ConnectedBases

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 as 8% of males and more than 1% of all people have difficulty distinguishing colors. We can make it easier for our audiences to interpret our figures and use our bioinformatics web applications if we give a little forethought and check to make sure that they will be able to discriminate what we identify with color.

Generally, I don’t use color in figures for journal articles or posters, but I do tend to use color in slide presentations. Now, I can make sure that my work is more accessible to those who might be colorblind.

Both software links above via Daring Fireball.

Update: I re-wrote this article and submitted it to MacResearch.org.

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 the links below to your bookmarks bar, as pictured here:

Then, there are 2 ways to use the bookmarklet:

• Highlight text within a webpage, then click the bookmarklet, and a NCBI search will be started using the selected text as the search parameters.
• Click the bookmarklet and a pop-up window will appear, into which you can paste your search term(s) or sequence. Click “OK” and the specified search will load in your current window.

1. Search Pubmed–The starting point for any biomedical scientific literature search.
2. Search PubMedCentral–A great tool to find articles that may only mention your term of interest in the discussion, methods, or figures of the paper.
3. BLASTN–Find nucleotide matches to your nucleotide sequence.
4. BLASTP–Find protein matches to your protein.
5. BLASTX–Find protein matches to the 6 frame translation of your nucleotide sequence in Genbank.
6. Search All Entrez–Find all references to a set of terms in all NCBI Entrez databases
7. Search Entrez Protein–Use accession numbers, protein functions, and other keywords to find proteins of interest.
8. Search Entrez Nucleotide–Use accession numbers, gene identifiers, and other terms to find nucleotide sequences.
9. Search Entrez Genome–Use variety of terms to find genomic sequences, integrated genetic and physical maps, and sequence maps.
10. Search Entrez Gene–Search the NCBI database of genes from RefSeq genomes.

Obviously, NCBI and NLM provide dozens of resources, but hopefully these search tools will be useful to you. I have tested these in Firefox 2.0 and Safari on Mac OS X 10.4.9.

These bookmarklets were adapted from those available at Jesse’s Bookmarklet Site.

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 created in Mail.app, with the URL of the uploaded file in the body of the message. This script works with Mac OS X 10.4 “Tiger” and doesn’t require any other software.

This updated version only asks for your NetID once, and then remembers it thereafter. To reset the set NetID, double-click on the droplet, and enter the new NetID.

Download Attach to My WebSpace

AttachToMyWebSpacewas inspired by Sender, a product of Stairways Software designed to work with Interarchy.

Leave any other questions in the comments section or send me an email.

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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 created in Mail.app, with the URL of the uploaded file in the body of the message. This script works with Mac OS X 10.4 “Tiger” and doesn’t require any other software.

The source code is also in the disk image.

I have an svn server set up in case anyone would like to collaborate, and I can set you up with an account if you drop me an email or comment.

AttachToMyWebSpace was inspired by Sender, a product of Stairways Software designed to work with Interarchy.