Tools and How-Tos for Biologists |
American Type Culture Collection |
Ever wonder where it is you're supposed to get these organisms you want to work with? Well, if you're not collecting clinical isolates or field samples, this is likely it. The ATCC is probably the largest storehouse of microbial samples there is. Beware of a couple of things, though. One, it costs money to order from here, of course. Two, do some tests to doublecheck that what you receive is what you ordered. These poor guys are pretty heavily overworked, and, anyway, it's only prudent. It is also incidentally a very good place to check characteristics about strains you already have or inherited from someone else; the trick is you have to be able to find your strain, which means you likely need to know its ATCC number. |
Basic Sciences |
This is a quality set of web tools provided by Northwestern University Medical School, including a really great oligonucleotide melting temperature calculator. The thing I like about this Tm calculator is that it also checks for hairpin formation or self-annealing, which is a great time (and dollar) saver. |
BCM Search Launcher Sequence Utilities |
This site hosted by the Baylor College of Medicine performs a couple of tricks, but my favorite is the six-frame nucleotide sequence translator. It'll take a FASTA-formatted nucleotide sequence and translate it into the amino acid sequences corresponding to the three possible forward frames as well as the three possible reverse complement frames. Great tool for finding your reading frame and it works FAST.
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BioEdit |
BioEdit is a nice piece of freeware from North Carolina State that I use all the time. It's a sequence alignment viewer and editor that also does ClustalW alignments. The ClustalW algorithm's not the fastest (it has an older client) and it could use a little more oomph in the search department, but for the low, low cost of $0.00 it's worth a look-see, trust me. Note: I am having trouble getting its ClustalW accessory program to run under WindowsXP. |
BioMath Tools |
This is a series of bio-mathematical tools provided by Promega, for those annoying conversions you're sick of doing on paper... |
Calculating Concentrations for PCR |
This is a step by step description of the slightly complicated calculations needed to take dried PCR primers and make them the proper concentration in OD units per milliliter. (Dimensional analysis with a twist.)Also covers dNTPs. |
Caltech Genome Research Laboratory |
Protocols for establishing and sequencing a BAC library can be found, cleverly enough, under "Protocols". |
ChemFinder |
Chemfinder is an Internet-based chemistry reference. It can pick out a chemical from formula, common, name, IUPAC name, etc. and return it to you with useful information like density, boiling point, toxicity, etc. I use this all the time. If you have their plug-in, it also draws the structure for you, which is very nice. |
ClustalW (Download) |
This is the download site for the ClustalW multiple alignment tool, which is a pretty universal standard for comparing sequences to one another to determine homology, identity, etc. etc. etc. It's free, and it's small, so it downloads quickly. Downside: It's DOS-based, not Windows-based, so you have to know how to run DOS programs. Also, I believe it follows the old DOS file name rules - no spaces, one period, first half no more than 8 characters, etc. I'm having problems with it under XP, too. I think since XP finally dumped DOS entirely real DOS-based programs have 'issues'.
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ClustalW (Web) |
This is a free on-line ClustalW alignment web tool provided by the European Bioinformatics Institute of European Molecular Biology Laboratory. It can also make cladograms and such forth, and both the alignments and the trees are also provided in a downloadable format, so you can choose to view your results in your web browser or pull them down and view them in an editor on your own system. Very well done, and shockingly fast for a web tool. |
ExPASy |
ExPASy is a Swiss server providing a lot of free bioinformatics tools, not the least of which would be the SWISS-PROT and TrEMBL protein sequence databases. SWISS-PROT contains actual sequences whereas TrEMBL contains extrapolated ones. |
InterProScan |
InterProScan is a nice little tool that I use in place of ProSite now. Offered by EBI, InterProScan takes your amino acid sequence and makes predictions on its possible activity as a protein based on motifs, domains and comparisons against other known protein sequences. It returns hits of different types with links to examples, so it's nice in that you actually get some corroboration in your result with one search. |
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This is a fantasterrific service for people looking to figure out, play around with or break metabolic pathways. It has a variety of organisms for which there's this nifty set of interconnected 2-D pathway diagrams that let you pick out the enzymes important to your application, and then you can look them up tout suite. I was so happy to find this particular site. Plus, there's apparently more to it I haven't got around to exploring yet. :) |
NCBI BLASTN |
This is NCBI's blastn page, where you can run a given nucleotide sequence against the largest genetic data repository in the world at NIH to see with what genes and what organisms your sequence matches up. I use this all the time. Very well done. |
PCR Optimization |
This is a new script I found on a Russian webpage I haven't tested yet but looks promising. It takes some information about your PCR concentrations and quantities and tells you if the mix is "in balance", i.e. if you don't have enough primer to consume your nucleotides or whatever. It then tells you about how many PCR cycles you'd actually need to consume your materials usefully, and at what point you hit plateau. I'm going to try this out and let you know how it works out for me. Note: Not great so far.
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PHYLIP |
PHYLIP is another extremely commonly employed client for determining phylogenetic relationships, making trees, figuring out molecular clock numbers, and so on. It's very useful and absolutely free. It's also very, very disorganized and includes maybe 15 or 20 separate DOS executables with different purposes that have to be used in certain orders and only accept certain filetypes. They also tend to drop your results in files of preset names and you have to know which one you want. Luckily, it also comes with literature, but the literature's pretty scattered, too. Be prepared to spend a little time learning to make it work. It's a very good program, though. |
Primer3 |
Primer3 is an automatic PCR primer/probe design system that can take an input sequence of bases and calculate a good primer or probe set within user-set parameters. Mechanically, it churns out good primer sequences, but specificity is another matter the user still has to insure for himself. |
PubMed |
This is the NIH's searchable database of biology-related publications. They've got abstracts for everything you're likely to care about in here. On top of that, they have searchable databases of published gene and protein sequences as well as BLAST searching. If you're a biologist and you're not using this, I don't know how you get through the week. Seriously. |
Quadratic Equation Solver |
Solves quadratic equations if you feed in A, B and C. Gives back decimal answers. I like it! |
Restriction Enzymes Web Page |
This website has a tremendous number of available restriction enzymes with their recognition sequences and cut points. I was floored when I saw the sheer quantity. It's great. Everything's in one place.
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Reverse Complement |
This is a Harvard Medical School webpage that autocalculates the reverse, complement or reverse complement for a given nucleotide sequence. I use this quite a bit. |
SDBS |
SDBS is a searchable database of IR, NMR and MS spectra for various organic compounds. You can search by peaks and values. It's one-stop shopping if you're trying to match your unknown chemical. |
Superfamily |
Superfamily is another tool for trying to nail down what a hypothetical protein is. You input your hypothetical or experimentally determined protein sequence and then it feeds back the broad family of proteins to which it thinks your protein belongs ("DNA-dependent RNA polymerase transcription factors", for instance) and shows you which segments make it think that. It'll also give you what the subcategories of that family are as possibilities. |
TAIR |
For you people that inexplicably prefer your cells with nuclei and organelles, the Arabidopsis Information Resource is a pretty cool site that includes not only a wealth of information about Arabidopsis thaliana but also an array of analysis tools (or links to analysis tools) to get in there and start mucking about with things Man Was Not Meant To Wot.
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TIGR Comprehensive Microbial Resource |
This is the list of published prokaryotic genomes sequenced by the Institute for Genomic Research. Good place to start if you're working on a common organism. A couple of clicks will also get you to TIGR's eukaryotic genomes as well.
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VectorDB |
This site is a fairly large if not particularly aesthetic listing of vectors available for DNA cloning, transformation and so forth. The information you get is fairly bare-bones and there's quite the bias toward E. coli in the bits I care about, but it's certainly a good place to start looking. |
Satellite Data and Geographic Tools |
FireLine Wildland Fires (US System) |
This website provides numerical data on wildfires occurring in the United States and Canada. The data's provided in text files, so don't expect cool pictures, and the format can sometimes leave something to be desired. If it's wildfire numbers you're looking place, though, this is a good place to start. |
Geonames |
A USGS site to look up a specific place to get its latitude/longitude. Works for more than just populated places, too. |
GOES |
This is NOAA Geostationary Satellite Server, which is a nifty site for viewing bird's eye views of weather systems. It's particularly keen for looking at hurricanes. You could see really clearly, for instance, how Hurricane Isabel was bigger than Florida... |
LUCI Fire Maps |
This is the primary page for NASA's Landsat 7 orbital global mapping instrument, and the first stop on your search for satellite pictures of the earth. They also have a sampler pack of interesting or attractive images of certain locales.
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LUCI Fire Maps |
This is a University of Maryland website that provides a convenient interface for viewing and retrieving MODIS fire map information by geographic breakdown. It gives access to a nifty scalable map interface that can provide user-selected data overlays. |
NOAA OSEI |
The NOAA Operational Significant Event Imagery website provides web-based access to imagery data for a wide variety of natural disasters, from earthquakes to dust storms to floods. It's not my favorite archive interface, as you have to search through FTP-style menus to find the image you want, but the data's there and it's free. |
Space Imaging |
Space Imaging is a private global mapping company with a pretty good orbital platform at its disposal, IKONOS, I think it is. If you're looking for decent resolution shots, this is a good place to look, and they've got a good gallery of cool shots for advertising purposes. |
TerraServer |
This site allows you to query for a specific placename and retrieves USGS overhead imagery for the area. Retrieving the image online is free, and then you can also opt to buy paper copies or framed copies or whatever, I do believe.
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TOMS |
The Total Ozone Mapping Spectrometer gives a visual display of satellite data for the evolution of either ozone or particulate aerosols in a desired area. It's nice for finding or confirming wildfires and their durations, as the trail of aerosol or radius of ozone cloud can lead you right back to them.
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Scientific Societies for Biologists |
American Chemical Society |
As you may have guessed from the title, this is a prominent (probably the prominent) society for chemists. Don't let that fool you, though. Biochemistry and molecular biology have become so prevalent in the larger field of biology that you're as likely to get interesting stuff and useful contacts from ACS as you are with ASM. Something to seriously consider. Their magazine, Chemical and Engineering News, is worth the student membership fee by itself. I am a society affiliate of this organization. |
American Society for Microbiology |
I think that ASM is really the central biological society. Then again, I would think that since I focus on microbiology. ASM deals with all biology on the microscale, be it eukaryotic or prokaryotic. The society also has a strong presence in molecular biology and genetics and publishes several influential biological journals. It is worth your time to check this out even as an undergraduate, because this is how you learn what it is you really should be learning. I am a student member of this organization. I especially like their ASMNews mail list, which contains ready hyperlinks to the interesting biology stories of the week on the Internet. |
Federation of American Scientists |
The Federation of American Scientists is a scientific watchdog group, monitoring the role of science in warfare and intelligence in this country and around the world. They also monitor government policy affecting science as well as emerging infectious diseases. I am a member of this organization. |
Sigma Xi, the Scientific Research Society |
Sigma Xi is a very well-respected organization which accepts scientists of all stripes and counts multiple Nobel laureates among their numbers. They also publish a magazine you may have seen called the American Scientist. Now, besides the fact the people are cool and networking opportunities abound, Sigma Xi has a lot of money. A lot. Scholarship money included, subtle hint to all you students out there. I am an associate member of this organization. |
Society for Industrial Microbiology |
This is a fairly straightforward name, and the society is exactly what it sounds like. This is the scientific association of microbiologists who employ their talents industrially. This includes everything from genetic engineering to bioremediation to improving silage. They also publish the Journal of Industrial Microbiology and Biotechnology which is free with membership. I am a student member of this organization. |
Union of Concerned Scientists |
The Union is an organization of environmentally concerned scientists. They perform watchdog activities on activities that affect the environment in a manner similar to the way FAS watches scientific warfare. I am not a member of the UCS because I don't agree with their stance on genetic modification of foods and I'm not all that sure about their nuclear power policies, either. They do, however, deserve equal time, so here they are. It's not like I know everything, no matter what I may tell you in person. |
Institutions and Programs |
American Military University |
This is an underrated resource that I truly wish I had known about when I was stationed in Korea. This distance learning institution is geared toward the military student and as such has associate's, bachelor's and master's degrees with that student in mind. They have distance education bachelor's degrees in 39 majors, plus they have minors available as well. |
Bacillus Genetic Stock Center |
Ohio State's BGSC is a massive collection of Bacillus species collected in their Department of Biochemistry. Just their catalogs are extremely informative and downloadable. They also have some nifty movies on Bacillus for videophiles.
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Columbia's Columbia Video Network |
Graduate school online is becoming a more and more popular option for people that are working and just don't have the time to stop. The trick, though, is that you miss out on the brand name schools. Well, Columbia now has several engineering master's degrees available by video streaming over the internet. Check it out. |
EcoBot |
This is a cool British project to make full autonomous robots - complete to being able to hunt and scavenge their own organic fuel sources!
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Harvard's Cell and Molecular Biology |
The Department has two nifty programs, one in Genetics & Genomics and the other in Molecular, Cellular & Chemical Biology. Both are sponsored by the department, o'course, but the former is collaborative with the Department of Evolutionary and Organismic Biology, if I recall correctly, and the latter with Chemical Biology. Worth a stop in if you're shopping for programs. |
Johns Hopkins University Applied Physics Laboratory |
My current place of employment. They are a self-funded research center of JHU that does scientific contracting for the Feds. They (we, I suppose) do some really, really nifty stuff. Check it out. |
JHU's Biomedical Engineering |
If you were to say that this is the best biomedical engineering program on Earth, I doubt you'd get a tremendous amount of argument. This isn't my thing, but for those you whose thing it is, take a gander. |
JHU's Chemical and Biomolecular Engineering |
If you want to do anything at Hopkins that doesn't expressly involve humans or medicine, your choices are fairly scarce. Fortunately, there's the Whiting School of Engineering, which has picked up the biotechnological football and started sprinting with it. Plus, for biotechnological engineering, it really doesn't get any better than these people. Check out the Cell & Molecular Biotechnology track. |
JHU's Molecular Microbiology and Immunology |
This program is way more into pathogens than I personally care for, but it's got a name that can't be beat and a spectacular faculty. The only trick: if you're into prokaryotes, this isn't really your gig. They do mostly eurkayotes and viral work, at least at last glance. |
MIT's Biology |
This is probably one of my favorite straight biology departments. It's got both pure and applied biology, as well as a nice combination of top flight professors and diverse research interests. This one's high on my list. |
National Technological University |
This is an on-line graduate school for scientists and engineers interested in part time study. The concept is kind of neat - instead of providing courses themselves, they act as a clearinghouse for science courses offered online by a number of universities like the University of Delaware, North Carolina State or University of Wisconsin-Madison. They use those as the basis to grant you a Master's in your discipline upon completion of the right array of curriculum. |
Princeton's Geosciences |
My soon-to-be-current program. A la Caesar, all Geosciences are divided into three parts: Atmospheric & Oceanic Sciences, the solid earth folks (seismology, vulcanology, etc.) and biogeochemistry, which includes my favorite, geomicrobiology. Any non-geomicrobiology-is-keen-thinking people are woefully misguided. This is, in fact, where it's at. |
Stanford Center for Professional Development |
Stanford uses this center to offer a variety of engineering master's degrees online to working folks. They have a number of options for course delivery available, including online, videotape, and videoconferencing as well as microwave broadcast if you happen to be around Stanford. For engineering students, you could do worse than a Stanford degree... |
Thayer School of Engineering at Dartmouth |
The Thayer School of Engineering at Dartmouth doesn't seem like an intuitive place for a microbiologist to show interest, but their Chemical and Biochemical Engineering section is right up there with the best metabolic engineers a person is likely to find. Check it out. |
UMCP College of Life Sciences |
The University of Maryland College Park is the school from which I received by bachelor's. They are particularly strong in this field, I think, and growing stronger. People looking for future schools to attend would do very well to drop by here. I've been nothing but pleased with College Park, and I found my degree was very competitive when applying to the Big Dog schools. |
UMCP's Molecular and Cell Biology |
This is an interdisciplinary program at my undergraduate alma mater which has quite a few nice points to it. One is that the program's cross-linked with the engineering school and the UM Biotechnology Institute to provide wide biotechnological support; another is that there are opportunities for microbiological research in everything from plant pathogens to human etiological agents to Archaea. |
UMD Science in the Evening |
The Science in the Evening program at College Park is probably the single best night-time science program in the Baltimore-DC area. It has the best selection of classes of any I could find and let me knock 36 or so credits of solid science out of the way while working. The biologically curious working person should give this a whirl. |
UMUC |
This is the homepage for the University of Maryland: University College, U of M's answer to education for working people. They provide quality education not only to the people of Maryland but also over the Internet in a variety of majors. They've been great for people on the move, such as myself. Strong in computing but weak in science, I'm afraid. |
University of Wisconsin-Madison's Bacteriology |
Wisconsin-Madison's fairly low key for its biology facilities being as highly rated as they are. U of W-M's usually in the top five for microbiology and top ten in any random biology or biology-related field. Plus, thanks to the cattle, dairy & beer industries of Wisconsin, they have a highly biotechnological focus I like. For me, it was either Princeton or here, and it was an agonizing choice. |
Yale's Biological and Biomedical Sciences |
The BBS program is part of the med school, which usually means the dial on its microbiology program is fixed to the "pathogenic" setting, but this department seems to have room for a wider variety of interests than most med school biology departments, which I like, and most of y'all out there are into the whole pathogenic thing, anyway. :D |
Scientific Publications |
ASM Press |
ASM puts out some of the better books in the biological business. Pricey suckers, let me tell you. If you thought you were going to escape the world of $150 texts just by graduating, you were fooling yourself. However, from grad student or research assistant forward, the lovely thing known as the grant will help you with this, so you can look at prices like these and not laugh out loud. Once you get past the price and look at the titles of these books, though, you start to see where the price tag comes from. ASM Press also puts out ASM's journals, which range across the whole field of biology and are well-respected. My personal favorite is Applied and Environmental Microbiology. Good stuff in there. |
Astrobiology.com
| This is a small, kind of niche website, but I like it. Its focus is all the news on astrobiology that's fit to print, and it has links to places like NASA Astrobiology and other astrobiology resources for the space-bug curious.
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Bad Bug Book |
This is a public resource made available by the Food and Drug Administration Center for Food Safety and Applied Nutrition (FDA/CFSAN). It's also less well known as the Foodborne Pathogenic Microorganisms and Natural Toxins Handbook. This is a good introductory site for a variety of foodborne pathogens that can at least get you going in the right direction toward a more sophisticated primary source. |
BioTechniques |
This journal on biotechnology is free for anyone who is a current laboratory researcher. Let me say again, free, as in, "no money". I subscribed just for that. |
Chemical and Engineering News |
This is a news site produced by the American Chemical Society. It has some good coverage of chemistry and biochemistry news in both scientific and political stripes, but the downside is that you have to have a subscription or an ACS member number to get to the deeper stuff. Members also get a paper copy mailed to them weekly. |
The Formation of Vegetable Mould Through the Action of Worms, With Observations on Their Habits |
Darwin's other major discovery: the mass action of earthworms on soil. |
Nature |
One of the world's pre-eminent journals, and it's on the web. The best thing is that you can get articles from back issues in PDF format, and if you have a subscription, they're free. The website has subdivisions for all their periodicals, from Biotechnology to Genetics. |
The New Scientist |
Britain's answer to Scientific American is freely available online. They give concise articles on scientific developments updated daily, frequently with citations for the original jornal article. I read this every day. Seriously. They put up about five new articles a day and I'm usually interested in two or three of them. |
Planetary Protection Provisions for Robotic Extraterrestrial Missions |
How we keep out neighbors' houses pristine when we stop by for a visit.
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Science |
The other of the world's pre-eminent journals, also on the web. If you're caught up on these, you're caught up on the latest and greatest of science. PDFs and archives againa available for subscribers.
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Space.com |
Up to the minute coverage of what's going on with space, space research, space programs and stuff like that there. I check it quite a lot, m'self.
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The Scientist |
This is another free magazine you can get by being a laboratory researcher. I've subscribed to it but I haven't received my first issue yet, so I can't really tell you how it is. I can, however, tell you I heard about it because a project manager from DARPA told my principal investigator if she isn't subscribed to it, she's nuts.
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Graduate Fellowships and Scholarships |
AIAA Willy Z. Sadeh Graduate Student Award
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For this one, you have to be at least a year into a full-time grad program in space engineering, space life sciences, or space policy with a minimum 3.3 GPA to qualify. This is one of AIAA's many, many scholarships. |
DoHS Graduate Fellowships |
This is an oddly interesting one put out by DoHS, and a good one, I think. Their idea is that supporting basic research increases Homeland Security, and they're right. This is kind of rare insight for bureaucracy, really. |
Dr. Wes Eckenfelder Jr. Scholarship |
This annual scholarship program is for PhD students working in an environmentally related discipline. Must be a US citizen for this one. |
EPA Graduate Fellowships |
They offer the STAR and GRO environmentally-related fellowships. It looks to me like they want paper applications sent snail-mail. Very retro-tech. |
Francois Fiessinger Scholarship |
This annual scholarship program is for PhD students or recent PhDs working in an environmentally related discipline. The annual deadline is August 1st each year, so think sharp. :) |
Geological Society of America Grants |
These are grants available from GSA to student members. Must be a GSA member in North America. |
NASA Graduate Student Research Program |
This is the website for application for NASA grad school fellowships. This site wants a couple of research proposals aimed at specific research centers plus prospective budgetary reqs. Be aware. US citizens only. |
NSF Graduate Research Fellowship Program |
This is the application page for NSF graduate student research fellowships. This is a first stop for most of us, which makes it very competitive. You'll need 3 rec letters for this. US citizens or permanent aliens, I think, but don't hold me to that. Check, anyway. |
Stress Deflators and Miscellany |
PhD Comics |
For those of you familiar with the twisted world of learning and mayhem that is grad school, this comic will be uproariously funny. If not, well, it won't be, but try it anyway, what the heck, right? |
Full Frontal Nerdity |
Three geeks. No lives. Roll for initiative. |
Nodwick |
A weekly comic that parodies D&D. A wizard, a cleric and a fighter that can't plan their way out of a paper bag without their porter, Nodwick, who has the lifespan of a Kenny. |
Penny Arcade |
A web comic about video gamers for video gamers. Parents beware: it can get a bit vulgar. |
SinFest |
This comic reminds me a lot of Bloom County from the '80s. A political strip with a short, glasses-wearing protagonist. I like Fundie and Evil Fanboy particularly. Warning: This has about the same level of tastelessness as South Park. Not for the easily offended. |
PvP Online |
A gamer comic inexplicably set in an office setting. Great folks, though. You'll like this one if you are a gamer... or know one... or have seen one once at the mall. :D |
MegaTokyo |
This is a rather odd, manga-style web comic ostensibly about video gamers... somehow. Give it try. It's beautifully drawn, if nothing else. |
Dilbert |
Scott Adams's shrine to his own creation. Hey, free Dilbert. Can't ask for better than that. |
The Onion |
Formerly a joke student newspaper of the Unversity of Wisconsin at Madison, this paper puts out much better commentary on the world than most real newspapers, even if their stories are completely fictional. I look forward to it every week. |
The Online Books Page |
Want to read a book but forgot to bring one with you? Never fear. Try the Online Books Page at UPenn. Peruse free e-books while chomping your lunch. |
The Skeptic's Annotated Bible |
An online Bible that highlights internal errors and inconsistencies. |
Yahoo! Games |
An insidious force! Be wary, for it will consume your brain at first glance. Especially What Word! and Text Twist, which suck all my attention out through my eyes and mousing hand. |
We Like Tha Moon |
Just click on it. |
The Great Gene Test |
Find out if you're the BMW of humans or a chimpanzee who's figured out the stapler. |
NationStates |
For you Civilization-SimCity-type large scale simulation fans, Jennifer Government: NationStates is a web-based government simulation game. Log on, create a nation, compete with the other nations in the world. Beware, though, for this server is slow as molasses. |
Aetolia |
Aetolia is, for those of you who remember The Day (as in Back In The Day), a text-based free telnet MUD. Old-school style. It's fun, though, and you can do it from any computer which has a telnet client (read: any computer). I like this one a lot. |
DHMO.org |
A spoof site dedicated to the outright banning of Dihydrogen Monoxide (DHMO). |
The Keirsey Temperament Sorter |
An on-line, slightly modified form of the Briggs-Meyer personality test with explanations of the personality templates used. I always come out an INTP on the BM test, and am damn proud of it. :) |
The Official US Time Clock |
Counting down the minutes until you get out of work? I know I am... at least as of right now. This page gives the time as of the United States atomic clock +/- 0.2 seconds. So when your boss tells you it's not quitting time yet, tell him physics begs to differ. |
NetFrog |
Feel like dissecting a frog but just don't want to get formaldehyde on your desk or table? Well, lucky for you there's NetFrog, the online frog dissection application from the University of Virginia. Hack apart an amphibian in the comfort of your home or office over tea and scones. No animals will be harmed in the dissection of this frog... |