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Entamoeba histolytica Genomic AnalysesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The sequencing of the Entamoeba histolytica genome, as well as the development of genome-wide techniques to allow study of gene expression, has led to many advances in our understanding of the biology of this parasite. Recent work used genomic technologies (DNA microarrays and proteomics) to study important aspects of amebic biology, including pathogenesis, host interaction, phagocytosis, stage conversion, responses to stressful stimuli, and mechanisms of gene regulation. These studies identify pathways involved in regulating major functions in this important human pathogen.from Anaerobic Parasitic Protozoa: Genomics and M...
Source: Microbiology Blog: The weblog for microbiologists. - November 5, 2009 Category: Microbiology Tags: Amebic biology Proteomics DNA microarrays Source Type: blogs

LentivirusesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
comprise a genus of diverse viruses in the Retroviridae family which are united in their ability to infect and persist in macrophages. Infections are characterized by immune system dysfunctions following sometimes lengthy incubation periods. The viruses in this genus include primate lentiviruses such as HIV as well as animal lentiviruses including equine infectious anemia virus (EIAV). An intriguing feature of lentiviruses is their ability to hijack macrophages so that they are simultaneously involved in the dissemination and control of virus spread throughout the host, leading to disease induction and/or transmission to ...
Source: Microbiology Blog: The weblog for microbiologists. - November 4, 2009 Category: Microbiology Tags: Lentiviral-macrophage interaction Macrophage biology Source Type: blogs

Scientists of note now on ScienceBlogsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Pamela Ronald of Tommorow's Table, author of Tomorrow's Table: Organic Farming, Genetics, and the Future of Food. Additionally, David Sloan Wilson, has moved his blog to ScienceBlogs. It's called Evolution for Everyone, after the book of the same name. You can read my review of his book here. Read the comments on this post... (Source: Gene Expression)
Source: Gene Expression - October 21, 2009 Category: Geneticists and Genetics Commentators Tags: Biology Source Type: blogs

Disease Diagnosed By Gene SequenceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This is such a cool application of genetics! By sequencing all the genes of a patient, scientists diagnosed a congenital disease that could not be identified using clinical observations. Because of the “molecular diagnostics technique”, doctors were able to provide a treatment tailored for the disease. The patient, an infant, was persistently dehydrated and failing to gain weight, and researchers uncovered a gene mutation that was responsible to the infant’s condition called congenital chloride diarrhea. Instead of sequencing all the thousand base pairs in a genome, researchers focused only on DNA that encode...
Source: Genetics and Health - October 21, 2009 Category: Geneticists and Genetics Commentators Authors: Grace Ibay Tags: DNA Genetic Diseases and Conditions Molecular Biology and Biotechnology congenital chloride diarrhea gene mutation molecular diagnostics sequence encoding dna Source Type: blogs

Systems Biology Graphical NotationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I haven’t updated this blog for a while, the reason being the usual for many researchers working in the US: grant writing. Part of this grant writing involved producing diagrams to illustrate various processes occurring at different scales in prostate tissue. These diagrams describe rather sophisticated intra and extra cellular interactions in the simplest possible manner. Yet these diagrams can be complicated and selecting the right symbols and colours to describe these interactions in a visually appealing but consistent manner can be far from trivial. As someone with a background in computer science I appreciate t...
Source: Cancerevo: Evolution and cancer - October 21, 2009 Category: Cancer Authors: David Basanta Tags: systems biology computational biology diagram notation graphs standard Source Type: blogs

Discussion with a Cancer SurgeonEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This weekend, I had the opportunity to sit down with a friend, a cancer surgeon who works at a major teaching hospital in the US. He, his wife and two kids were up visiting us for the weekend. Over coffee, I was asking him about the state of cancer therapeutics. Although he himself does not administer drugs or design treatments, he is part of a larger team which includes molecular oncologists that perform this task. What I heard was quite surprising. Read the rest of this post... | Read the comments on this post... (Source: The Daily Transcript)
Source: The Daily Transcript - October 20, 2009 Category: Medical Scientists Tags: Pure Biology Source Type: blogs

All Your Ribosomes Belong to UsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
So more than a week has gone by and there has been little press about the science Nobels. And I must say that this year's Medicine and Chemistry prizes are some of the most important in quite a while. But even between the two, the Chemistry is especially important. Why? I'm not sure. Maybe they were overshadowed by Obama's award??? Or maybe science journalists are sleeping on the job. Ribosomes ... boring. Nothing could be further from the truth. Ribosomes are arguably the most important biological molecule that we know of. I don't have much time to write long essays on the subject so I'll just throw some ideas at yo...
Source: The Daily Transcript - October 16, 2009 Category: Medical Scientists Tags: Pure Biology Source Type: blogs

Dyslexic Molecular Biologist Carol Greider Wins 2009 Nobel Prize in MedicineEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
“It's going to be hard work whether you think it's fun or not, so you might as well have fun while you're doing the hard work.” - Carol Greider, PhD, 2009 Nobel Prize Winner in MedicineHer application package was a bit unusual, Greider says. “I had great research experience, great letters of recommendation, and outstanding grades, but I had poor GREs.” Although she did not know it growing up, Greider suffers from dyslexia, which affected her scores on standardized tests. Only two schools—the California Institute of Technology (Pasadena, CA) and the University of California, Berkeley— offered her an interview......
Source: Eide Neurolearning Blog - October 12, 2009 Category: Neurologists Tags: molecular biology Nobel Prize science physics spatial Source Type: blogs

microRNAsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Until 2001, few people had heard the term micro ribonucleic acids, but these little chunks of nucleic acid, just 21 to 23 bases long, have been conserved throughout evolution. They don’t code for proteins, but they do seem to be involved in the regulation of immunity, the development and differentiation of immune cells, antibody production and the release of chemicals involved in the inflammatory response. So micro by name, but not by nature, you might say. Indeed, microRNA, or miRNA, represent something of a new paradigm in the regulation of a vast array of responses of physiological and hence medical importance. Th...
Source: Sciencebase Science Blog - September 28, 2009 Category: Medical Scientists Authors: David Bradley Tags: Science biomedicine miRNA molecular biology Source Type: blogs

Synthetic biology goes mainstreamEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
If The New Yorker is giving the topic coverage.... (though a lot of probably is more Craig Venter's celebrity status) (Source: Gene Expression)
Source: Gene Expression - September 22, 2009 Category: Geneticists and Genetics Commentators Tags: Synthetic biology Source Type: blogs

Does Tamiflu resistant swine flu virus really spread less well?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
There is no way to keep up with all the flu news, so we pick and choose, usually based on some kind of point we want to make. That's both the good and the bad of this blog: the news comes with a point of view. But so does most news, and we try to make ours both explicit and scientifically as accurate as we can with the information at hand. Today is a typical example. Bloomberg is reporting that any swine flu virus resistant to oseltamivir (trade name Tamiflu), the only antiviral pill effective at all for the infection, transmits less well than swine flu that's sensitive to Tamiflu. The source of this information is Dr. Dav...
Source: Effect Measure - September 16, 2009 Category: Epidemiologists Tags: Biology Source Type: blogs

Lost World, 2009Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The story about the giant rat discovered in an isolated crater in Papua New Guinea is fascinating. It's kind of atypical in these days, but if you read through really old copies of National Geographic from the early 20th century it you observe that it occurred all the time back then. I would of course much rather live now at the turn of the 21st century than the turn of the 20th, but there's a certain amount of zoological and anthropological wonder that we'll not be able to attain because so much of the sample space of possibilities has been mapped out. Read the comments on this post... (Source: Gene Expression)
Source: Gene Expression - September 8, 2009 Category: Geneticists and Genetics Commentators Tags: Biology Source Type: blogs

The Role of Transforming Growth Factor-Beta -Mediated Tumor-Stroma Interactions in Prostate Cancer Progression: An Integrative ApproachEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Can biologists and mathematicians accomplish more together than working separately? My answer to that question has always been a resounding yes but today I am backing up that statement with a piece of research: the result of a collaboration involving mathematicians and biologists (and a pathologist) in Tampa, Nashville and Houston. Basanta, D., Strand, D., Lukner, R., Franco, O., Cliffel, D., Ayala, G., Hayward, S., & Anderson, A. (2009). The Role of Transforming Growth Factor- -Mediated Tumor-Stroma Interactions in Prostate Cancer Progression: An Integrative Approach Cancer Research, 69 (17), 7111-7120 DOI: 10.1158/0...
Source: Cancerevo: Evolution and cancer - September 4, 2009 Category: Cancer Authors: David Basanta Tags: integrative biology cancer stroma tumour interactions paper article Source Type: blogs

Did You Ever Wonder What Your Hair Looks Like Close Up?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This really appeals to the scientist in me. You can see all of the important hair structures like the cuticle, the cortex and even the melanin that gives hair it’s color. It also shows you why you can’t fix a split end. Once the hair fiber has been broken, no amount of hair treatment is going to rebuild a broken strand. (Source: thebeautybrains.com)
Source: thebeautybrains.com - August 5, 2009 Category: Physicians With Health Advice Authors: Mid Brain Tags: Beauty Research Biology of Hair Source Type: blogs

Drug synergies tend to be context specificEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A little over a year ago I mentioned a paper published in MSB on how drug-combinations could be used to study pathways. Recently, some of the same authors have now published a study in Nature Biotech analyzing drug combinations under different contexts (i.e. different tissues, different species, different outputs, etc). The underlying methodology of the study is essentially the same as in above mentioned paper. The authors try to study the effect of combining drugs on specific phenotypes. One example of a phenotype could be the inhibition of growth of a pathogenic strain. Different concentrations of two drugs are combined...
Source: Public Rambling - August 1, 2009 Category: Bioinformaticians Tags: chemogenomics systems biology Source Type: blogs

Artificial SpermEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Read this news story about how human sperm have been made in the lab (Source: Jemma's Biology Blog)
Source: Jemma's Biology Blog - July 9, 2009 Category: Medical Scientists Tags: Topic 3 - Voice of the Genome BIOLOGY NEWS Source Type: blogs

Conversations from Penn State: Emerging DiseasesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In the current episode of the Penn State University interview series called “Conversations from Penn State“, Peter Hudson, who is Willaman professor of biology and director of Penn State’s Huck Institutes of the Life Sciences, discusses the dynamics of infectious diseases, their spread, and their transmission from animals to humans. (Source: virology blog)
Source: virology blog - June 22, 2009 Category: Virology Authors: Vincent Racaniello Tags: Information biology infectious disease penn state university peter hudson video viral virology virus Source Type: blogs

Transgenic MonkeysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
News story about how transgenic monkeys may be used to find cures for human diseases.What does transgenic mean? (Source: Jemma's Biology Blog)
Source: Jemma's Biology Blog - June 11, 2009 Category: Medical Scientists Tags: Topic 3 - Voice of the Genome BIOLOGY NEWS Source Type: blogs

Can I Tan Sunless Safely?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Mid Brain muses: According to this article, the Fake Bake sunless tanning market is hot. Over the last few years major skin care manufacturers have discovered how to combine a skin moisturizer with a sunless tanner to make an effective light sunless tanner that gives a steady color change. These new tech products prevent the streaking effect that has been a major drawback of traditional sunless tanners. They also provide daily moisturization so there’s a reason to use them everyday. You get healthy skin and a natural looking color. How do sunless tanners work? To understand sunless tanning it is helpful to have a si...
Source: thebeautybrains.com - May 20, 2009 Category: Physicians With Health Advice Authors: Mid Brain Tags: Beauty Industry Biology of Skin How cosmetics work Questions DHA self tanner tan sunless Source Type: blogs

Teen-age children as experimental subjectsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We always enjoy home science experiments and it was fun the other night to learn about a new experiment we could try with our teenage daughter and an iPhone. As it turned out, the joke was on us. Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World)
Source: Discovering Biology in a Digital World - May 6, 2009 Category: Medical Scientists Tags: Biology (Macroscopic ) Source Type: blogs

Why are the schools closing and other good H1N1 links...Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Over at DailyKos, DemfromCT has an excellent post explaining why it may be beneficial for schools to close temporarily, even if they only have one confirmed case of swine influenza: H1N1: Why Do Schools Close, And When Do They Open? DarkSyde also has one up on the basic biology and evolution of the flu. Nick Kristof discusses our lack of attention to public health and what it means in the event of a pandemic in today's NY Times. [Updated: and via the comment theads, this post which further discusses what I mentioned here regarding testing--and how the confirmed cases are only the tip of the iceberg (complete with dia...
Source: Aetiology - May 3, 2009 Category: Epidemiologists Tags: General biology Source Type: blogs

Adamantane resistance in flu explainedEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nick Anthis has a very nice (and very readable!) overview of why flu viruses (including the new A/H1N1 strain) are resistant to adamantane, one of the antiviral drugs that can be used to treat influenza infections. Read the comments on this post... (Source: Aetiology)
Source: Aetiology - May 1, 2009 Category: Epidemiologists Tags: General biology Source Type: blogs

Noninvasive Down Syndrome test no go (for now)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I blogged about this a few months ago, but Dan MacArthur reports that the firm which was going to roll it out first claims that it doesn't really work as advertised. Read the comments on this post... (Source: Gene Expression)
Source: Gene Expression - April 30, 2009 Category: Geneticists and Genetics Commentators Tags: Biology Source Type: blogs

Drink wine to live longer!Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I'm in the mood for a "feel good" story with the past week's fixation in swine flu. Half A Glass Of Wine A Day May Boost Life Expectancy By Five Years: The Dutch authors base their findings on a total of 1,373 randomly selected men whose cardiovascular health and life expectancy at age 50 were repeatedly monitored between 1960 and 2000. Here are the findings: Read the rest of this post... | Read the comments on this post... (Source: Gene Expression)
Source: Gene Expression - April 30, 2009 Category: Geneticists and Genetics Commentators Tags: Biology Source Type: blogs

Pray the virus awayEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Carl Zimmer points out that Marianne Williamson is making some real strange suggestions in regards to the swine flue in The Huffington Post: l) Pray it away. Just pray it away, asking God as you understand Him, the Divine Physician, Jesus or whatever other form of divine imagery works for you. Simply ask that it be removed from our midst. 2) Send love to Mexico. Between what's actually been happening there with the drug wars, plus all the "Mexico is dangerous" thoughts we've loaded onto it over the last several weeks, it needs a major dose of love - the most powerful medicine of all - to dissolve the fear thoughts that h...
Source: Gene Expression - April 29, 2009 Category: Geneticists and Genetics Commentators Tags: Biology Source Type: blogs

Vitamin D & asthmaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Serum Vitamin D Levels and Markers of Severity of Childhood Asthma in Costa Rica. See ScienceDaily. Anecdote: my own asthma has gotten much better since I started Vitamin D supplementation. Not only have I had many fewer bouts of bronchitis the past few years, but my basal respiratory functioning is much improved. Read the comments on this post... (Source: Gene Expression)
Source: Gene Expression - April 27, 2009 Category: Geneticists and Genetics Commentators Tags: Biology Source Type: blogs

Swine flu and deaths in healthy adults--cytokine storm?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Discussion after the jump... Read the rest of this post... | Read the comments on this post... (Source: Aetiology)
Source: Aetiology - April 26, 2009 Category: Epidemiologists Tags: General biology Source Type: blogs

Swine flu: a quick overview--and new New York and Kansas casesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Sorry for the radio silence--I've been working on grants and manuscripts like a fiend, and so have tried to limit as many distractions as possible (which, unfortunately, includes blogging). However, the swine flu news is right up my alley, so I do just want to say a few words about it, and point you to some excellent stories already up elsewhere. First, in case you've not been paying attention to the news in the last few days, there have been 8 reported cases of swine influenza infections in humans (6 in California and 2 in Texas, with additional suspected cases) and reports from Mexico suggesting as many as 1000 ill and...
Source: Aetiology - April 25, 2009 Category: Epidemiologists Tags: General biology Source Type: blogs

The Semantic Web of Life ScienceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This summary was born out of a question on Twitter and percolated to FriendFeed, which was “Who is using RDF and integrating other resources at the minute and what are those resources? From this question, several resources were highlighted. UniProt. The comprehensive resource of protein information is available as an RDF distribution and each Protein record has a corresponding RDF download option. Phil pointed out Semantic Systems Biology, As systems biology is largely concerned with representing networks and interactions at a systems level, a language like RDF would seem an obvious choice to represent this type of kno...
Source: peanutbutter - April 25, 2009 Category: Bioinformaticians Authors: peanutbutter Tags: bioinformatics life-science semantic web Biology Resource Description Framework RDF Twitter FriendFeed systems biology open data Linked Open Data Source Type: blogs

Swine flu...2009 as annus horribilis?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
See FuturePundit & Effect Measure. Also see H5N1. CDC recommends (especially for residents of California & Texas): Read the rest of this post... | Read the comments on this post... (Source: Gene Expression)
Source: Gene Expression - April 25, 2009 Category: Geneticists and Genetics Commentators Tags: Biology Source Type: blogs

Injection, Collection, and SexEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
That's how new life forms are created every day in the wild, folks. Human researchers of course have added a few twists on the theme. If we can't induce bacteria or animal cells to collect new bits of DNA on their own, we turn to electroshock therapy. With plants.... aw heck, we just shoot them. And where did this crazy rant come from you ask? Last Saturday morning, at the crack of 9 am I got to be interviewed on a radio program with two of the main spokespeople from the DIY bio movement, Mackenzie Cowell and Meredith Patterson. The program was "The Food Chain" (you can listen to it here: ) Read the rest of this post....
Source: Discovering Biology in a Digital World - April 22, 2009 Category: Medical Scientists Tags: DIY biology Source Type: blogs

Tropical latitude = more girlsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The New York Times has a story about a new paper, Humans at tropical latitudes produce more females: Skews in the human sex ratio at birth have captivated scientists for over a century. The accepted average human natal sex ratio is slightly male biased, at 106 males per 100 females or 51.5 per cent males. Studies conducted on a localized scale show that sex ratios deviate from this average in response to a staggering number of social, economical and physiological variables. However, these patterns often prove inconsistent when expanded to other human populations, perhaps because the nature of the influences themselves exhi...
Source: Gene Expression - April 21, 2009 Category: Geneticists and Genetics Commentators Tags: Biology Source Type: blogs

This should not be here … or Notes to a bioinformatician – two years laterEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Image via CrunchBase I was contacted a couple of months (maybe more) to write a guest entry for their blog. I did that and on March 11th I sent the text you see below. It’s not my best creation (and not the worst, believe me), but as they’re taking so long to publish it and I don’t want it to go to waste, I’m publishing it. — Exactly two years ago (or almost exactly), I posted a follow-up blog entry to Notes to a young computational biologist. I still believe that 97% of all advice is worthless, but I also believe that it’s worth sharing your experiences as it might be useful to some...
Source: Blind.Scientist - April 17, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Biology Computer programming FriendFeed twitter Source Type: blogs

Dealing with Change in Your LifeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Does the idea of a change in your life or career send you running for the hills? Do you get nervous, feel unsettled or anxious about change? Would you prefer that things just stay the same? Well you are not alone. Millions of people feel the same way you do. Why is Change so Difficult to Embrace? Change often stirs up feelings of uncertainty, doubt, fear and trepidation. Emotions most of us don’t like to experience very much. Change can be scary as it often means you have to step outside your comfort zone. People Love Sameness Most people prefer sameness, routine, certainty and familiarity. Just think about organiz...
Source: Armstrong Method - April 7, 2009 Category: Life Coaches Authors: admin Tags: blogs benefits effectively embrace empowering inevitable payment quantum biology sameness staff stomach structures territory Source Type: blogs

What Books Would Be Good For Self-Study in Bioinformatics?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Despite my lack of commitment to this site, it seems that I’m still getting comments every now and again. And I appreciate the interest. It really helps me realize the potential interest in the kind of things I’ve written about here. Most recently, I got a comment from Sudhang requesting books for the computer programmer who wants to self-study in the field of Bioinformatics. The following is my list. It may seem like its a bit everywhere but that’s kind of what you get with the field of Bioinformatics. Molecular Cell Biology. One would get glossy eyed trying to read through this book, but you need to ha...
Source: biowhat.com - April 4, 2009 Category: Bioinformaticians Authors: Ryan Castillo Tags: Statistics Computer Science Bioinformatics Biology Source Type: blogs

Brain News: Lifelong Learning for Cognitive HealthEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Here you have the March edition of our monthly newsletter covering cognitive health and brain fitness topics. Please remember that you can subscribe to receive this Newsletter by email, using the box at the top of this page. I know I am biased - but do believe this Newsletter issue might well be our best so far. I hope you find the time to enjoy it! Bird's Eye View Top Articles and Resources in March: Highlights - a) great articles in SciAm Mind and the Wall Street Journal, b) new resources (book and free DVD) by the Dana Foundation, c) research studies on how our cognitive abilities tend to evolve as we age, the impact o...
Source: SharpBrains - March 31, 2009 Category: Neurologists Authors: Alvaro Fernandez Tags: Cognitive Neuroscience Education Health & Wellness Brain Fitness Newsletter ADHD drugs aging Biology book brain care brain fitness book brain fitness guide brain news Brain Plasticity Brain Training brett steenbarger cogn Source Type: blogs

BioModels Workshop 2009: Day 2Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Today was great fun - lots of presentations and lots of lively discussions, of which we were all a part, but which Nicolas Le Novère ("shown" left, courtesy of Falko Krause :) ) also enjoyed. Here are the notes! CellML: Catherine Lloyd Most o... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics)
Source: Systems Biology & Bioinformatics - March 29, 2009 Category: Bioinformaticians Tags: bioinformatics saint arcadia systems biology libannotationsbml cellml biomodels workshop 2009 semanticsbml Source Type: blogs

BioModels Workshop 2009: Day 1Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
BioModels Database Introduction: Nicolas Le Novere Repository of quantitative models only for the moment: no implicit statement of biochemical accuracy as a consequence of being in the database, but must be of biological interest and only those ... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics)
Source: Systems Biology & Bioinformatics - March 28, 2009 Category: Bioinformaticians Tags: bioinformatics systems biology biomodels workshop 2009 Source Type: blogs

SBML Hackathon 2009: FinishedEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The SBML Hackathon was a really interesting experience for me. I haven't had much time to collect my thoughts, as we've gone straight on to the next phase: the BioModels Workshop or, for some, the trip home. This was my first Hackathon, and I fou... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics)
Source: Systems Biology & Bioinformatics - March 28, 2009 Category: Bioinformaticians Tags: bioinformatics systems biology sbml hackathon 2009 Source Type: blogs

SBML Hackathon Day 2Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Things changing with SBML Level 3 A complete list is available at http://sbml.org/Community/Wiki/SBML_Level_3_Core/Workplan These are just the ones I found the most interesting as we went through the whole list. + Move species type and compart... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics)
Source: Systems Biology & Bioinformatics - March 28, 2009 Category: Bioinformaticians Tags: bioinformatics systems biology sbml hackathon 2009 libsbml Source Type: blogs

SBML Hackathon 2009: Afternoon SessionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Falko Krause presented ubuntu 4 systems biology, a live cd with some applications pre-installed, so you can try it out without having to actually install it. He says if you have any software you'd like to include, to let them know and they'll inc... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics)
Source: Systems Biology & Bioinformatics - March 27, 2009 Category: Bioinformaticians Tags: bioinformatics systems biology sbml hackathon 2009 Source Type: blogs

The BioSysBio conference 2009Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Image via Wikipedia The premise of the BioSysBio conference is to bring together the best young researchers working in Synthetic Biology, Systems Biology and Bioinformatics, providing a platform to hear and discuss the most recent and scientific advances and applications in these fascinating fields. This years BioSysBio 09 has just taken place in Cambridge, UK. The program was more slanted towards synthetic biology rather than more traditional systems biology, which I think reflects the growing momentum that synthetic biology has gained in the past year. I think this is a good progress and I was secretley glad as I di...
Source: peanutbutter - March 26, 2009 Category: Bioinformaticians Authors: peanutbutter Tags: bioinformatics conference report Biology Cambridge Twitter Drew Endy Synthetic Biology FriendFeed RNA Christina Smolke biosysbio systems biology Source Type: blogs

SBML Hackathon 2009: Introduction and libSBML 4 OverviewEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Keep track of the tweets at http://search.twitter.com/search?q=%23sbml Nicolas' Introduction Sponsored by Elixir ("a sustainable infrastructure for biological information in Europe"). Very nice graph of the minimal cost of storage and other IT r... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics)
Source: Systems Biology & Bioinformatics - March 26, 2009 Category: Bioinformaticians Tags: bioinformatics systems biology sbml hackathon 2009 libsbml Source Type: blogs

Keynote: Towards Scalable Synthetic Biology and Engineering Beyond the Bioreactor (BioSysBio 2009)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Adam Arkin UC Berkeley People have been doing "Old School" synbio for a long time, of course: take corn (which came from Teosinte), dogs. But is selective breeding actually equivalent, in some sense, to "old school" synthetic biology? He argues t... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics)
Source: Systems Biology & Bioinformatics - March 25, 2009 Category: Bioinformaticians Tags: bioinformatics systems biology synthetic biology biosysbio 2009 Source Type: blogs

De novo DNA Synthesis using Single Molecule PCR (BioSysBio 2009)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
T Ben Yehezkel et al. Weizmann Institute of Science When looking at the number of clones needed to sequenced in order to get one error-free molecule, the proportion of perfect molecules decrease exponentially with length. They have an error-corre... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics)
Source: Systems Biology & Bioinformatics - March 25, 2009 Category: Bioinformaticians Tags: bioinformatics systems biology biosysbio 2009 dna synthesis Source Type: blogs

Second-Generation Sequencing of Mutants: the $1000 Mutant Genome (BioSysBio 2009)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
J A Pachebat et al. University of Cambridge HGP finished 2004, and took $300 million. Same method in 2007 for $10 million. However, there is a new generation of techniques that are much cheaper and faster. Very nice hierarchy, or family tree, of ... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics)
Source: Systems Biology & Bioinformatics - March 25, 2009 Category: Bioinformaticians Tags: bioinformatics sequencing systems biology biosysbio 2009 amoebae Source Type: blogs

Building a New Biology (BioSysBio 2009)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Drew Endy Stanford University, and BioBricks Foundation Overview: Puzzle related to SB and informing some of his engineering work. Then a ramble through the science of genetics. Last part is a debrief on BioBrick public agreements. Part 1. If SB... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics)
Source: Systems Biology & Bioinformatics - March 25, 2009 Category: Bioinformaticians Tags: bioinformatics systems biology synthetic biology biosysbio 2009 biobricks Source Type: blogs

Why Secure Synthetic Biology? (BioSysBio 2009)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Piers Millett Biological Weapons Convention Implementation Support Unit, UN Biology is inherently dual-use: can be used for beneficial and malignant purposes. Synbio is value neutral - it's the purpose it's put to that determines if it is bad or ... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics)
Source: Systems Biology & Bioinformatics - March 25, 2009 Category: Bioinformaticians Tags: bioinformatics systems biology biosecurity biosysbio 2009 biological weapons convention Source Type: blogs

What if everything you thought you knew about the genome was wrong?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
For the past few months, the shake-up that began with Next Generation DNA Sequencing has been forcing me to adjust to a whole new view of things going on inside of a cell. We've been learning things these past two years that are completely changing our understanding of the genome and how it works and it's clear we're never going back to the simple view we had before. What's changed? The two most striking changes, to me at least, are the new views of the way the genome is put together and what the cell does with the information. Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World)
Source: Discovering Biology in a Digital World - March 24, 2009 Category: Medical Scientists Tags: Genetics & Molecular Biology Source Type: blogs

Look into the future (and the past) with Gene GenieEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
What do the missing Romanov children, genetically engineered humans, financial risk taking, and poop have in common? You can read about all these topics from this month's Gene Genie carnival at Mary Meets Dolly. Who would have thought that mutations could be so much fun? Read the comments on this post... (Source: Discovering Biology in a Digital World)
Source: Discovering Biology in a Digital World - March 22, 2009 Category: Medical Scientists Tags: Genetics & Molecular Biology Source Type: blogs