008662 http://www.medworm.com/index.php?rid=4841987&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FPnFE-Cg3WGw%2F Good morning, everyone, and how are you today? Here on the Pharmalot corporate campus, we are engaged in the off-to-the-school-house hustle. This calls, of course, for a cup or two of stimulation. How else to gear up for those meetings and deadlines? So please feel free to join us. And here is another invitation: our webinar next week on the injectable drug delivery market. Meanwhile, we offer you these tidbits of the world at large. Have a great day and do stay in touch… North Carolina Delays Vote On Preemption Bill (Associated Press) CDC Blog On Zombie Apocalypse Proves Apocalyptic (AdWeek) Takeda To Buy Nycomed For $13.6 Billion (Reuters) Bill Gates Calls For A ‘Decade Of Vaccinations’ (Pharma Times) J&J Failed To Warn Parents Of Motrin Risks: Lawyer (Bloomberg Ne... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4841987 Thu, 19 May 2011 11:47:58 +0100 4841987 http://www.medworm.com/index.php?rid=4753970&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FN7yYPeyVrt4%2F During a lengthy inspection last fall of a supplier of active pharmaceutical ingredients, the FDA found something curious. The Baltimore facility run by ChemPacific, which also has operations in China, was failing to complete batch records for various lots of Norepinephrine Bitartrate. Entries were incomplete or missing, records were backdated and the in-house quality unit failed to detect the problems. In other words, ChemPacific was cited for playing fast and loose with its paperwork. In one specific example, the FDA noted that Chinese characters signifying a “need to change” were written on different batch records. And someone at the supplier told FDA investigators that the characters indicated these marked pages were to be replaced with a corrected batch record page. Interestingly... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4753970 Tue, 26 Apr 2011 15:00:24 +0100 4753970 http://www.medworm.com/index.php?rid=4653606&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FHbgOGFlE5sE%2F The ongoing shortage of prescription medicines continues to wreak havoc in the form of rising medication errors and are costing US hospitals an extra $200 million by forcing them to purchase more expensive generics or other therapeutic substitutes, according to a survey by the Premier alliance of hospitals and healthcare provideres. Why is this happening? At least 42 percent of sterile injectable drug shortages last year were due to product quality problems, such as particulates, microbial contamination, newly identified impurities and stability changes. Another 9 percent were due to problems with raw materials and 5 percent were attributed to the shutdown of a manufacturing site. Keep in mind, Premier notes, that foreign markets are the source for up to 80 percent of the raw materials req... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4653606 Tue, 29 Mar 2011 11:52:12 +0100 4653606 http://www.medworm.com/index.php?rid=4642729&cid=t_104627_113_f&fid=34634&url=http%3A%2F%2Fwww.emrandhipaa.com%2Femr-and-hipaa%2F2011%2F03%2F24%2Foperating-system-of-healthcare-it%2F Likewise, says Allscripts’ Tullman, “today we’re building the operating system for the future of healthcare. This country can’t afford its healthcare system anymore, so something’s got to change. We can no longer buy our way out of the problem.” – Source: Information Week The above comments sparks all sorts of interesting thoughts and questions for me. The first is “What is the Operating System of healthcare IT?” Obviously, we’re quite sure Tullman hopes that it’s the suite of Allscripts products. Although, how ironic is it that one company can have 5-10 (I lost count) different EMR software. I’ve never known an operating system to have 5-10 completely different software. Seems like something needs to change there. Unl... EMR and HIPAA blogs http://www.medworm.com/rss/comments.php?id=4642729 Thu, 24 Mar 2011 19:29:51 +0100 4642729 http://www.medworm.com/index.php?rid=4592691&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2F5cPetg5jHnI%2F For those wondering about the difficulties confronting the FDA as the agency attempts to monitor the supply chain, the chart offers some insight. From roughly 1,200 foreign manufacturing plants in 2001, the number grew to more than 3,500 in 2008 - a 185 percent increase. Yet the number of FDA inspections rose 23 percent, leading to a 57 percent drop in the inspection rate. [UPDATE: In 2001, 20.7 percent of facilities were inspected, but only 8.9 percent in fiscal year 2008]. In China alone, the problem is daunting. There are nearly 1,000 manufacturers of drug substances eligible for FDA inspection. And for 89 percent of audited Chinese-made drug substances, US and European pharmaceutical purchasers fail to demand the mandatory Chinese license and certificate, according to Philippe André o... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4592691 Tue, 15 Mar 2011 12:15:33 +0100 4592691 http://www.medworm.com/index.php?rid=4522286&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2Fc4iwc7RTeus%2F Two years ago, Pfizer trumpted a deal in which Aurobindo, a large supplier of active pharmaceutical ingredients that is based in India, would make a few dozen generic meds for the brand-name drugmaker. The move was part of a grand plan to expand into generics with lower manufacturing costs and revive growth as patents on big-selling, brand-name meds began expiring. “These agreements represent solid, measurable progress, and a strong commitment to achieve our growth objectives,” said David Simmons, who heads the drugmaker’s emerging markets and established products units, in a statement. Established products is a Pfizer euphemism for generics and branded generics. “We will dramatically change Pfizer’s Established Products portfolio to an engine of positive growth.” Since... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4522286 Fri, 25 Feb 2011 15:51:21 +0100 4522286 http://www.medworm.com/index.php?rid=4424441&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FrMRhvr_EIp8%2F One of the companies at the center of the Heparin scandal nearly three years ago just can’t seem to get it right. Last fall, the FDA sent an inspection letter to Scientific Protein Laboratories because the supplier of active pharmaceutical ingredients received info that additional lots were contaminated in October 2008 - months after the scandal broke - but failed to adequately investigate for a year. Now, the FDA has issued a January 20 warning letter in which SPL was upbraided for failing to consider widening its internal investigation into contamination into other lots for another eight months. This is serious; the blood thinner, you may recall, was linked to more than 80 deaths and hundreds of serious reactions in patients in late 2007 and early 2008. In the spring of 2008, an FD... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4424441 Tue, 01 Feb 2011 17:24:42 +0100 4424441 http://www.medworm.com/index.php?rid=4419352&cid=t_104627_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F01%2F31%2Ffarewell-friendfeed-its-been-fun%2F I’ve been a strong proponent of FriendFeed since its launch. Its technology, clean interface and “data first, then conversations” approach have made it a highly-successful experiment in social networking for scientists (and other groups). So you may be surprised to hear that from today, I will no longer be importing items into FriendFeed, or participating in the conversations at other feeds. Here’s a brief explanation and some thoughts on my online activity in the coming months. The value of FriendFeed FriendFeed is simply an aggregator, displaying items from other online services. There’s nothing special about that: other sites do the same thing (although many have fallen by the wayside) and were FriendFeed to disappear, those items would still exist at thei... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4419352 Mon, 31 Jan 2011 13:34:07 +0100 4419352 http://www.medworm.com/index.php?rid=4414546&cid=t_104627_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fseven-slices-of-science-stuff.html from David Bradley Vuja de – Thinking outside the box with new eyes? Haven't we see this managerial psychobabble before or is it just vuja de? Alchemist Newsletter – An element close to every Alchemist's heart, quicksilver, or more properly mercury, featured in the chemistry news roundup this week, as does the creation of life from the primordial soup and how that may have begun. In the world of agrichemicals there is a possible sting in the tale for a relatively new class of pesticides, although no definitive evidence is yet available. In materials science tiny, but microscopic particles can undergo self-assembly it seems, while depressing news emerges from Europe regarding the lack of efficacy of an antidepressant drug marketed there. Finally, a new, free chemical... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=4414546 Sat, 29 Jan 2011 16:00:08 +0100 4414546 http://www.medworm.com/index.php?rid=4405960&cid=t_104627_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F01%2F27%2Fapis-have-let-me-down-part-22-friendfeed%2F In part 1, I described some frustrations arising out of a work project, using the Array Express API. I find that one way to deal mentally with these situations is to spend some time on a fun project, using similar programming techniques. A potential downside of this approach is that if your fun project goes bad, you’re really frustrated. That’s when it’s time to abandon the digital world, go outside and enjoy nature. Here then, is why I decided to build another small project around FriendFeed, how its failure has led me to question the value of FriendFeed for the first time and why my time as a FriendFeed user might be up. At the beginning of each year, I frequently experience a period of angst with respect to my social network and other web activity. Specifically, I ask... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4405960 Thu, 27 Jan 2011 09:06:30 +0100 4405960 http://www.medworm.com/index.php?rid=4405961&cid=t_104627_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=4338265&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2F4f2wrjzvvuk%2F In recent months, the FDA has come under still greater pressure to monitor foreign plants. The US General Accountability Office has issued a scathing report (see this), House Republicans have chastised the agency for failing to fully probe the Heparin scandal (read here) and one Congressional committee is particularly interested in oversight failures in Puerto Rico (look here). So how does the FDA respond? The agency recently issued warning letters to four different manufacturers of active pharmaceutical ingredients and slammed them for a host of significant deviations from Current Good Manufacturing Practice. These included failures to establish a stability program to monitor the APIs; maintain adequate laboratory controls and maintain adequate records; or demonstrate that analytical test... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4338265 Wed, 12 Jan 2011 14:46:55 +0100 4338265 http://www.medworm.com/index.php?rid=4314221&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2F6v6OHNUJQ_Y%2F Greetings, everyone. How are you this morning? We trust you feel invigorated as another day gets under way. As usual, we are brewing a delicious cup of stimulation and poking around for interesting items. Heard something fascinating? Send us a note. Meanwhile, we hope your workload is manageable and much gets accomplished. Catch you soon… Pfizer Faces 1,200 Chantix Lawsuits (Birmingham News) Spectrum To Make Biosimilar Of Roche’s Rituximab (Reuters) Roche Wins Wider Approval For Actemra (Bloomberg News) Evidence Links Avastin To Heart Failure In Breast Cancer Patients (HealthDay) EMA Worries Over Foreign APIs (InPharma-Technologist) J&J Files For FDA Approval Of Bloodthinner (Associated Press) Celgene Submits New Applications For Cancer Meds (Reuters) Xoma Inks $505M Diabe... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4314221 Wed, 05 Jan 2011 12:48:44 +0100 4314221 http://www.medworm.com/index.php?rid=4265915&cid=t_104627_113_f&fid=34634&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FEmrAndHipaa%2F%7E3%2F2vWy6L-H1x4%2F I still have a hard time calling myself a writer or even press (although it’s convenient for getting into conferences). Plus, I think I reach, influence and interact with as many or more people than the traditional healthcare journalist. However, there’s something liberating about being called a blogger instead of a journalist because the standard and approach is different. At least I thought that was the case until I read this article on Forbes.com which declares Allscripts new API as “Open Source’s Debut in Healthcare.” Ok, to be fair, it was written written on a Forbes healthcare blog and not their magazine, but as a blogger I’m embarrassed that a Forbes blogger would write such a terrible article. Let me set the record straight. Allscripts launched a... EMR and HIPAA blogs http://www.medworm.com/rss/comments.php?id=4265915 Mon, 13 Dec 2010 19:24:38 +0100 4265915 http://www.medworm.com/index.php?rid=4238151&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2F4wnU_lg3IY0%2F Rise and shine, everyone. Another brand new day is on the way and, once again, we are hustling the short people off to their various school houses. This calls, of course, for a cup of stimulation. So please join us, or grab a bottle of water if you prefer. Meanwhile, here are a few tidbits to get us all started. Have a great one and drop us a line if you hear anything interesting… Sanofi Unwilling To Meet Genzyme Demands (Bloomberg News) Enzon Pharma Cuts Workforce By 26 Percent (Reuters) Johnson & Johnson Faces Thousands Of Levaquin Lawsuits (Minneapolis Star-Tribune) Kindler Departure Sparked By Succession Issue? (Bloomberg News) Glaxo Buys Chinese Drugmaker For $70M (Reuters) Chris Viehbacher Is Named New PhRMA Chief (The Hill) Medicaid Drugs Are Going To Drug Dealers (Associ... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4238151 Tue, 07 Dec 2010 12:56:32 +0100 4238151 http://www.medworm.com/index.php?rid=3885498&cid=t_104627_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F08%2F20%2Fbackup-your-citeulike-library-using-mongodb-and-ruby%2F Well, that was easy. #!/usr/bin/ruby require "rubygems" require "mongo" require "json/pure" require "open-uri" db = Mongo::Connection.new.db('citeulike') col = db.collection('articles') j = JSON.parse(open("http://www.citeulike.org/json/user/neils").read) j.each do |article| article[:_id] = article['article_id'] col.save(article) end Filed under: programming, ruby Tagged: api, backup, citeulike, json, mongodb (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3885498 Fri, 20 Aug 2010 01:50:57 +0100 3885498 http://www.medworm.com/index.php?rid=3862139&cid=t_104627_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FTYnPBOOMfqE%2F Next time I create an API to my (few) applications, include dozens of Easter Eggs, no documentation. Some has to think about the children! (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=3862139 Thu, 12 Aug 2010 19:20:10 +0100 3862139 http://www.medworm.com/index.php?rid=3798733&cid=t_104627_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F07%2F29%2Flazy-post-a-life-scientists-best-of%2F When stuck for ideas or pressed for time, a blogger can always fall back on a round-up of activity from elsewhere on the web. Yes, it’s time for a “best of the past 14 days” from the FriendFeed Life Scientists group. Just a slight twist to make it more exciting (?) – we’ll automate the process using the API and a little Ruby. #/usr/bin/ruby require "rubygems" require "json/pure" require "open-uri" bestof = JSON.parse(open("http://friendfeed-api.com/v2/feed/the-life-scientists/summary/14").read) 0.upto(9) {|entry| url = bestof['entries'][entry]['url'] body = bestof['entries'][entry]['body'] puts "<li><a href='#{url}'>ff#{entry+1}</a> - #{body}</li>" } Run, copy output and paste to ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3798733 Thu, 29 Jul 2010 07:10:20 +0100 3798733 http://www.medworm.com/index.php?rid=3767238&cid=t_104627_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F07%2F20%2Fanalysing-the-ismb-2010-meeting-using-r%2F The colossus of bioinformatics meetings, ISMB, convened in Boston this year from July 9 – 13. As in recent years, the meeting was covered online at its website, FriendFeed and Twitter. I thought it would be fun to run a quick analysis of activity at the FriendFeed room using R. 1. Fetch the data We can use the FriendFeed API to fetch data in JSON format. R provides two useful packages: RCurl, for making the HTTP request and rjson (or RJSONIO), to parse the results into a list. Since we don’t know in advance how many entries to expect, we set some arbitrarily large maximum number of entries, loop towards it and break when no more entries are returned. library(RCurl) library(rjson) ismb.url <- "http://friendfeed-api.com/v2/feed/ismb2010" ismb.data <- list() fo... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3767238 Tue, 20 Jul 2010 07:24:19 +0100 3767238 http://www.medworm.com/index.php?rid=3172020&cid=t_104627_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fdo-it-yourself-board-presentation-meaningful-use Just as I did with the American Recovery and Reinvestment Act, I've prepared a presentation that you can use for your Board and stakeholders to review the requirements of the Interim Final Rule and Notice of Proposed Rulemaking. Feel free to use it without attribution to me. This should save thousands of hours since everyone will be preparing the same material. Download it here. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=3172020 Thu, 14 Jan 2010 15:53:35 +0100 3172020 http://www.medworm.com/index.php?rid=3149253&cid=t_104627_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F07%2Fhow-to-archive-data-via-an-api-using-ruby-and-mongodb%2F I was going to title this post “How to: archive a FriendFeed feed in MongoDB”. The example code does just that but (a) I fear that this blog suggests a near-obsession with FriendFeed (see tag cloud, right sidebar) and (b) the principles apply to any API that returns JSON. There are rare examples of biological data with JSON output in the wild, e.g. the ArrayExpress Gene Expression Atlas. So I’m still writing a bioinformatics blog ;-) Let’s go straight to the code: #!/usr/bin/ruby require "rubygems" require "mongo" require "json/pure" require "open-uri" # db config db = Mongo::Connection.new.db('friendfeed') col = db.collection('lifesci') # fetch json 0.step(9900, 100) {|n| f = open("http://friendfeed-api.com/v2/feed/... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3149253 Thu, 07 Jan 2010 00:17:46 +0100 3149253 http://www.medworm.com/index.php?rid=3079512&cid=t_104627_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F12%2F11%2Fapis-i-wish-the-life-sciences-would-learn-from-social-networks%2F I was prompted by a thread on the apparent decline of FriendFeed to look for evidence of declining participation in my networks. First, a quick and dirty Ruby script, tls.rb to grab the Life Scientists feed and count the likes and comments: #!/usr/bin/ruby require 'rubygems' require 'json/pure' require 'net/http' require 'open-uri' def format_date(d) if d =~ /(\d{4}-\d{2}-\d{2})T(\d{2}:\d{2}:\d{2})Z/ return "#{$1},#{$2}" else return d end end def count_items(i) if i.nil? return 0 else return i.count end end n = ARGV[0] u = "http://friendfeed-api.com/v2/feed/the-life-scientists?start=#{n}" f = open(u).read j = JSON.parse(f) j.each_pair do |k,v| if k == "entries" v.each do |entry| date = format_date(entry['date']) likes = count_it... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3079512 Fri, 11 Dec 2009 02:50:49 +0100 3079512 http://www.medworm.com/index.php?rid=3067307&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FvI8bsLiCTUw%2F The increasing reliance on active pharmaceutical ingredients from overseas - notably, China - is prompting a row in Europe, where the Active Pharmaceuticals Ingredients Committee, a trade group, wants the European Commission to require repeated, mandatory inspection of overseas API facilities, Outsourcing Pharma reports. The debate comes amid ongoing concerns over the safety of APIs emanating from China, where reports of counterfeit or diluted ingredients has caused a repeated ruckus, such as with the Heparin scandal last year (some background). Recently, AstraZeneca disclosed plans to rely on China for APIs (see here). The European Commission excluded overseas mandatory inspections from a draft directive because they would be too expensive. However, this was based on a figure that Chris O... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3067307 Tue, 08 Dec 2009 14:06:55 +0100 3067307 http://www.medworm.com/index.php?rid=3040020&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FyGEhZnz1GK0%2F The move comes two years after the big drugmaker insisted it wouldn’t outsource this activity there. Recently, though, AstraZeneca been building up its manufacturing presence in China with a big factory in Wuxi, which in addition to making APIs, also does medicine formulation and packaging, The Times of London reports. The move is part of a cost-cutting drive begun in 2007, which happened to coincide with increasing concerns over manufacturing safety and quality at Chinese facilities. At the time, AstraZeneca was caught in a fit of embarassing backpedaling after insisting API production wouldn’t be outsourced to China, even though plans had been made (see here and here). The drugmaker may attempt to assuage concerns by running its own facilities, but this step underscores a dif... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3040020 Mon, 30 Nov 2009 13:49:45 +0100 3040020 http://www.medworm.com/index.php?rid=2948307&cid=t_104627_87_f&fid=36050&url=http%3A%2F%2Fwww.blisstree.com%2Fbreastfeeding123%2Fremaining-attached-after-weaning%2F October is Attachment Parenting Month and I could not pass up this opportunity to talk about some ways to stay close to your children after they have weaned. Attachment Parenting International explains: “Attached at the Heart Through the Years” is the theme for AP Month 2009 and a statement that healthy, secure attachments between parents and children is a dynamic process that extends throughout childhood and does not end with baby bonding. During AP Month, parents are challenged to re-examine their daily activities and traditions and learn new ways to grow with each other and remain close and supportive. I found breastfeeding to be a natural and easy way to bond with my children and to stay close to them through toddlerhood. Remaining close and attached was practically effor... Breastfeeding 1-2-3 blogs http://www.medworm.com/rss/comments.php?id=2948307 Sat, 31 Oct 2009 20:22:31 +0100 2948307 http://www.medworm.com/index.php?rid=2876142&cid=t_104627_113_f&fid=34634&url=http%3A%2F%2Fwww.emrandhipaa.com%2Femr-and-hipaa%2F2009%2F10%2F01%2Finterview-with-srssoft-emr-ceo-evan-steele%2F I’ve been finding what SRSsoft and in particular their CEO, Evan Steele has been saying about the ARRA EHR stimulus money on the SRSsoft blog called EMR Straight Talk really interesting. They’re an EMR company that I think has taken a different approach to marketing their EMR software. So, I thought it would be interesting to interview Evan on a number of relevant topics related to his EMR and the ARRA stimulus money. Let me know if you like the following interview and I’ll think about doing more of them. Describe what you define a hybrid EMR is. Hybrid EMR satisfies the demands of high performance physicians by providing process efficiency. This benefit is delivered through click minimization, ergonomic design, product flexibility and a non-proprietary, open software pla... EMR and HIPAA blogs http://www.medworm.com/rss/comments.php?id=2876142 Thu, 01 Oct 2009 15:09:17 +0100 2876142 http://www.medworm.com/index.php?rid=2477493&cid=t_104627_86_f&fid=38272&url=http%3A%2F%2Flaikaspoetnik.wordpress.com%2F2009%2F06%2F14%2Fquoteurl-a-simple-way-to-quote-save-and-publish-tweets%2F Ever tried to catch and publish a twitter conversation? Hard, isn’t it, especially at WordPress.com where the lay-out is often difficult to control, if you just copy and paste. Tweets also tend to disappear after approximately 3-4 weeks.  Thus if you want to capture them you should do it (relatively) soon after they have been tweeted. A [...] (Source: Laika's MedLibLog) Laika's MedLibLog blogs http://www.medworm.com/rss/comments.php?id=2477493 Sun, 14 Jun 2009 19:28:42 +0100 2477493 http://www.medworm.com/index.php?rid=2150752&cid=t_104627_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F02%2F02%2Fbrief-notes-on-export-from-friendfeed%2F During discussion of the ISMB 2008 room, Thomas asks: “Does FF really provide long-term archival?” Lars points out that it’s as permanent as anything else on the Web, Dorothea points out that FriendFeed offer no guarantees and Deepak discusses the FriendFeed API. Question: how useful is the FriendFeed API as a tool to, for example, archive a FriendFeed room? We can access the ISMB 2008 room via the API using a URL like this: curl “http://friendfeed.com/api/feed/room/ismb-2008?format=xml” > ismb.xml We can also retrieve items in other formats by substituting “xml” in the URL with one of: json, atom, rss. Note that where a FriendFeed post contains a “N more comments” link, those comments are actually present on the page and revealed... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2150752 Mon, 02 Feb 2009 02:01:45 +0100 2150752 http://www.medworm.com/index.php?rid=1947765&cid=t_104627_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F11%2Fpython-training-for-cheminformatics.html "the best choice of high-level programming language for computational chemistry is Python" [A. Dalke]Many cheminformatic/modeling toolkits provide Python interfaces, as shown in the summary below. This is a good reason to consult Andrew for a training sessions, or checking Andrew's or Noel's blogs from time to time. The various open source projects, from which a few are stalled, support Python, as well as the academic/commercial OEChem toolkit. Two very important modeling programs supporting Python are Schrödinger's modeling suite and PyMol. For a training on the last two programs, you best contact the software support teams directly.Please let me know, if other molecular modeling/ cheminformatics/ statistical modeling programs should be mentioned here ![source: EuroQSAR poster, A. Dalk... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1947765 Sun, 09 Nov 2008 15:23:00 +0100 1947765 http://www.medworm.com/index.php?rid=1930403&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F440022434%2F In an essay that takes a top-down view of the agency and its myriad problems protecting the supply of pharmaceuticals, Gardiner Harris of The New York Times reviews the highlights - or lowlights - of the past year or so: the Heparin deaths, the Ranbaxy scandal and the withering criticism from Congress. And he notes some of the issues bedeviling the FDA as it struggles to cope with the growing role played by Chinese suppliers: antiquated FDA computer systems, an inability among FDA staff to decipher names of Chinese plants, difficult travel conditions for agency inspectors, and, of course, the debate over sufficient FDA funding. For instance, this year, 18.2 million shipments of food, devices, cosmetics and drugs are expected to enter more than 300 US ports, but the FDA had 454 investigator... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1930403 Sun, 02 Nov 2008 15:17:56 +0100 1930403 http://www.medworm.com/index.php?rid=1385832&cid=t_104627_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F273939264%2F Linkfest I am sure there is something profound to be said about writing a gazillion books algorithmically, but it mostly escapes me Michael Barton riffs on Git and Github (and yes I have an account) Cascading is a large dataset build tool and a processing API for Hadoop Sun Microsystems has a Platform as a Service? Check out Project Caroline MetaBase - the place where life science databases go meta Papyrus, a student oriented feed reader Multimedia Hadoop Summit - Tons of great material Social Graph Foo Camp videos - See previous Word for scientific publishing Blogspotting Toby Segaran’s blog Venture Hacks - A long time favorite Events Barcamb2 7th International BIOKKD 2008 Self Assembly Well, you’ve already heard about my appearance on Jon Udell’s podcast. P... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1385832 Sun, 20 Apr 2008 07:18:29 +0100 1385832 http://www.medworm.com/index.php?rid=1378006&cid=t_104627_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F271811959%2F Lots of talk on data lately. Paul Kedrosky, for example, wants to bring on the data blogs. So in that spirit I wanted to mention some cool data-related sites and APIs and put up some data of my own. Google has its charts API. Swivel and Many Eyes are also familiar to many people who read this blog. To that list I would like to Trendrr, which I first read about on ReadWriteWeb. Haven’t quite tried it out yet, but it definitely looks very interesting. There are a lot of public datasets available, and while accessing them or finding them isn’t as easy as one would like, and the fact that more data should be openly available is always there, it is becoming increasingly available to do things with those data via APIs or services like Freebase (I think that’s where Freebase re... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1378006 Thu, 17 Apr 2008 03:25:52 +0100 1378006 http://www.medworm.com/index.php?rid=1297715&cid=t_104627_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F03%2F12%2Fevolution-of-an-idea%2F It’s great to sit back and watch ideas and software unfold. Just over a year ago, Euan asked whether anyone was employing AJAX in graphical genome browsers. The old-style “reload on refresh” browsers (UCSC, Gbrowse, Ensembl) were starting to look a bit Web 1.0. This sparked plenty of discussion, including a pointer to X:Map: a very nice alternative view of Ensembl data using the Google Maps API. Jump forward to today and thanks to Euan’s del.icio.us feed via FriendFeed, I discover Genome Projector, which takes the zoom-able Google Maps idea to a new level. And that’s how social networks let you discover stuff. Brilliant. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1297715 Wed, 12 Mar 2008 12:07:40 +0100 1297715 http://www.medworm.com/index.php?rid=1146221&cid=t_104627_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F01%2F12%2Fnature-old-and-new%2F Complete Nature archive 1869-present now online Euan lets slip that a Nature Network API is in the works. Can’t wait. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1146221 Fri, 11 Jan 2008 14:16:01 +0100 1146221 http://www.medworm.com/index.php?rid=1142707&cid=t_104627_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F214411038%2F Israel’s Teva Pharmaceuticals, the world’s largest generics maker, plans to invest over $1 billion in India over the next two years to acquire Indian drug companies and set up manufacturing facilities, The Business Standard reports. Around $250 million to $300 million will be used to establish manufacturing facilities and the rest to fund acquisitions in India. A few weeks ago, Teva had acquired over 100 acres of land near Gwalior, Madhya Pradesh, to set up API manufacturing facilities that will match the production capacity of domestic generic majors such as Ranbaxy, Cipla, Dr Reddy’s, Sun Pharma and Wockhardt, sources told the paper. Work would start at the site after government clearance is obtained. “Teva considers India an interesting geographical region and is looking to bro... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1142707 Thu, 10 Jan 2008 13:37:59 +0100 1142707 http://www.medworm.com/index.php?rid=726298&cid=t_104627_122_f&fid=35074&url=http%3A%2F%2Fbrainmaps.blogspot.com%2F2007%2F07%2Fintroducing-brain-maps-api.html The Brain Maps API lets you embed Brain Maps in your own web pages with JavaScript. Future versions will enable you to add overlays to brain maps (including markers and polylines) and display shadowed "info windows". The Brain Maps API is a free service, available for any web site that is free to consumers.Additional information is at http://brainmaps.org/index.php?p=brain-maps-api (Source: Brain Maps) Brain Maps blogs http://www.medworm.com/rss/comments.php?id=726298 Wed, 11 Jul 2007 04:57:00 +0100 726298 http://www.medworm.com/index.php?rid=586225&cid=t_104627_86_f&fid=34461&url=http%3A%2F%2Fdigicmb.blogspot.com%2F2007%2F05%2Fsecond-life-search-toolbar-sl-resources.html toolbar powered by Conduit This Toolbar provides (almost) all Search Tools to find information about Second Life, Blogs, RSS Feeds, Links, Podcasts, Video's and Images. Do you want to find out HOW Second life can be useful for EDUCATION, TEACHING, SCIENCE and RESEARCH? And you want to see examples of that? Do you want to know what is available for sale IN and OUTSIDE Second Life? Or are you looking for Auctions, Classifieds, Events, Groups, Help? Try this toolbar and keep up with what is happening in Second Life. SEE THIS SHORT DEMO! Or add the Second Life Search Module to Your Netvibes account: News about Second Life Search? Have a look at SecondLifeSearch.blogspot.com Tags: Secondlife, Second Life, Search Toolbar, search, Toolbar, Sl, SL Se... DigiCMB blogs http://www.medworm.com/rss/comments.php?id=586225 Tue, 01 May 2007 22:06:00 +0100 586225 http://www.medworm.com/index.php?rid=502965&cid=t_104627_97_f&fid=35050&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmaGazette%2F%7E3%2F104654104%2Fmanufacturing_agreement_with_s.html Vion Pharmaceuticals, Inc. (Nasdaq: VION) has recently extended its manufacturing agreement with SAFC (a member of the Sigma-Aldrich Group) for its lead anticancer agent Cloretazine® (VNP40101M). The extended agreement will allow SAFC to continue the manufacture of Cloretazine® (VNP40101M) active pharmaceutical ingredient (API) to September 2009. SAFC is the custom manufacturing group within the Sigma-Aldrich Group focused on both biochemical production and the manufacturing of complex, multi-step organic synthesis of APIs and key intermediates. Vion Pharmaceuticals is committed to developing and commercializing innovative cancer therapeutics. Find more details from the press release (a pdf file). (Source: PharmaGazette) PharmaGazette blogs http://www.medworm.com/rss/comments.php?id=502965 Mon, 26 Mar 2007 11:31:24 +0100 502965 http://www.medworm.com/index.php?rid=486181&cid=t_104627_132_f&fid=35022&url=http%3A%2F%2Fplindenbaum.blogspot.com%2F2006%2F12%2Fjava-16-mustang-jaxb-and.html JAXB provides a convenient way to bind an XML schema to a representation in Java code. It makes it easy for you to incorporate XML data and processing functions in applications based on Java technology without having to know much about XML itself. The Architecture for XML Binding is now included in the new Java1.6. I wanted to test JAXB to see how it could be used to parse the NCBI/TinySeqXML format. First I created a XSD description of a TSeq:Source tinyseq.xsd (...) <xs:element name="TSeqSet"> <xs:annotation> <xs:documentation>Set of sequences</xs:documentation> </xs:annotation> <xs:complextype> <xs:sequence> <xs:element ref="TSeq" maxoccurs="unbounded"> </xs:element> </xs:sequence> <... YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=486181 Fri, 15 Dec 2006 05:00:00 +0100 486181 http://www.medworm.com/index.php?rid=486180&cid=t_104627_132_f&fid=35022&url=http%3A%2F%2Fplindenbaum.blogspot.com%2F2006%2F12%2Fjava-16-mustang-staxand-bioinformatics.html about StAX via xml.com ; Most current XML APIs fall into one of two broad classes: event-based APIs like SAX and XNI or tree-based APIs like DOM and JDOM. Most programmers find the tree-based APIs to be easier to use; but such APIs are less efficient, especially with respect to memory usage. (...) However, the common streaming APIs like SAX are all push APIs. They feed the content of the document to the application as soon as they see it, whether the application is ready to receive that data or not. SAX and XNI are fast and efficient, but the patterns they require programmers to adopt are unfamiliar and uncomfortable to many developers. (...) StAX shares with SAX the ability to read arbitrarily large documents. However, in StAX the application is in control rather than the parser. The ap... YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=486180 Fri, 15 Dec 2006 05:00:00 +0100 486180