## Thursday, December 20, 2012

### Self-Publishing: A Personal Experience

December 20, 2012 1:52 pm

As some of you may know, a year ago I published my book 'Enzyme Kinetics for Systems Biology' and I am about to release the second edition. Next year the hope is to publish another title. Self-publishing my own book has been something I've wanted to do for many years and I thought I'd share some of the experiences and rational for my decision.

Although it has been possible to self-publish almost since the beginning of the written work, recent developments have made it much easier, credible and worthwhile to do. A combination of the internet, print on demand and sophisticated writing tools has made self-publishing an intellectually rewarding and sometimes a highly profitable adventure.

The first question is ask is why didn't I just go with a traditional publisher and I've been asked often enough? The main reason for self-publishing is control, these include things like:

Style of the book and text
Book size
Book price
Ability to offer discounts
Choose between Black/White or Color or have both
Publish however I like, free pdf, print or kindle version etc.
The royalties are much much better

These reasons are all well and good but there are also a couple of more subtle reasons which really made a difference to me, these include:

1. The first is that all figures and text in the book remain my property. In a traditional publishing model, the publishers get copyright which means I cannot reuse the figures or text anywhere else. The first edition has 97 figures. I created each one so I am not inclined to simply hand over copyright to an organization that contributed nothing to their creation.

2. Once in the hands of the publisher, the publisher will decide how many copies will be printed (i.e sold) and whether there will be a second edition or not. If the book goes out of print, I cannot take control back and you'll never see the book published again.

3. Once published it is not possible to update the book with revisions. For example, there will no doubt be some typographical errors in the text. A traditional publisher will not release a new revision with corrections or minor updates.

I have discussed these issues with a number of publishers especially with respect to holding copyright and the ability to create revisions but they they were not interested in changing.

In the next blog I will talk more about the mechanics of self-publishing.

## Wednesday, December 5, 2012

### LaTeX and Chemistry

Originally Posted on  by

I recently had the need to draw some chemical equation in a LaTeX document. In the past I’ve used ChemDraw and loaded the image into my document as a png file. Last time I used ChemDraw was on my old computer and I didn’t have it on my new machine. So rather than download a copy and remind myself how to use it, I decided to see what was going on in the LaTeX community with respect to chemistry support. The answer is a lot. What I found was a number of new packages. One particular package, chemfig, written by Christian Tellechea, caught my attention. One needs to read the documentation before using this package but its mode of operation is fairly straightforward. Other related tools can be found at Clemens Niederberger

For those who are curious, chemfig is built on tikz, an excellent general-purpose drawing package. The main command in chemfig is:

   \chemfig{atom1 bond type[angle,coeff,tikz code]atom2}


Atoms can continue to be added to the list. A very simple example is:

\setatomsep{2em}
\chemfig{CH_3-CH_2-COOH}


\setatomsep just set the bond length which I made a little longer compared to the default. Or expressed in a different way using the angle option:

\chemfig{H-C(-[2]H)(-[6]H)-C(-[2]H)(-[6]H)-C(-[7]H)=[1]O}


For my purpose I need to draw a transaminase reaction, for this, I used the following code:

\setatomsep{1.8em}
\schemestart
\chemname{\chemfig{[6]COO^{-}-[6]CH(-[0]NH_3^{+})%
-[6]CH_2-[6]CH_2-[6]COO^{-}}}{glutamate}
\+{0pt,0pt,-48pt}
\chemname{\chemfig{[6]COO^{-}-[6]C(=[0]O)-[6]CH_3}}{pyruvate}
\arrow
\chemname{\chemfig{[6]COO^{-}-[6]C(=[0]O)-[6]CH_2-[6]CH_2%
-[6]COO^{-}}}{$\alpha$-ketoglutarate}
\+{0pt,0pt,-48pt}
\chemname{\chemfig{[6]COO^{-}-[6]CH(-[0]{NH_3^{+}})%
-[6]CH_3}}{alanine}
\schemestop


which yielded:

It could probably be tuned up a bit, for example, the molecules are a bit close to the addition' symbols. One thing I couldn’t get working very well was coloring atoms and groups of atoms.

If you use MiKTeX on windows all you have to do is include the following line at the start of your document:

\usepackage{chemfig}
`

and MiTeX will automatically download the package. Further details of the package including the fairly long manual can be found at CTAN.