tag:blogger.com,1999:blog-90483196730341418262012-02-16T02:51:55.756-08:00Collection of Useful and Best web sites in Life ScienceAbout ushttp://www.blogger.com/profile/09516317622129179424noreply@blogger.comBlogger691100tag:blogger.com,1999:blog-9048319673034141826.post-13025115793287915112010-11-22T07:06:00.002-08:002010-11-24T15:53:00.777-08:00

For far too long, the chloroplast has been keeping the spotlight squarely on himself. Everybody knows what a chloroplast is, but many fail to realize that the chloroplast is just one type of the organelles known as plastids. Plprot, the plastid protein database, features three types of plastids in addition to the chloroplast: the proplastid (the precursor to all other plastids), the

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Here’s a website that took a page from Hollywood when it comes to advertising its movies. Rather than touting “Academy Award winner So-and-So,” it boasts the “Nobel Prize-winning worm C. elegans.” The entire site is, in fact, dedicated to this small scientific celebrity, showcasing the little critter in a number of time-lapse videos. These videos have been made by members of the worldwide

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For as much as cancer has (sadly) become part of our existence, there are many people who do not understand just what it is. Enter Inside Cancer, a wonderful website for anybody who wants to learn about the basics of cancer, as well as a fantastic website for educators. Inside Cancer is a nicely designed multimedia website that is divided into four sections: hallmarks of cancer, causes and

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Do you find yourself on the PROWL for online protein analysis tools? (Hey, I have to take the easy puns where I can get them…) If so, then you need to scurry over to the website of the Chait laboratory at The Rockefeller University. This laboratory, dedicated to the development of “proteomic tools for dissecting cellular function, with a special emphasis on the mass spectrometry (MS) of

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It is unlikely that an ambiguous title like “ArgusLab” drives too much traffic to this website, which s a shame. ArgusLab is, in fact, the name of a molecular modeling program authored by Mark Thompson (as opposed to the name of a laboratory, as would be the obvious suspect). It is free to download, although it is unfortunately only PC-compatible. Do not be deterred by the blank screen that

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It falls between the trial-by-fire period of graduate school and the (hopefully reachable) light-at-the-end-of-the-tunnel dream job. Yes, that’s right—it’s the postdoctoral position. Fearing the dreaded possibility of being stuck in postdoc limbo, researchers at this stage of their career often don’t have access to (or don’t know where to go to find) resources related to career development.

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How exactly does one plant science, I wonder? I’ll have to think on that one… What I can speak to is plantingscience.org, a wonderful website on which students, teachers, and researchers can put down their roots. The idea behind this burgeoning online community is simple: connect research mentors, educators, and students so that young minds can grow into mature scientists. The website

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I can always appreciate a website with a clever logo—such as the Genetic Alliance’s DNA strand in which people substitute for the base pairs. And when the rest of the site delivers, well, that just makes my day. Genetic Alliance is a nonprofit health advocacy group that provides resources about health in general, but with a specific emphasis on genetic disorders. The disease info search

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The warm summer weather invites us to go outdoors where one can spend hours admiring blooming flowers and trees in the park. But, if allergies keep you homebound, you can spend your time perusing the pollen-free plants of the New York Botanical Garden’s C.V. Starr Virtual Herbarium. Geared toward researchers, as opposed to people who simply enjoy looking at photos of pretty plants, the

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Kudos to the people behind AntWeb for setting their sights high: “Over time, this site will grow to describe every species of ant known.” Yes, AntWeb may be quite a way off from total ant characterization, but the current collection is more than enough to ensnare me. Working with a current inventory of 206,261 specimens, AntWeb provides wonderful, up-close images of ant species from around

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Remember when life was simple—when a mouse was just a mouse? There were none of these knock-out or conditional knock-out complications. Well, we’ve learned a lot from each modified musculus strain individually, but sometimes it’s nice to take a step back and observe on a broader scale. That’s exactly what the Europhenome Mouse Phenotyping Resource provides: a wide scope of phenotypes across

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Scientists have a knack for creating self-explanatory names for things, and the defensins are no exception. It doesn’t take an immunologist to guess that this family of peptides does something to protect us, and indeed they do. Defensins are antimicrobial peptides that are found in a wide variety of organ-isms (including us), and now, thanks to the collaborative efforts of the

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It was a happy accident that I came across SlideWorld, a wonderful website with a less-than-descriptive name. (For all I knew, it could have been the website for a water park!) SlideWorld is a search engine for medical PowerPoint presentations. Boasting 7,650,583 presentations, SlideWorld allows one to enter the site as either an “empowered patient” or a “medical professional,” and

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Who knew that the trees were at war? (At least, that’s the first image that came to mind when I read that the Gymnosperm Database is “the web’s premier source of information on conifers and their ‘allies.’” It was an entertaining thought…) In all seriousness, though, the Gymnosperm Database is a wonderful botany website, and it is strongly infused with the candor of its creator, Christopher

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Aren’t mosquito bites just the worst? No, I correct myself—contracting malaria from mosquito bites is the worst! Well, hey—don’t blame the mosquito. We should be focused on the parasite, Mr. Plasmodium falciparum. Many scientists are, in fact, entirely focused on Plasmodium falciparum, and the WHO/TDR Malaria Database is a wonderful online resource for malaria researchers. The site includes

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For all of the acronyms, made-up names, and nomenclature I have encountered in science, I can’t remember the last time I came across a name so visually succinct as BioTapestry. The many (many, MANY) genetic interactions within organisms are very much akin to threads that are elegantly woven to form intricate tapestries. And thus, there seems to be no name more befitting an interactive tool

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Far from having a stern librarian to “shush!” you and your friends, the Macaulay Library is, in fact, the noisiest library around! Housed at the Cornell Lab of Ornithology, the Macaulay Library’s online archive is the world’s largest archive of animal sounds and video. Rather than simply being limited to bird sounds (as one might expect from an ornithology laboratory), the Macaulay Library

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If you want to explore the complex landscape of gene interactions, Cytoscape makes for an excellent compass. Developed by a consortium funded by the National Institute of General Medical Sciences (NIGMS) of the NIH and the NSF, Cytoscape is an open-source software platform to visualize and analyze complex networks such as biological pathways and molecular interactions. A unique feature of

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Isn’t it frustrating to be putting together a document or presentation, only to realize that it could really use some good images and alas, you can’t find any? Thankfully, there’s ImageBank, hosted by The Higher Education Academy at the UK Centre for Bioscience. This collection of images offers the perfect remedy to that graphically challenged scientific talk or bland lecture. One can browse

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I am a firm believer that one can never watch too many scientific animations, and for that reason I find the Howard Hughes Medical Institute’s BioInteractive website to be an online gold mine. The information is generally divided into 13 topics (neuroscience, infectious diseases, stem cells, evolution, obesity, cancer, genomics and chemical genetics, sex determination, biological clocks,

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How to describe this site? Well I think the opening page says it all: “Think of us as one of your labmates—except, we don’t fall asleep in group meetings…” (Yes, we’ve all been there.) Benchfly is a multifaceted resource for scientists, although the primary component of the site consists of video tutorials. Whether you want to know how to pack a capillary column, clean a rotovap, or smear

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I know what you’re thinking—cycad? What in the world is a cycad? Well, although you may not know the name of this group of plants, you’ve probably seen them before. Often mistaken for palms or ferns, these plants have short trunks and are crowned with a cluster of leaves that look like, well, palm or fern leaves. More than half of the cycad species also happen to be threatened or endangered.

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This website holds a certain “innate” appeal for immunology researchers as it is an excellent database for gene interactions and pathways related to innate immunity. A collaboration between groups at Simon Fraser University, the University of British Columbia, and the Teagasc Animal Bioscience Centre in Ireland, Innate DB provides users with many ways to explore the information contained

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The rise of biotechnology has clearly changed the research landscape. Accordingly, science education must be willing to adapt to the constantly evolving technologies and techniques. The BioTech Project at the University of Arizona provides resources for teachers to introduce concepts of biotechnology in the laboratory to students of various ages. The “Laboratory Activities” tab provides

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Before you explore this one, read the author’s preface entitled “Why Chemical Logic?” In it, he provides a rational explanation for his arrangement of topics in teaching biochemistry and explains why they differ from more modern presentations. The approach is interesting and radical, starting with lipid structure and then moving to protein structure, carbohydrate structure, DNA/genomics/

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A schizophrenic site, Vaccines and the Infectious Diseases They Prevent provides a considerable amount of useful medical information about seven devastating diseases, but its URL and the opening page leads visitors to believe it only concerns tetanus. Fortunately, that is not the case, as a click on the small panel of disease names at the top of the opening page reveals. Diseases include

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ou want quirky? OK. Start with the title of this educational site. I’m not quite sure what it means. It certainly doesn’t describe (at least as I see it) the contents of the site, which are animations relevant to cell biology. Topic areas include amino acids/proteins, cell function overview, cell anatomy, cell membranes, chromosome structure, glycolysis, evolution, and more. Each of these

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Oh, those crazy geneticists! Who thinks of naming a gene “Hedgehog”, anyway? The name may be frivolous, but the Hedgehog Signaling Pathway is certainly not, as it is required during the embryogenesis of many organisms. The Hedgehog Signaling Pathway Database, through the San Francisco State University, provides a number of online tools for researchers studying this pathway. There are

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Who knew that nuclear hormone receptors could be so fun (or colorful)? There is plenty of information to explore on this relatively new online resource, edited by a professor at Penn State University. The site is beautifully organized and easy to navigate. If you have no idea what a nuclear hormone receptor is (sometimes called NR–don’t ask me why the “H” wasn’t considered worthy enough to

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Now here’s a site where you can really go fishing for information! (I wish I could take credit for that pun, but it also happens to be used a few times on the website…) FishBase is a massive database for everything you ever wanted to know about our finned, fishy friends. To understand the scope of the database, here are the current statistics (as of November 2009): 31,400 species, 279,800

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Now I’m not generally a betting gal, but I would bet that most of you reading this are unfamiliar with bean beetles. (Am I right?) Well, bean beetles, or more properly Callosobruchus maculates, get their name because the larvae develop and feed exclusively on the seeds of legumes. These bugs might be agricultural pests in Asia and Africa, but they happen to also be very useful experimental

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Can the experiences of cells in one generation pass on characteristics to the next one? If you asked that question just a few years ago, the consensus answer would likely have been ‘no,’ but advances in the study of epigenetics are rapidly revealing instances where environment affects phenotype long after the fact. Rooted in complex modifications resulting in activation/inactivation of

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Paul McCartney's ex, Heather Mills, says that meat putrifies in your stomach for 40 years. Roger Moore (James Bond actor) claims that foie gras causes Alzheimer's disease. Celebrities get a disproportionately large amount of media coverage and therefore such statements can be anything from annoying to dangerous. Battling outrageous claims in the media is the Sense About Science page, which

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Extension services at land-grant universities invariably have entomologists who do everything from advising on insect infestations to identifying specimens submitted to them. “What's That Bug?” is to the Web what extension entomologists are to universities, offering a full range of services, essentially for free (donations are requested). Features include identification of creepy crawlers

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If fondness is measured by the amount of effort that goes into a web site, Derrick Ditchburn certainly has an enormous affection for nature. Ditchburn and his son are the two principals of the Dereila Nature Inn, a site that describes itself as “A Virtual Inn for Nature Lovers,” and it's loaded with cyber delights. Test your knowledge of birds with the eight-bird crossword puzzles. Assemble

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Commonly found in fresh water, Tetrahymena are ciliated protozoans that are important model organisms for biomedical research. It was in Tetrahymena that Thomas Cech, Nobel Laureate in chemistry, discovered ribozymes and it was in this same organism that much understanding of telomeres has been realized. Tetrahymena also was the system where the function of histone acetylation was revealed. If

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The protein folding problem isn't normally associated with fun. Indeed, the intractable nature of predicting folding commonly leads to frustration, but Foldit is a welcome and thoughtful exception. Created as a tool that is both educational and has research applications, Foldit comes as a downloadable program (Mac, Windows, Linux) available upon free registration. After firing it up, users are

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You've got a great lab web page loaded with content. You want users to find information, so you need a search function, but getting one from providers on your terms can be a problem. What to do? Consider JRank, which aims to be all things to web page creators and has a useful set of indexed information for other users as well—check out the site's impressive collection of online encyclopedias and

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Regulating gene expression by transcription factors is fundamental to the survival of every cell. The web is bursting with tools for identifying these proteins and their DNA-binding sites, but few offer a visual perspective. Since seeing is believing, and insightful for understanding too, Paul Boardman at Manchester University developed SightSeer, a tool for imaging mapped transcription factor

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Derek Wong is a medical virologist in Hong Kong who worked in the lab that discovered the first-ever human avian influenza infection (H5N1), and he has studied SARS as well. Putting his credentials to work, Derek created Wong's Virology, a web site full of information about viruses, directed largely toward undergraduate and post-graduate students. The site includes practice exams aimed at

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Whether you pronounce it “AY-POP-TOE-SIS” or “AP-O-TOE-SIS,” scientists with a morbid interest in cell death will enjoy CellDeath.de, an initiative started and maintained by Ph.D. students. The site is clearly a work-in-progress, as evidenced by some blank pages and outdated conference dates/publications. However, the scaffolding is in place to make this site a hub for apoptosis research.

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Every now and then I find a site, which has such a wide audience and addresses a broad Internet-related concern that I feel compelled to write about it, even though it doesn't directly deal with biotechnology. The issue I'm talking about is the need to register at sites. I've complained about this on numerous occasions because of the tendency of some sites to sell that information, ultimately

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By its own description the National Biological Information Infrastructure (NBII) is a "broad, collaborative program to provide increased access to data and information on the nation's biological resources." Towards this end, three of the topics covered on the site (botany, genetic biodiversity, and fisheries/aquatic resources) are grist for this month's Best of the Web mill. Each of the main

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Remember when you were in school and genetics equated to Punnett squares over, and over, and over again? (Not that I’m complaining —I could happily Punnett all day.) Well, anyone who remembers genetics as merely Mendel and peas should definitely check out this site, one of the wonderful DNA Learning Center sites through the Cold Spring Harbor Laboratory. Actually, anyone who ever wanted to know

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Immunology at NIH, at first glance, would, logically, seem to be devoted mostly to the topic of immunology, but on closer examination, the site appears instead to be more about the people involved in the discipline than about immunology itself. The opening page provides four research snapshots, but clicking on them reveals little about immunology. For example, the heading titled Structural

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The American Museum of Natural History has, as one might expect, an attractive site, with many visually pleasing pages on general topics in natural history. It was a pleasant surprise, though, to discover that, in addition to general information on things like volcanoes, astronomy, and tsunamis, the Science Bulletins section of the site has helpful coverage of biology and molecular biology that

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It doesn't take an electron microscope to produce beautiful and educational images of tiny life forms. That message is clearly in focus at Micrographia.com, where an eclectic collection of (mostly) microorganisms is on display 24/7. From the movie of a tiny juggling act on the opening page to an expansive set of images sorted biologically, Micrographia wows with its pictures, and there's no

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“What if they gave a war and nobody came?” In the new millennium, that rather irreverent 1960s question has been turned on its head to “what if we had a database and no one annotated it?” Welcome to PDBWiki, the web site that aims to enhance the quality of data in the Protein Database (PDB) through community-supplied knowledge. With over 61,000 entries, PDB has a lot of room for commenting and

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One of the most significant properties of almost all species of bacteria is their ability to expand rapidly from a single cell into a choking overpopulation in a short time frame—under the right conditions. Spanning a continuum from planet-saving good to tasty food components to pathogenically bad, bacteria's space in the ecosystem is enormous. Covering this territory is the Virtual Museum of

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I haven’t covered a totally fun/silly site in a while, so I guess it is time to do so (or so my justification for including a weird site goes). Iowa State’s Tasty Insect Recipe is one of the more unusual sites I’ve covered here. Dealing, perhaps disturbingly, with the prurient interest of eating bugs, the site has been noticed by many people besides me, including Jay Leno, as seen on the opening

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If you’ve read this column for any period of time, you know that I like the offbeat. Consequently, I couldn’t resist this offering, which provides a musical introduction to protein structure. Yes, there are many sites like this one with similar ideas, but I’ll wager that none of them produce its interesting melodies. “A Protein Primer” accomplishes its magic by assigning increasing pitch to amino

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Never again will you have to wonder where in the world you can find the Arabian tiger snake or the Bibron’s keel-scaled boa (if, by chance, you were actually in search of them). Using the World Wildlife Fund’s WildFinder tool, you can search for specific species and obtain a global view of the regions in which they reside. Alternatively, you can search for a specific region to find which species

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I’ll be honest—this site isn’t exactly pretty to look at. (But then again, are parasites supposed to be pretty?) Produced as part of a zoology course at the University of Alberta, Principles of Parasitism offers a nice collection of animations and movies to introduce one to the world of all things parasitic. From protozoa to digenea, from nematoda to arthropoda, you’ll find an assortment of

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On the subject of anatomy, I’d bet this site contains one area you’ve never considered. Comparative Placentation, according to the description on its site, “was created to assist with the examination and evaluation of the many different types of mammalian placentas.” Okay, but who would care about such a subject? I’m glad you asked—veterinary pathologists. Imagine the challenge of veterinarians

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We’re going on an African safari! On this excursion, though, we’re not concerned with lions or giraffes. Instead, we’re going to take a gander at the avian biodiversity of the African continent. In order to promote conservation, the groups Bird Explorers, Birding Africa, and the African Bird Club created this database, which now includes 11,196 images. These images showcase 1,845 species. That is

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A self-described education resource to promote bioscience literacy, ActionBioscience is a product of the American Institute of Biological Sciences. The site is well along it way to achieving its aim, with seven hyperlinked bioscience challenges – Biodiversity, Environment, Genomics, Biotechnology, Evolution, New Frontiers, and Education. Under each of those headings resides dozens of

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This site reminded me of a metabolic pathway map (cue the groans from anyone who had to memorize one of those), in that it took a bit of time to assimilate all of the information presented. That’s because Biochem4Schools is an umbrella site, meaning that its only content is a compilation of biochemistry-related websites. Not that I’m complaining—there are a LOT of great links. The only problem is

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One can’t help but be lured into this entertaining, informative website. Using microscope images and videos as teaching tools, the Microscope Imaging Station provides a nice introduction to a variety of topics in biology. Although aimed at a younger audience, scientists of all ages can appreciate the wonderful images and informative blurbs with whimsical, news-like headlines. (For instance, some

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Like DaVinci's Vitruvian Man shown stretching out to the 24 human chromosomes on the opening page of the Human Chromosome Launchpad, visitors too can “reach out and touch” a lot of information at the well-designed Oak Ridge National Laboratories site. Cybernauts traveling here expecting only DNA sequences are in for a pleasant surprise. With an eye for hierarchy, the site's designers have

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This is an excellent site that will make researchers who study mice jump for joy (and just might make researchers who choose other model organisms a bit envious). The Edinburgh Mouse Atlas Project offers many tools for researchers, divided into the 3-D embryo anatomy atlas and the EMAGE gene-expression database. The embryo anatomy atlas does offer three dimensions (as promised), as one can move

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A vague website title, to be sure, but once you determine what it is (it’s a site for a research center that studies human evolution by investigating similarities with apes), you can appreciate the site’s resources. The Living Links Center is part of the Yerkes National Primate Research Center, the nation’s largest primate center. In addition to providing information about current research

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A site whose teaser URL derives less from the philosophical question that humans have asked about their existence for ages, than from Erwin Schrodinger's 1944 tome that formed the framework for investigating molecules as the basis of biology, What is Life takes a conceptual view of living things. It affords visitors the ability to explore topics ranging from our evolving concept of a gene to man,

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Combine the work of numerous volunteers and one part-time paid engineer and you'll probably be hard-pressed to duplicate the functionality of Calflora, the online go-to source of information about California plants. Considering the broad range of environments in the most populous U.S. state, the matter of comprehensive coverage is not a trivial one. There is a lot of territory here! Calflora

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Jim Haseloff, Ph.D., of the University of Cambridge, provides a wide range of resources on his lab’s home page. The site is nicely organized into seven categories: Haseloff lab, synthetic biology, plant systems, imaging, design, construction, and teaching. Highlights of the site include software tools found under the “design” tab, as well as Powerpoint presentations and other learning materials

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Microscopes, antibiotics, vaccines, and biotechnology bring awareness of the microbial cosmos—in which the Earth is bathed—to those of us who perceive things macroscopically. For better or worse, microbes rule this bio-oasis we call home, so it's not surprising when they stage a protest from time to time. Unfortunately, if the “natives are restless,” the results are sometimes catastrophic.

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As pandemics go, H1N1 fits into the category of a fairly manageable one (there is a vaccine, after all). Yet, the public perception of the illness is disturbingly inaccurate, thanks to its scary portrayal in the media. Paddling upstream against the current of misinformation about this important public health matter is the Influenza Research Database, which deals with research data and serves

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Speaking of microscopic domains, Nikon sponsors an annual photography contest for images taken through the ‘scope that are as stunning as they are other-worldly. The winner for 2009's Small World Competition has just been announced (an anther from Arabidopsis thaliana, pictured here) and it—along with the many outstanding runners-up—are available for view at Nikon's easily navigable web site.

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Well, it’s not the prettiest website, but who ever said that primer websites had to be pretty, right? MethPrimer is a straightforward program for designing bisulfite-conversion-based methylation PCR primers, either for methylation-specific PCR (MSP) or bisulfite-sequencing PCR (BSP)/bisulfite-restriction PCR. The primer design program is pretty standard—paste a DNA sequence, choose

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So, you finally obtain data. Now it’s time for statistical analysis—but wait! You can’t remember what a t-test is, or how to perform hierarchical multiple regression analyses. Well never fear. Thanks to the generosity of Daniel Soper, Ph.D., an assistant professor at California State University, Fullerton, all you need to remember is how to click over to Dr. Soper’s statistics calculators page.

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