helpful links
organization + collaboration tools
+Slack – A great team communication and file sharing app. Strengths include: live conversations, project organization, and searchable message history.
+Asana – Nice web app for organizing and sharing project data and status updates. Its strength is that it has flexible task organization options, which includes lists and boards.
+Trello – Trello is a useful web app for organizing project ideas and status updates. Trello's minimalist board style layout is well-suited for short to mid-range projects as well as project design
DNA editing software
+ApE (A Plasmid Editor) – Essential for organizing, engineering, and sharing DNA constructs. Friends don't let friends edit DNA in MS Word!
genome browsers +
sequence analysis tools
+NCBI (National Center for Biotechnology Information) – This is where you can access DNA and protein sequences and use workhorse analysis tools like BLAST.
+IMG/M (Integrated Microbial Genomes & Microbiomes) – Great resource of genome and metagenome sequences with a variety of analysis tools and export options.
+Biopython – An incredibly powerful suite of molecular bioinformatic tools. The utility of Biopython cannot be overstated. You will first need Python (pre-installed with Mac OS X). Interactive computing with IPython also allows for fast and dynamic data exploration. Writing and organizing Python code is made even more convenient using Textwrangler (for Mac).
+ExPASy – A bioinformatics resource portal where you can find a range of web-based analysis tools.
PCR (polymerase chain reaction)
+primer3 – A go-to primer design tool that is quick, easy, and reliable.
+NEB Tm calculator – Calculates PCR annealing temperatures based on user-defined primer sequences and any of the NEB polymerases.
restriction digest
+NEB Double Digest Finder – A nice tool to quickly track down the right buffers for multi-enzyme digests.
teaching + learning
+NEB video library – A fantastic resource of informative videos on various molecular techniques and reagents.
vendors + products we like
+NEB – All-around great molecular biology products. We mainly rely on NEB for restriction enzymes and DNA polymerases.
+Zymo – Zymo makes some of the best kits for mini-prepping, gel purification, and DNA clean and concentration.
+IDT – We mainly order primers from IDT, but they have a nice selection of products for synthetic biology applications.
+GenScript – An amazing place where they synthesize huge pieces of custom DNA sequences.
+Promega – The Wizard Genomic DNA Purification Kit is awesome.
+x-tracta Gel Extractor – Awesome little tool for cutting out bands from DNA gels. These can be bought from most general supply vendors.