There are many advantages associated with publishing with an Open Access journal...but I'm not going to go into these now (see recent posts on PMR's blog [e.g.
this one] for a comprehensive background if the advantages are not self-evident). Here the point I want to make is that the authors of OA papers can do things with their papers which are not allowed by traditional publishers.
As a trivial example, authors of OA publications can
legally distribute copies of their papers - sort of handy if you're a scientist, eh? :-) With most Open Access publishers, the author does not transfer copyright to the publisher but rather licenses it to them under a Creative Commons License. In other words, the author retains the right to do whatever they want with the paper: they can copy+paste the text into their blog (
insert example here if someone can send me one), they can insert the paper as an appendix to another publication (as I did with the
Open Babel book), they can magnify it to A0 size and present it as a poster or art installation or whatever... (I've sometimes wondered why Open Access journals don't make more capital out of this difference between themselves and closed journals - for example, they could hand out the top 10 most accessed papers at conferences.)
Well, in the spirit of exercising my right to recycle my OA papers as I like, I've put together a book (well, a PDF at least) consisting of the various PDFs stitched together with a Table of Contents. Here is the result (a 15MB
PDF):
If I wanted to, I could upload this to Lulu and allow people to order a copy in the post, all nicely bound with a cover. Maybe another day.
Notes: The PDF was created based on comments on the
Debian message board. To avoid confusion over page numbers, I added the short form of the appropriate reference to the footer of all of the papers. The following Python script was used to automate some of the steps:
import os
latex="""\\documentclass[12pt,a4paper]{book}
\\usepackage{multido}
\\usepackage[hmargin=.8cm,vmargin=0.5cm,nohead,nofoot]{geometry}
\\usepackage[explicit]{titlesec}
\\newcommand*\\Hide{%%
\\titleformat{\\chapter}[display]
{}{}{0pt}{\\Huge\\thispagestyle{empty}}
\\titleformat{\\part}
{}{}{0pt}{}
}
\\begin{document}
\\pagestyle{empty}
\\title{Open Access Publications of\\\\Noel O'Boyle}
\\maketitle
\\tableofcontents
%s
\\end{document}
"""
data = {
"BO.pdf": [15,
"""Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
N. M. O'Boyle, R. Guha, E. L. Willighagen, S. E. Adams, J. Alvarsson, J.-C. Bradley, I. V. Filippov, R. M. Hanson, M. D. Hanwell, G. R. Hutchison, C. A. James, N. Jeliazkova, A. S. I. D. Lang, K. M. Langner, D. C. Lonie, D. M. Lowe, J. Pansanel, D. Pavlov, O. Spjuth, C. Steinbeck, A. L. Tenderholt, K. J. Theisen and P. Murray-Rust.
J. Cheminf. 2011, 3, 37."""],
"GM.pdf": [12,
"""Userscripts for the life sciences
E. L. Willighagen, N. M. O'Boyle, H. Gopalakrishnan, D. Jiao, R. Guha, C. Steinbeck and D. J. Wild.
BMC Bioinformatcs. 2007, 8, 487."""],
"Cinfony.pdf": [10, """Cinfony - combining Open Source cheminformatics toolkits behind a common interface
N. M. O'Boyle and G. R. Hutchison.
Chem. Cent. J. 2008, 2, 24."""],
"Confab.pdf": [9, """Confab - Systematic generation of diverse low-energy conformers
N. M. O'Boyle, T. Vandermeersch, C. J. Flynn, A. R. Maguire and G. R. Hutchison.
J. Cheminf. 2011, 3, 8."""],
"AntColony.pdf": [15, """Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction
N. M. O'Boyle, D. S. Palmer, F. Nigsch and J. B. O. Mitchell.
Chem. Cent. J. 2008, 2, 21."""],
"DataAnalysis.pdf": [2, """Review of ``Data Analysis with Open Source Tools"
N. M. O'Boyle.
J. Cheminf. 2011, 3, 10."""],
"MACIE2005.pdf": [2, """MACiE: a database of enzyme reaction mechanisms
G. L. Holliday, G. J. Bartlett, D. E. Almonacid, N. M. O'Boyle, P. Murray-Rust, J. M. Thornton and J. B. O. Mitchell.
Bioinformatics. 2005, 21, 4315-4316."""],
"MACIE2007.pdf": [6, """MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms
G. L. Holliday, D. E. Almonacid, G. J. Bartlett, N. M. O'Boyle, J. W. Torrance, P. Murray-Rust, J. B. O. Mitchell and J. M. Thornton.
Nucleic Acid Res. 2007, 35, D515-D520."""],
"OB.pdf": [14, """Open Babel: An open chemical toolbox
N. M. O'Boyle, M. Banck, C. A. James, C. Morley, T. Vandermeersch and G. R. Hutchison.
J. Cheminf. 2011, 3, 33."""],
"PyChem.pdf": [2, """PYCHEM: a multivariate analysis package for python
R. M. Jarvis, D. Broadhurst, H. Johnson, N. M. O'Boyle and R. Goodacre.
Bioinformatics. 2006, 22, 2565-2566."""],
"Pybel.pdf": [7, """Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit
N. M. O'Boyle, C. Morley and G. R. Hutchison.
Chem. Cent. J. 2008, 2, 5."""]
}
order = [["Cheminformatics toolkits", ['Pybel', 'Cinfony', 'OB']],
["Enzyme reaction mechanisms", ['MACIE2005', 'MACIE2007']],
["QSAR", ['PyChem', 'AntColony']],
["The Rest", ["GM", "Confab", "DataAnalysis", "BO"]]
]
def formatjournal(text):
"""Format the journal metadata
>>> formatjournal("Chem. Cent. J. 2008, 2, 5.")
'\\\\textit{Chem. Cent. J.} \\\\textbf{2008}, \\\\textit{2}, 5.'
"""
broken = text.split(" ")
pages = broken[-1][:-1]
year = broken[-3][:-1]
volume = broken[-2][:-1]
journal = " ".join(broken[:-3])
return "\\textit{%s} \\textbf{%s}, \\textit{%s}, %s." % (journal, year, volume, pages)
def test():
import doctest
doctest.testmod()
if __name__ == "__main__":
# Sanity checks
N = 0
for x, y in data.iteritems():
assert os.path.isfile(x)
N += y[0]
assert len(data) == sum(len(y) for x, y in order)
# Write latex
output = []
for a, b, in order:
output.append("\\part{%s}{\\Hide" % a)
for paper in b:
pages, biblio = data["%s.pdf" % paper]
broken = biblio.split("\n")
title = broken[0]
output.append("\\chapter{%s}" % title)
authors = broken[2]
journaldata = formatjournal(broken[3])
output.append("""\\multido{}{%d}{\\null\\vfill
%s
\\newpage}""" % (pages, journaldata))
output.append("}")
with open("generated.tex", "w") as f:
f.write(latex % "\n".join(output))
# Join Papers together
pages = 1
paper_idx = 1
names = "A=generated.pdf"
cat = "A2 A2 A2 A2"
pages += 4
for a, b in order:
cat += " A2 A2"
pages += 2
for paper in b:
# New chapters always on odd-number pages
if pages % 2 == 0:
cat += " A2"
pages += 1
## print pages
paper_idx += 1
papername = chr(64+paper_idx)
names += " %s=%s.pdf" % (papername, paper)
cat += " %s" % papername
pages += data["%s.pdf" % paper][0]
print >> open("run.bat", "w"), "pdftk %s cat %s output combined.pdf" % (names, cat)
print """Now run...
pdflatex generated
pdflatex generated
run.bat
pdftk combined.pdf burst output tmp\\file_%03d.pdf
pdftk generated.pdf burst output tmp\\numbers_%03d.pdf
bash-3.2$ cd tmp && for i in `seq -w 1 109`; do pdftk file_$i.pdf background numbers_$i.pdf output new-$i.pdf; done
pdftk tmp\\new-???.pdf output new.pdf
"""
Cinfony presents a common API to several cheminformatics toolkits. It uses the Python programming language, and builds on top of Open Babel, the RDKit, the CDK, Indigo, OPSIN and cheminformatics webservices.
