geneious // stirplate.io // benchling.com
I've been a cheerleader for the amazing Geneious software platform for awhile now. If you do a lot of cloning...or primer design...or sequencing, its really streamlined, with some great visuals. I even use it to generate images for powerpoints sometimes, for say zooming in on a gene region. Another great aspect is they keep evolving- each update is better and better- and they just announced for R8 (still in beta) that there will be a crispr design plugin as well as NGS assembly with scaffolding. I'm really looking forward to trying it out.
Two new websites have come on my radar recently that attempt to broach a few difficulties I believe many labs deal with.
1. stirplate.io (this one is more for my biologist / bench inclined scientists) offers a simple solution for RNAseq analysis [extra points for a beauitful website design as well]. Keith Gonzales started stirplate after building a few similar platforms for labs he worked in previously. They parallel process your fastq's on the cloud for super-fast turn around times- and unlike Galaxy, only requires a few minutes of your time. They take care of your alignment, counting, DESeq differential expression analysis, clustering etc in about 1-2 days.
2. benchling.com is an online tool for organizing your protocols, files, etc. A note from Saji, the Founder and CEO:
When I was doing research, my data, and my lab’s, was spread out in many different places and in a variety of file formats. Staying organized was tough and knowledge transfer was a headache when lab members left.
Many of our users are in similar situations. We’ve worked closely with them to import their existing data into Benchling, and I wanted to offer the same assistance to you. We’re happy to help migrate your data by writing scripts to sanitize your data, adding importers for odd file types, and doing manual cleanup.
Here's a bit of background on us. We're a group of MIT CS/Bio alums who are fed up with the terrible quality of software in biology. We've made it our mission to build beautiful tools for working with DNA that are easy to use and enable collaboration.
Lots of very exciting new options out there for researchers to stay organized and be more efficient! Feel free to email me if you have any questions about using these platforms.