Inserting plain text references in Paperpile

I used to use zotero for reference management, but now I use paperpile since it is a bit more stable. One peculiarity of paperpile is that it only provides plug-in for google docs (an advantage in my opinion) since it is easier to collaborate over google docs.

I often encounter having to insert references from a formatted paper in some document format like ms word where the original dynamic references inserted by a reference manager was lost. Doing this manually is very tedious.

There is a work around for this that worked very well when I used it:

Sign up for crossref: http://www.crossref.org/SimpleTextQuery/

and paste the reference list in the window of the crossref site, which returns nicely formatted references.

Then I ran makebib http://www.snowelm.com/~t/doc/tips/makebib.perl.cgi

on the output and uploaded the resulting bibtex file to Paperpile.

Very easy!

PCR simulation with WebPCR

It is handy to have a bioinformatics tool to simulate various aspects of the Polymerase Chain Reaction (PCR). Errors are easily introduced in the primer design step so it is useful to have a simulation tools that can predict the sequence of the PCR product so that it can be verified.

I have put a PCR simulation script online called WebPCR . It is written in Python and runs using Flask on PythonAnywhere. 

The PCR simulation script used is from the pydna package.

The WebPCR window accepts a list of sequences in FASTA or Genbank format (or a mixture of both formats).

The last of the sequences in this list is assumed to be the template sequence while all preceding ones are assumed to be PCR primers.

The simulator will return a text based report describing the PCR product from each primer pair that is able to form one:

Two PCR programs are suggested for each PCR product, one for Taq polymerase and one for polymerases containing a DNA binding domain such as the Phusion DNA polymerase.

WebPCR has some capabilities not found in any or most other simulators:

• Tailed primers are handled correctly
• Inverse PCR of circular templates

The WebPCR  script has to be told that the template is circular. This can be done in two ways, depending on the format of the template sequence:

For FASTA format template sequence, simply add the keyword "circular" in the FASTA header:

For Genbank format template sequence, the DNA topology is set to either "linear" or "circular" in the LOCUS line: