http://connectedbases.com Mac OS X, Microbiology, and the space between Fri, 20 Jul 2007 16:03:45 +0000 http://backend.userland.com/rss092 en In the Letters section of the May issue of Microbe, Tatiana Tatusova at NCBI writes a great summary and comparison of GenBank, RefSeq, UniProt, and Swiss-Prot in an article titled "GenBank, RefSeq, TPA, and UniProt: What's in a Name?". Certainly, a useful introduction to these resources. http://connectedbases.com/2007/07/20/database-soup-genbank-refseq-tpa-and-uniprot/ An interesting discussion has arisen on Electronic Laboratory Notebooks (ELNs) and why "wet lab" biologists don't use them. Neil points out several advantages of ELNs, which I will paraphrase: Easily share data with lab members/collaborators Search experiments by date, title, keywords, tags Link experiments to related resources: "protocols, MSDS data, risk assessments, plasmid maps, ... http://connectedbases.com/2007/07/19/electronic-laboratory-notebooks-dont-work-in-the-wet-lab/ Over at RRResearch, Dr. Redfield is looking to download lots of incomplete H. influenzae genomes. So, I left a comment describing how I would solve the problem. Here, I expand the comment with a screencast (5 minutes) that show the procedures I take to download 288 nucleotide records from ... http://connectedbases.com/2007/07/18/screencast-download-unfinished-genomic-sequences-at-ncbi-entrez/ Color Oracle is a free software utility to simulate how the colorblind might see your artwork or figures available for Mac OS X (10.3.9 or better), Windows, and Linux. Another similar utility for this is Sim Daltonism (Mac OS X 10.2.8 or better). According to Wikipedia article, as many ... http://connectedbases.com/2007/05/21/color-oracle-make-sure-your-figures-are-colorblind-friendly/ I was looking through Nucleic Acids Research this morning, and I saw an abstract for taveRNA, which I remembered as a graphical design interface for bioinformatic workflows (PMC). But instead, it was a set of web-tools for understanding RNA structure (inteRNA, pRuNA, alteRNA). Both sets of tools share ... http://connectedbases.com/2007/05/11/make-your-project-google-able/ NCBI's PubMed is essential to the biomedical researcher, and luckily, NCBI offers many interesting ways to increase productivity, especially through MyNCBI. MyNCBI is a service that allows personalization of NCBI resources to aid your research, saving you time and hassle. Some of the ways you can use it include: 1. Save ... http://connectedbases.com/2007/03/18/5-ways-to-turbocharge-your-pubmed-searches-using-myncbi/ Do you ever remember reading a paper, but can't remember enough about it to find it easily in a normal Pubmed search? Do you have a paper copy of an article that lacks full bibliographic information? PubMed offers Single Citation Matcher, which provides a great interactive interface to finding that article ... http://connectedbases.com/2007/02/07/find-half-remembered-journal-articles-with-single-citation-matcher/ Spend a lot of time using the web interface to NCBI BLAST or other NCBI services? Want to minimize the time you spend opening BLAST or PubMed search pages? Bookmarklets ? are a handy way to quickly search for information. Save these bookmarklets for easy use by dragging any of ... http://connectedbases.com/2006/11/29/10-bookmarklets-to-quickly-search-ncbi-resources/ Attach to My WebSpace is an AppleScript Droplet to copy files to a users web folder at MyWebSpace at the University of Wisconsin-Madison so that the file is publically available. The file is renamed in a web-friendly form (spaces removed, etc). Finally, a new message is ... http://connectedbases.com/2006/11/14/attachtomywebspace-updated/ The End of Free Will?: Has research on our minds removed choice from the marketplace? University of Wisconsin-Madison Genetics Professor Sean B. Carroll, talks about evolution and the human genome. He's the author of a new book, "The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution,". Science Laureates ... http://connectedbases.com/2006/11/02/best-recent-science-podcasts-no-2/