Converting a spreadsheet of SMILES: my first OSM contribution
I’ve long admired the work of the Open Source Malaria Project. Unfortunately time and “day job” constraints prevent me from being as involved as I’d like.
So: I was happy to make a small contribution recently in response to this request for help:
Can anyone help @O_S_M to convert this spreadsheet ( malaria.ourexperiment.org/biological_dat…) into chemical structures with data? #openscience #realtimechem— Alice Williamson (@all_isee) June 24, 2014
Note – this all works fine under Linux; there seem to be some issues with Open Babel library files under OSX.
First step: make that data usab...
Source: What You're Doing Is Rather Desperate - July 1, 2014 Category: Bioinformaticians Authors: nsaunders Tags: open science programming statistics cheminformatics conversion malaria osm smiles Source Type: blogs
Insurance Coverage for Oncofertility: Concerns about Socioeconomic Disparities
<p>In a recent <a href="/BioethicsBlog/post.cfm/the-importance-of-assisted-reproductive-technologies-for-women-in-developing-countries">blog</a>, I asserted that assisted reproductive technology (ART) should be a higher priority for the global South because of the severe health, social, and economic effects infertility can have on women there. The most common response to this claim is that resources should first be devoted to treating and preventing life-threatening conditions, such as malaria and HIV/AIDS, rather than conditions that are perceived as merely social and/or psychological. The...
Source: blog.bioethics.net - June 16, 2014 Category: Medical Ethics Authors: Hayley Dittus-Doria Tags: Health Care Reproductive Medicine Fertility health insurance syndicated Source Type: blogs
Vinod Khosla – Still Stirring Things Up
Vinod Khosla (Wikipedia)
Vinod Khosla’s still at it. This time its the Stanford Big Data in Biomedicine Conference.
I don’t really blame him – he’s got quite a thing going on the speaker circuit. As long as he keeps getting invited to give keynote addresses at healthcare summits, he’ll keep cranking through his slide set and stirring up the hornet’s nest by saying that 80% of docs will be replaced by digital devices. Which coincidentally, his venture capital firm finances. Except now he’s calling it big data, since that’s what the most recent summit he spoke at was abou...
Source: The Blog That Ate Manhattan - May 29, 2014 Category: Primary Care Authors: Margaret Polaneczky, MD Tags: Second Opinions Big Data doctors Stanford Vinod Khosla Source Type: blogs
Forthcoming Conferences June 2014
June 01 - 05, 2014 6th Singapore International Water Week SIWWSingapore, Singapore Further informationJointly organised by the International Water Association (IWA) and PUB, Singapore's national water agency.Suggested reading: Applications of Molecular Microbiological Methods Microbial Ecological Theory Foodborne and Waterborne Bacterial Pathogens June 01 - 06, 2014 BiopolymersNewport, RI, USA Further informationGordon Research Conference. Biopolymers. Mechanisms of Biomolecular Interactions: From Physical Principles to Biological Insights.Suggested reading: ...
Source: Microbiology Blog: The weblog for microbiologists. - May 14, 2014 Category: Microbiology Source Type: blogs
Call me intolerant . . .
. . . if you will.Last Sunday I was channel surfing toward the news when I saw the victor in that weekend's golf tournament getting interviewed. The teevee guy asked him the standard question, why did he think his game had been so good?It turns out it's because this particular golfer has "gotten closer to God." He realized he couldn't do it on his own so he started relying on God to guide his swing.Here's what I think, punk. You are a malignant narcissist. You are actually claiming, before a national television audience, that the immortal, omnipotent creator of the universe of billions of galaxies, each of billions of star...
Source: Stayin' Alive - May 11, 2014 Category: American Health Source Type: blogs
Disease eradication
World Malaria Day was a couple of weeks go, and I missed posting on it due to my recent indisposition. Yeah, yeah, I don't usually pay much attention to these artificial occasions --- National Pickle Week, Administrative Assistant's Day, yadda yadda -- but the WHO and the Global Fund used the day to push hard to get attention and maybe raise some dough. Here's the UN Special Envoy's statement on the day, which was April 25. Malaria matters because it is a leading killer of children and because endemic malaria is a major factor that holds down poor regions of the world. With lots of people debilitated, economic welfare suff...
Source: Stayin' Alive - May 8, 2014 Category: American Health Source Type: blogs
Low tech biotech
Citizen science and the DIY (do-it-yourself) movement combine in the quest to create simple, low-cost, assembled-from-basic-materials equipment capable of carrying out sophisticated diagnostic tests or other applications. Open access data can be an important component of making such equipment cost effective.
For example, this synthetic biology project funded on Kickstarter last year to engineer glowing plants as an alternate light source uses the open data of the National Center for Biotechnology Information (NCBI) databases.
On the other hand, while doctors in various medical departments and citizen tinkerers alike may ...
Source: Open Medicine Blog - - April 26, 2014 Category: Medical Publishers Authors: Carlyn Zwarenstein Source Type: blogs
Strange Adventures and Assorted Announcements
Photo: X-ray Delta One By Crabby McSlackerSo Happy Saint Patricks Day! Although aside from a green shirt that makes an appearance in a photo or two, I'm afraid we're not doing much on that theme today.This post is partly about seeking out "adventure!" But, if you are an anxious person, fear not. I haven't changed my opinion that there is absolutely nothing wrong with embracing your comfort zone, and staying way the hell away from "adventures" other people suggest if they seem too risky or otherwise unappealing.However, there is still a lot of excitement and novelty to be had in the world from within your comfor...
Source: Cranky Fitness - March 17, 2014 Category: Consumer Health News Authors: Crabby McSlacker Source Type: blogs
50 Cent Origami Microscope for Third-World Diagnostics
No, Curtis James Jackson III didn’t decide to invest in science and sponsor a microscope. It’s an actual microscope that costs around $0.50 USD to produce ($1 for higher magnification), and can be assembled in under 10 minutes. The Foldscope, developed by the Prakash Lab at Stanford University, provides over 2,000X magnification with submicron resolution, weighs 8.8 grams, fits in a pocket, is battery-powered for up to 50 hours on a single button cell, and is rugged enough to withstand being dropped from three stories or being stomped on by a mad scientist’s boot.
Once assembled, the Foldscope is operated...
Source: Medgadget - March 11, 2014 Category: Technology Consultants Authors: Ben Ouyang Tags: Diagnostics Genetics Pathology Public Health Source Type: blogs
Media release: Travel-acquired infections and illnesses in Canadians: surveillance report
This study, then, provides information that until now we have had to infer from travel-acquired illness in other groups.
The study uncovered a number of surprises for travelling Canadians and Canadian immigrants. For example, travel to visit friends and relatives carries a particularly high risk of illness. Serious diseases, like malaria, malaria or enteric fever, are in fact common imported illnesses. And diseases significant to public health, like hepatitis B and tuberculosis, are common as well among returning travellers.
“In order to maximize opportunities for prevention of these types of potentially serious infectio...
Source: Open Medicine Blog - - February 11, 2014 Category: Medical Publishers Authors: Carlyn Zwarenstein Source Type: blogs
Some pharmacological history: an exam from 1959
Last year, I was sent my answer paper for one of my final exams, taken in 1959. This has triggered a bout of shamelessly autobiographical nostalgia.
The answer sheets that I wrote had been kept by one of my teachers at Leeds, Dr George Mogey. After he died in 2003, aged 86, his widow, Audrey, found them and sent them to me. And after a hunt through the junk piled high in my office, I found the exam papers from that year too.
George Mogey was an excellent teacher and a kind man. He gave most of the lectures to medical students, which we, as pharmacy/pharmacology students attended. His lectures were inspirational.
...
Source: DC's goodscience - February 6, 2014 Category: Professors and Educators Authors: David Colquhoun Tags: B.L. Welch George Mogey H.O. Schild Pharmacology statistics University of Leeds inference J.W. Trevan UCL University College London Source Type: blogs
Some pharmacological history: an exam from 1959
Last year, I was sent my answer paper for one of my final exams, taken in 1959. This has triggered a bout of shamelessly autobiographical nostalgia.
The answer sheets that I wrote had been kept by one of my teachers at Leeds, Dr George Mogey. After he died in 2003, aged 86, his widow, Audrey, found them and sent them to me. And after a hunt through the junk piled high in my office, I found the exam papers from that year too.
George Mogey was an excellent teacher and a kind man. He gave most of the lectures to medical students, which we, as pharmacy/pharmacology students attended. His lectures were inspirational.
...
Source: DC's goodscience - February 6, 2014 Category: Science Authors: David Colquhoun Tags: B.L. Welch George Mogey H.O. Schild Pharmacology statistics University of Leeds inference J.W. Trevan UCL University College London Source Type: blogs
Answer to Case 290
Answer: P. falciparum with early trophozoites (ring forms) and schizonts. Also shown (last photo) is a monocyte with malaria pigment (hemozoin). Although the differential diagnosis includes infection with 2 different Plasmodium species (notably with P. falciparum and P. malariae), the relatively high percent parasitemia and characteristics of the schizonts are most suggestive of a single infection with P. falciparum.Marco Ligozzi mentions that "P. falciparum schizonts are rarely seen in the peripheral blood and their presence may indicate a potentially severe malaria." Similarly, Anonymous notes tha...
Source: Creepy Dreadful Wonderful Parasites - February 2, 2014 Category: Pathologists Source Type: blogs
Answer to Case 288
Answer: Plasmodium ovaleMarco Ligozzi and Dr. Rajani nicely described the features of P. ovale:"The parasitized erythrocytes are oval in shape and fimbriated at the end," "Schuffner's stippling is present, more evident especially at the edges of the erythrocyte"and malaria "pigment is scattered, coarse."Of note, Dr. Rajani points out that Schuffner's dots are "relevant to P. ovale infection; yet, these dots also appear in cases of P. vivax infection." Therefore it is incumbent upon us to look at other features that would allow us to differentiate P. ovale from P. vivax. The features that I find most usefu...
Source: Creepy Dreadful Wonderful Parasites - December 29, 2013 Category: Pathologists Source Type: blogs
Adb To Link For Expanding Hiv/aids Treatment In Myanmar
Using 10 million U.S. dollars’ grant from the Japanese fund, ADB will establish innovative partnership between government and NGOs to deliver better services to 739 villages in five townships in Mon, Kayin and Shan ethnic states. It is projected that by 2017, communities will see strengthened health system that can plan for and manage response to HIV/AIDS and STI with the number of trained health service providers increasing by 30 percent, the number of patient consultation increasing by 80 percent and behavior change campaign to help reduce exposure to HIV, STI, TB and malaria. Estimation shows that 240,000 people i...
Source: aids-write.org - December 25, 2013 Category: HIV AIDS Authors: aidswrite Tags: current news hiv news Source Type: blogs
