I think I should list here some useful biology-related software packages and databases that I use:
- Fiji, a batteries-included distribution of ImageJ. When I was an undergraduate at the Rochester Institute of Technology (RIT) doing my research in oncology, I used Fiji to read Leica LIF files (generated from TCS SP5 Leica Laser Confocal Microscopy). I also used Fiji to run pseudo-quantification on my image samples. A new GUI for ImageJ is being actively developed, known as ImageJFX. There is a complex software for analyzing data known as CellProfiler and I think I would like to learn using it in the future.
- SnapGene Viewer. This is the stripped-down version of the SnapGene, but still awesome. I use this to visualize my plasmids and plan for restriction digest experiments. The upside of using the full-blown SnapGene is that it allows you to plan cloning experiments in silico, e.g. planning for OE-PCR, Gateway cloning, etc. Other alternatives include: Serial Cloner (free & open source) and Unipro UGENE (free & open source).
- UCSF Chimera. I like this a lot than using PyMol. And today, 05 February 2018, I just realized that there is a new version of PyMol, the PyMol 2.0. It looks better. There is BioBlender if you are into that kind of thing (Blender FTW!). There is another protein visualization software that I would like to try: CueMol.
- ChemAxon. I used ChemAxon Marvin in the past for drawing organic molecules. It helped me a lot to answer some nasty organic chemistry homeworks. Btw, they have a new product called BioEddie. It looks interesting.
- Ensembl Database. I taught myself how to use Ensembl's Variant Effect Predictor (VEP) to figure out which SNVs could be deleterious, thus figuring out the genotype for the observed phenotype. VEP provides output for gnomAD, SIFT, PolyPhen (PPh), among others.
- Autodock. So we got PyMol and/or UCSF Chimera to visualize proteins, then what? Well, enter Autodocks. This is a program that can automate ligand binding to receptor protein automagically. I would like to try Autodock Vina, which is essentially a faster version of the Autodock 4.
- Icy. I had a rough day counting cells from fluorescent images with Fiji by using the Multipoint Tool. I thought that it was ridiculous to shit and count 200 something cells. Then I found 2 alternatives: CellProfiler (overkill) and Icy (just nice). Icy's Spot Detector tool is very useful for this kind of job.