_ MacBio.Info _
Turn your Mac into a bioinformatics workstation without tearing your hair out!
Welcome to the pre-release version of MacBio.Info, a bioinformatics resource for Macintosh users. Our goal is to help biologists turn their Macs into powerful bioinformatics workstations, with the minimum of obscure jargon, esoteric instructions or hair pulling!
Where possible, we will do this by pointing to the hard work of many others who have made software available for Mac OS X, adding only some instructions and context to make it easy to select, install, and get started using these tools. We also aim to conduct forums for Mac bioinformatics users to help point out and fill gaps in Mac bioinformatics functions, and to offer community support.
Why the Mac?
Most 'serious' bioinformatics applications are written for Unix. Since Mac OS X is based on Unix, it is relatively easy to transform ('port') most Unix applications to the Mac. That gives the opportunity to run heavy duty applications on your very own desktop machine, and even take them on the road on a Powerbook laptop.
Unix, unlike the Mac, is renowned for user-unfriendliness, obscure commands, and text (rather than graphic) driven programs. So, many Unix programs look a bit ugly on the Mac, and many assume a lot of technical expertise to install and run them. MacBio.Info aims to cut out some of that difficulty by holding your hand if you don't feel expert enough to everything from scratch.
A draft layout
The following in part is a working draft of how we want the site to be, and in part is a quick-and-dirty catalog of bioinformatics sources for the Mac. Even at this stage, it is one of the better resources for Mac bioinformatics programs, but we aim to make it much much better and more user- and task-oriented: what you need to do to do you work, not what programs are availalble from where.
- Bioinformatics software list from Apple.
- BioTeam is a Mac-supporting bioinformatics consultancy. Their iNquiry commercial package includes Mac ports of a wide range of bioinformatics software, web interfaces and support for distributed multiprocessing. They also have put together a free package of tools, with decent instructions on installation (see the above link for details). This package provides Blast, FASTA and HMMer sequence comparisons, ClustalW multiple sequence alignment, the EMBOSS collection of utilities, Phylip phylogeny software and Primer software for PCR oligo design.
- Instructions for installing software (to cover compression schemes, disk images, compilation, environment variables, fink and more)
- Forums (combination of mailing lists and web forums to allow discussion of any issue around doing bioinformatics on the Mac).
Tools like Blast, FastA and Blat to search a query sequence against a database of sequences.
Aligning a family of sequences and derivatives of that - motif-finding, HMMs, phylogenetic trees
Practical tools to manage data from DNA sequencers
General packages, mostly commercial, to do lab-scale molecular biology - mapping vectors, restriction digests, simple protein analyses etc.
Tools to look at microarray and other gene expression data.