McLaughlin Lab

Streamlining Genius - Periodicals

 If you haven't read Good to Great by Jim Collins you don't know what a rock star you can be in any field.

Our favorite cyber organization genius is Lifehacker which has a great website to boot with info on free apps, great critiques on tech and handy how to genius stuff.

Not a book, but a magazine everyone should get is Wired with cool science buzz, and techy information thats great.

Organization - Apps, Sites and Other Peripheral Brains

Is your email your go to source of what needs to get done?  If so, FollowUpThen is your place to be.  Send yourself a list or reminder at a the time of your choosing and link it right into your Gmail threat.  Sweet!

Anatomy Structure and Function

Who doesn't love a bazillionaire who throws neuroscience the best tool in 20 years with The Allen Brain Atlas?  Human brain, mouse brain, developing brain...name your protein and find where and when it's expressed.  Snaps Paul Allen on philanthropy done right!

Our Genomic Repairman gives a shout out to two sites on this front.  Gene Expression Atlas - a semantically enriched database of meta-analysis statistics for condition-specific gene expression.

He also recommends gene expression omnibus a database of high throughput gene expression and hybridization arrays, chips and microarrays. From experience, this interface will require some tinkering or bribing a pro with a beer for a short tutorial as it's not the most intuitive for the newbies.

A little rusty on what projects where in the CNS?  Hit USC's brain architure management site to see all your projections.

Animals

Lee Silver's landmark book on Mouse Genetics is free online and takes you through everything you could want to know. Find it here.

Heterozygote, haploinsufficient double mutant mice all explained by the fine folks at Jackson Laboratories.  While there, check out their info on repositiories for aged animals, links to mutations for PD, spinal cord mutants and all manner of other great resources from Oak Ridge to Special Mouse Strains.

Once you get the critters, you'll want to make sure you are ubber nice to them so they can be happy and you can get reproducible results.  DAC has great staff and resources to enrich enviroments, but we like this video on handling especially for newbies. Shout out to Tommy Saborito for finding it!

Antibodies

How to Use 'Em

Starter information on thinking about antibodies, fixation and protocols from immunohistochemistry world.

Abcam has a great starting site for how Westerns work here.

Pick your perfect gel percentage based on DNA, RNA or protein size with this snazzy chart from Clontech.

Find your hard to find antibody here from the Antibody Resource Page.

And shout out to Cell Signaling for a positive control sheet from HEAVEN here

Calculators

Wolfram Alpha is Wikipedia from not a bunch of ding dongs in their basement making stuff up.  Use it for your refences, calculations and you know *real* facts.

Graph pad's site will allow you to recheck your science math backwards and forwards.

Cell Culture

Why do it in vivo when you can grow it in a dish?  We do love us some primary cultures and here is where we like to visit for fun.

Greg Brewer is a pioneer in making neurons grow like gangbusters.  Check out his work in this online chapter laying the foundation of how to culture cells.

Giant props to Johannas Hell for calling manufacturers on the carpet for their unreliable supplements and making his own - NS21 is the way to go and Nature has a great story on why.

We are big fans of Hibernate especially when you are making cultures from heterozygote matings and need to genotype fast before culturing.  Keeps your brain bits alive for 24h until you can PCR.

We have tried every lipid, salt and voodoo method to transfect primary neuronal cultures and the reigning champ is Amaxa.  Dissociate, zap and enjoy 30-40% efficiency.

For fans of cell lines, of course you should be getting clean happy cells from ATCC, but did you know that LGC's site provides photos and additional support for those cells? 

Cell Culture Boogers

 Find out what's wrong with your cells with this handy guide for beginners and pros.  Provided by our buddies at Corning.  Download it here.  Then memorize it.

Clinical Neurology

 Is it the 12 beers to celebrate your first paper or is it delerium? Find out on the Delerium diagnosis and research page.  (BTW, it's the beers)

Clinical Neuroscience Certificate Program

 We are proud to be spearheading an initiative to facilitate translational neuroscience research by addition of the Clinical Neuroscience Scholars program.  Predoctoral applications are due April 23, 2012 as a single PDF.  Information about the program can be found here.  The slides for the informational program on March 28, 2012 can be found here.

Computer Savers

 Descum your PC with ccleaner.  Its free, its awesome.

Save up to 5G of your data online for free using iDrive.

PC users....figure out why it takes a year for your computer to boot and what crashed it using Soluto for free.

Oh, and for those pesky shortcuts to make science symbols, use this site.

DNA

Bottoms up....learn how to cast, run and analyze your agarose gels here.

Got your gene but need to sub clone the sucker?  Here's our favorite site to cut and paste in an easy to use platform from Cyagen.  Clean graphics and easy for your newbies to understand. We also have come to like Vector Builder in 2013.

A public repository for plasmids saves you the hassle of mailing them out.  Simply turn your DNA over to Addgene and let them do all that pesky 'communicating' stuff we don't like as left brained folks.  Site has lots of cool DNA constructs and manipulation tools and links to boot.

Filtration

 Hate Goo?  Keep your solutions free of whatevs and separate proteins and organelles using Waters Filter Selector or buy a kit if you're super rich. We like the old fashion mitochondrial isolation protocol in our protocol section for the record.

Flow Cytometry

Our cytometry guru @Geeka tellls us that the places to go are Purdue's tremendously horrifically designed site (you can tell a boy made it; but the info is solid!).

For those who want their cytometry basics visit this free site to analyze, plot and replot your data.

You can also check out Geeka's special version of snark and science at her blog.

Freeing Your Radicals

Reactive oxygen species....oh, we could go on and on about how much we love (hate?) thee.  But be sure to check out the following sites for background, discussion, meetings and protocols.

New but intriguing is the Society for Free Radical Medicine and Biology's new online forum.  The Boss is grumpy that it is member only and thinks they are really missing the boat in appealing to a broad audience though.

Radical Update 2012

 The good people at Free Radical Biology and Medicine have put together a handy guide on what your dyes are and aren't measuring when you use them to measure ROS.  Find it here if you want to publish with them.

General Protocols

Protocols online is a great clearinghouse for information and bench protocols.

Cold Spring Harbor is the mac-daddy of published and online protocols.  Love their peer reviewed works....just hope your university has access to it.

Nature Protocols is rocking in print....not a huge fan of their online site as advice is sketchy and it is hard to navigate in its current format.

BitesizeBio falls into so many domains on education, protocols and networking I feel bad about 'just' putting it here, but if you're a Twitter person, they have a great feed.

Benchfly I guess if you are picking between being a lab rat or a bench fly, you will get more information at the Benchfly site where they have video protocols and great information for lab newbies.

OpenWetWare is a unique high potential site which combines lab protocols and notebook features online.  McLaughlinites don't believe in trusting some company to preserve our notebooks for us so we are hard copy, but it's highly functional and a great concept.

Molecular Station has some depth in odd areas for biochemistry and reagent prep, but its spotty in lots of places, but worth a look. 

Elabprotocols is not the biggest, but it has a great interactive component and clear protocols. 

Biowww.net is a mix of protocols and products with some depth in transfection and siRNA.  Jeannette likes it, so that's good enough for us.

Andrew Kropinski has done an amazing job of cultivating a great collection of protocols on everything from DNA to lipds and his site is a continously updating and great resource.

Grants

 Oh, did you want to BUY that reagent?  Yeah, you're gonna need some cash for that.  

For Vandy-ites, we recommend you check our in house well currated list of opportunities.

For others, we recommend you leave science so we can have more money.  Or you can look at ScanGrants, Grants.Gov, Women in Science, Open Educational Database and Powerball.

Graphics

For those who can never QUITE get the right colors, we love Kuler - upload your image and get a full range of matching colors.  Excellent for graphics and posters. ColorSuckr (yes, it's spelled right smarty pants) is another great nature inspired palette generator.

Also, if you aren't using Picasa for saving photos and playing with cool filters you are missing the boat.  Tons of free storage and the ability to download your photos in their original high resolution format. 

If the 50 fonts available in Microsoft aren't enough, check out Google Web Fonts.

Can't quite figure out your lasso tools, layers and other Photoshop mayhem, well You Suck at Photoshop.  Oh and there's a website for that which is AWE-some.  Say it right.  Aweeee (pause) some.  Now go there.

And your posters aren't as amazing as you think or your mom reassures you they are.  Fix them using pointers from The Scientist.

Microscopy Magic!

The Mac-Daddy site for all things cellular is The Cell: An Image Library.  So many awesome pictures, so little time to drool.  EMs, fluorescent staining, live cell imaging of all kinds of biological processes and organelles...its all there!

Using a fluorophore that might be bleeding into your other signals?  Check it here at Omega Filters.

Make up your data and save time!  Err, we mean virtually stain your cells and see how they would look at this ubber creepy and equally cool Molecular Probes Site.

We buy our 'scopes from Zeiss, but have to give snaps to Nikon's Microscopy U for excellent intro materials on imaging for folks at all levels from phase bright to confocal and FRET.

Mitochondria - Our Favorite Organelle!

Mitosciences has a great newsletter and some cool technologies to look at expression of components of the electron transport chain etc.

Seahorse Biosciences....when we finally win some big bucks with our well planned scratching lottery ticket strategy, we are SO getting one of these.  In the meantime, be sure to check out their killer webinar series.

Be sure you are on the email for the mitochondrial interest group out of NIH.  Great user forum and lots of the big guns actively participate.

Papers, References - Controlling the Chaos

The lab is sharply divided on this section with some 'old schooling' it sticking to Endnote until they get it right (2020 perhaps?) while others enjoy the following electronic resources.

Mac Folks, it goes without saying you are going to want Papers from the genius' at mekentosj.

Our new favorite site is LabGuru.  it lets you follow your minions on what they are doing electronic notebook style.  You can share jobs, results and attachments online as well as incorporate information on your DNA/Protein/Cells of interest, do some inventory control and develop protocols.  

For those that haven't turned their lives over to Steve Jobs, may we recommend Jake's favorite reference manager Zotero to take notes, make a library, share it  with your peeps and assemble a publication quality paper from all of it (actually it only does 3 of those things).  Great for most things, but still not an 'import style' for many journals and runs as a Firefox extension which isn't for everyone (like those who love Chrome for instance).

Mendeley trumps Zotero in finding similar papers to what you are reading, ranking their impact but is missing the ability to take notes from a webpage.  Our friend Mr. Gunn loves it, so we give it a shout out.

PCR

Design your primers using MITs Frodo or some of Molbios other recommended tools which you can find here.

Primer Blast is the oldest of the search tools from NCBI allowing you to integrate Primer 3.0 design with Blast to limit overlap with other genes. 

Jacquelynn claims that this video on PCR is 'good nerdy fun' and a great primer on primers. (Get it, you need primers for PCR and it is a primer on the content).  Whatevs, don't be a hater just check here

People Slightly More Insane than Us.

You have to love a man who thrives on snark and restraining orders so holla if you love David Thorne.

Got someone who just can't look it up themselves, Jake is a huge fan of the Google smackdown offered by Let Me Google That for You.

Periodic Table

 No one has made the Periodic Table more interesting than the University of Nottingham.  Check 'er out (thanks Scott Palubinsky!)

Proteins - one on one

Huge snaps to the queen bees of Twitter @SugarScientist and @biochembelle for their amazing recommendations in this area.

Structural Biology Knowledgebase, More of a specialists database than they probably intended this site contains information from the Protein Structure Initiative containing structure function info and help developing methods.

Protein Databank,  THE repository of protein structure coordinate with useful tools for quick looks at structures and ligands. 

Chimera, free for us academics a great molecular visualization program even for the wee babies of science.

The EBI Toolbox, tools for analyzing and aligning protein and gene sequences.

Check your ammonium sulfate protein precipitation calculations here.

Calculate what your protein Pi should be using this snazzy site.

Scripps site will give you all kinds of basic and higher order information about your protein here.

If cicular dichromism is your problem (and really - when isn't it!) check out this friendly site.

And while we can't straighten out your life, we can cut your peptide here and use Molinspiration to predict bioactivity of small molecules

Proteins - Networks

Science Magazines database of cell signaling is the mac-daddy of who your protein is and who they like to play with.  High quality.  Lovely pictures.  Clearly written by a woman.  :-)

Trying to figure out who your protein's friends are?  Check iHOP...not the pancake place...the information hyperplinked over proteins to put together known regulators.

Check out the good folks at the Badger Lab for assembling proprietary and open code resources for analyzing protein networks, predicting gene function....all kinds of great information.

Science Education

Tired of doing all that pesky 'research' to give a talk?  Check out Vadlo's site for other scientists background talks as well as some protocols. You can also check out TalkMiner which is home to our favorite slide show on CNS vascularization.

Also, mad, mad love to Khan Academy purveyer of all things from biology to physics in digestible nuggets for little tater tots to big kids too. Also, huge fans of Science Friday's Educator forum for videos and mini experiments for the minis in your life.

Society for Neuroscience's NERVE site has pretty graphic and digestible science nuggets for all.

SNPs (If you know this is pronounced 'snips', you're a geek

 Single nucleotide polymorphisms, or SNPs, they are what make all of us so very special and unique.  Some folks more special while some are decidedly less special.  If you are wondering if the protein you are working on has polymorphisms in the general public, you can use Exome Variant Server to enter your Entrez number and, easy peazy, you're good to go.  SNPs are not disease linked, but at least you can say 'my conserved Serine is mutated in 2% of the public' and then Voila!  Your research is translational. Snaps, not snips, to our buddy Nick Campbell for helping us with our SNPs.

Stats and Programming

When your good old t-test won't do...check out @nparmalee's buddies at R-project to enjoy data handling at its finest.

Someone pesky send you something where you need to know Unix and you don't.  No worries (okay, worry because they should know you don't know!) but catch up fast with help from the Korf lab.

Westerns - Your ultimate guide to the party

For newbies - check out a video on how to run a SDS-PAGE gel to separate your proteins.

Your boss won't be happy with just a gel, so don't forget this video on blotting.