Bio::Blogs #8
The eighth edition of Bio::Blogs was originally posted online on the 2nd of February at:
Editorial musings
Welcome to the eight edition of the
bioinformatics blog journal Bio::Blogs. The
archive from previous months can be found at
bioblogs.wordpress.com. When this carnival
was started, more than eight months ago, it had
the primary objective to serve as sort of display
for some of the best bioinformatics blog posts
on the web and to create incentives for other
people to promote their blogs and join in the
conversation.
Looking back at the past Bio::Blogs editions I
would like to think that we have manage to
come with with many interesting posts about
bioinformatic conferences, tools and useful
computational tips like the DNA analysis series
by Sandra Porter (I,II,III,IV,V,VI). Bio::Blogs has
also been use to promote tools that have been
published in blogs like the Genetic
Programming Applet from Pierre and research
like the correlation between protein-interaction
likelihood and protein age (I and II) that I
worked on.
Not everything went as I would hope. The
submissions to Bio::Blogs have not picked up as
I would expect. Some of this can be explained
by poor promotion of my part but it is also due
to the small size of the bioinformatics blogging
community. In any case I think it is worth
maintaining Bio::Blogs up and running for some
more time before thinking about stopping this
experiment.
In this edition a PDF version of all the posts has
been created for anyone interested in
downloading, printing and reading some fine
posts over coffee or tea. Leave comments or
send an email (bioblogs at gmail.com) with your
thoughts/ideas for the continuation of this blog
journal. I think this printed version also gives a
more concrete impression of the potential of
blogging for scientific communication.
News and Views
GrrlScientist submitted a report on a recent
Science paper describing how moths use their
antennae to help them stabilize their flight (see
page 3). Apart from some nasty experiments
were they authors removed and glued parts of
the antenna the work features some interesting
neurophysiology analysis used to characterize
the sensitivity of the antennae.
1

From my blog I picked an entry on network
reconstruction (see page 4). I think the
increasing amounts of omics data should be
better explored than it currently is and network
reconstruction methods are a very good way of
achieving this. In this paper, Jason Ernst and
colleagues used expression data to reconstruct
dynamic transcription regulatory interactions. I
will try to continue blogging about the topic in
future posts.
Comentaries
PLoS ONE was launched about two months ago
and it has produced so far an amazing stream of
publications. However the initially proposed
goal of generating discussions online to
promote post-publication reviews as been
lagging. Stew (on page 6) and Alf (on page 7)
wrote two commentaries (summited by Greg)
regarding the progress of PLoS ONE. They both
discuss the current lack of infrastructures to
stimulate the online discussions at the PLoS
ONE site. Stew goes even further by providing
to anyone interested a nice Gresemonkey script
to add blog comments to the PLoS ONE papers.
I hope Chris Surridge and the rest of the PLoS
ONE team start deploying soon some of the
tools that they have talked about in their blog.
They need to make ONE feel like home, a place
were a community of people can discuss their
papers.
From Deepak we have a post dedicated (on
page 8) to what he dubs EcoInformatics. The
importance of using computational methods to
analyze ecological changes from the molecules
Bio::Blogs #8
to the ecosystems. The problems range from
data access to data management and analysis.
The complexity and the different scales of
organization (i.e. molecules, environment,
ecosystems, disease) make this a very promising
field for computational biologists.
From ecological changes we move on to human
evolution. On page 10, Phil tries to introduce
the possibility of humanity using technology to
improve itself. Having a strong interest myself
in synthetic biology and man-machine
interfaces I would say that we are still far away
from having such control. It is nevertheless
useful to discuss the implications of emerging
technologies to better prepare for the possible
changes.
Reviews and tips
I start this section with a post from a brand new
bioinformatics blog called Bioinformatics Zen.
Michael Barton submitted his post on useful
tips to get organized as a dry lab scientist (see
page 12). I agree with most of his suggestions. I
have try to slightly fancier methods of
organizing my work using project managing
tools but I end up returning to a more
straightforward folder based approach as well.
Finally on page 14 Neil Saunders presents a nice
tutorial on building AJAX pages for
bioinformatics. It is a very well explained
introduction with annotated code. If you were
ever interested in learning the basics of AJAX
but never invested time in it, here is a good
chance to try it.
2

Gyroscopes Tell Moths How to Fly Straight
This blog post was originally posted online by GrrlScientist on the 9 of February 2007 at:
http://scienceblogs.com/grrlscientist/2007/02/gyroscopes_tell_moth_how_to_fl.php
Researchers have discovered that moth
antennae have gyroscope-like sensors to help
them control their flight through the air.
Because they fly at night, the source of their
smooth and graceful flight was a mystery
because they could not rely on visual cues.
But a research team headed by Sanjay Sane, a
biologist at the University of Washington,
Seattle, found a structure at the base of the
antennae that senses when the moth's body
begins to pitch or roll, it relays this information
to the brain, which causes the body to
compensate.
"Whenever a creature is moving about, it has to
have sensory information to tell it what it has
done," said Sane. "If a person unintentionally
turns around, the inner ear system or eyes will
provide that information and allow for a course
correction. Flying creatures need to know that
information too, and when the light is low, and
the visual cues are hard to see, they have to
depend more on the mechanosensory system."
In a particularly elegant series of experiments,
the researchers found that removing the
Bio::Blogs #8
th
antennae caused the moths to collide with
walls, to fly backwards or crash to the floor.
However, when the antennae were glued back
in place, the moths regained their
maneuverability.
Closer examination revealed that a structure,
called Johnston's organ, found at the base of
the moths' antennae, was crucial for flight
stability. This organ relies on vibrations from
the antennae, which remain in a fixed position
during flight, to detect the spatial relationship
of the moth's body to its antennae, behaving
like a gyroscope.
Johnston's organ sends this information to the
moth's brain, which then tells the moth to shift
its body back to the correct spatial position.
Previous studies found that two-winged insects,
such as house flies or mosquitoes, also use
gyroscope-like sensors to control their flight.
These are the "halteres" that are attached to
their hindwings.
Cited story.
3

in sillico network reconstruction (using expression data)
This post was originally posted by Pedro Beltrao on th 7th of February 2007 at:
http://pbeltrao.blogspot.com/2007/02/in-sillico-network-reconstruction-using.html
In my last post I commented on a paper that
tried to find the best mathematical model for a
cellular pathway. In that paper they used
information on known and predicted protein
interactions. This time I want to mention a
paper, published in Nature Mol. Systems
Biology, that attempts to reconstruct gene
regulatory networks from gene expression data
and Chip-chip data.
The authors were interested in determining
how/when transcription factors regulate their
target genes over time. One novelty introduced
in this work was the focus on bifurcation events
in gene expression. They tried to look for cases
where a groups of genes clearly bifurcated into
two groups at a particular time point.
Combining these patterns of bifurcation with
experimental binding data for transcription
factors they tried to predict what transcription
Bio::Blogs #8
factors regulate these group of genes. There is a
simple example shown in figure 1, reproduced
below.
In this toy example there is a bifurcation event
at 1 h and another at the 2h time point. All of
the genes are assigned to a gene expression
path. In this case, the red genes are those that
are very likely to show a down regulation in
between the 1st and 2nd hour and stay at the
same level of expression from then on. Once
the genes have been assigned it is possible to
search for transcription factors that are
significantly associate to each gene expression
path. For example in this case, TF A is strongly
associated to the pink trajectory. This means
that many of the genes in the pink group have a
known binding site for TF A in their promoter
region.
4

To test their approach, the authors studied the
amino-acid starvation in S. cerevisiae. In figure 2
they summarize the reconstructed dynamic
map. The result is the association of TFs to
groups of genes and the changes in expression
of these genes over time during amino acid
starvation.
One interesting finding from this map was that
Ino4 activates a group of genes related to lipid
metabolism starting at the 2h time point. Since
Ino4 binding sites had only been profiled by
Chip-chip in YPD media and not in a.a.
starvation, this is a novel result obtained using
their method.
To further test the significance of their
observation they performed Chip-chip assays of
Ino4 in amino acid starvation. They confirmed
Bio::Blogs #8
that Ino4 binds many more promoters during
amino acid starvation as compared to synthetic
complete glucose media. Out of 207 genes
bound by Ino4 (specifically during AA
starvation) 34 were also among the genes
assigned to the Ino4 gene path obtained from
their approach.
This results confirmed the usefulness of this
computational approach to reconstruct gene
regulatory networks from gene expression data
and TF binding site information. The authors
then go on to study the regulation of other
conditions.
For anyone curious enough about the method,
this was done using Hidden Markov Models (see
here for available primer on HMMs).
5
 Bio::Blogs #8

PLoS One / Postgenomic mashup

This post was originally posted by Stew on the 12th of February 2007 at:
http://www.ghastlyfop.com/blog/2007/02/plos-one-postgenomic-mashup.html

Chris Surridge has an interesting post over at

the PLoS blog about the comments (or the lack
thereof) on PLoS One papers. He mentions one
paper in particular that has a long discussion
thread associated with it on Gene Expression
but no real comments on the actual PLoS One
site.

As a temporary solution (?) to the problem of

blog comments not being immediately
accessible from the paper, summaries of
notable manuscripts are going to be posted to
the PLoS publishing blog with open comment
threads. Based on the three posts already up I
think this is a terrible idea.
Partly this is personal preference - I hate blogs
that just replicate tables of contents - but more
importantly I think that it misses the point.
People like the GNXP folks have taken the time
and trouble to build up a loyal community that
fosters debate and to create an environment in
which visitors enjoy interacting with the site
and with each other. Sticking up an abstract or
two on your own blog just isn't going to
compete with that, doesn't matter how much
traffic you get.
Blog properly - engage your audience - or don't
blog at all. It's a personal communication
medium, that's one of the reasons why people
feel more comfortable commenting in a
blogging environment. A link and an abstract on
a publisher's blog isn't personal, it's an advert.
The PLoS One blogs are generally a good read at
the moment, don't ruin them.
I'm not just PLoS bashing here: I like the ideas
behind PLoS One and we do the same 'if we
blog the abstract then people will comment!'
thing at Nature on some blogs (the ones I don't
read any more). The intention is good, it's just
misguided, IMHO.
Anyway, I think that a better solution would be
to embrace the existing science blogosphere
and to explore ways of working with it more
closely. As a proof of concept, here's a
Greasemonkey script that adds science blog
trackbacks to PLoS One.
It's doesn't look particularly nice, mainly
because I didn't have time to style things very
well. Feel free to do with it as you will, though
(you could get it working with PLoS Two, for a
start).

6

PLoS One
This post was originally posted by Alf on the 13th of February 2007 at:
http://hublog.hubmed.org/archives/001447.html
PLoS One's been launched in beta for a while
now, but there had been technical problems
that seem to have been fixed now. It's a great
idea: a much lower barrier of entry to article
acceptance, publishing articles of any length,
with peer review provided by readers
comments on the article after it's published and
publication charges paid for by the authors'
funding agencies.
Technically, PLoS should be built on solid
foundations, as it uses the NLM Journal
Publishing DTD to store articles as XML and
retrieves all objects (articles, figures, etc) using
DOIs. The underlying TOPAZ software is
supposed to be released as open source,
though there hasn't been anything made
available yet. Hopefully this project should
cross-pollinate well with OJS, which recently
had its own annotation system added thanks to
Geof Glass's work on Marginalia. PLoS only
producing RSS feeds and still not even getting
them right doesn't exactly inspire confidence
though.
As far as published articles go, some people
publish long, technical papers similar to those
found in existing journals; others publish short,
one experiment papers (which will hopefully get
even shorter, if methods and introductions can
be referenced elsewhere).
Bio::Blogs #8
There was one article that caught my attention
because of the wording of the funding section:
"The authors claim they did not receive any
financial funding." - suggesting, perhaps, that
the publishers weren't entirely sure about that
claim. This article in particular has quite a few
style errors (even one in the title), so while peer
review may come afterwards (and hasn't in this
case, yet, but maybe someone out there is
repeating the experiment themselves), there's
still a role for publishers in copy-editing articles
for readability. It would be good if authors have
enough control over their published papers that
corrections can be made at a later date, and
with archiving of open access articles using
LOCKSS, updated articles could feasibly be
distributed to multiple archives.
It's a shame that Chris Surridge is already
lamenting the lack of comments on papers,
when the infrastructure isn't in place to
properly handle discussions at the moment. It's
not surprising that people are more willing to
comment on papers within their own
communities where they can see that
discussion threads are treated as important,
permanent content and displayed
appropriately.
7

Ecoinformatics - Information for our planet
This post was originally posted by Deepak on the 4th of February 2007 at:
http://mndoci.com/blog/2007/02/04/ecoinformatics-information-for-our-planet/
As some of you know, I contribute to the Seattle
edition of Worldchanging. That has resulted in a
lot of research into science for sustainable
development. Since Just Science week starts
tomorrow, I thought it would be good to get the
ball rolling with something that combines
sustainability with science. A couple of weeks
ago I came upon a paper entitled The new
bioinformatics: Integrating ecological data from
the gene to the biosphere by a group of
researchers from UC Santa Barbara and UC
Davis. The abstract was interesting enough to
go get the paper and find out what the authors
really had to say about the subject.
Bioinformatics has been engine that has made
the entire genomics “revolution” possible. From
the various databases hosted by the NCBI and
the EBI, to tools like BLAST, and efforts like the
HapMap project, bioinformatics is an essential
part of modern biology. The huge amounts of
data from genome sequencing efforts provide
the fuel for follow on bioinformatics efforts.
Ecology is a field rich with information. Based
on the paper, one could argue that it is a form
of systems biology. Every ecological system is
finally balance, and being able to understand
the factors involved and how perturbing them
might impact the ecology is not a trivial
problem. In the review, the authors talk about
the demise of gorillas in Africa. There were a
number of factors involved, including Ebola and
hunting pressure. To understand the impact of
all the factors would require understanding the
epidemiology, genetics and transmission modes
of Ebola, the nutritional status and various
sociological factors of the local human
Bio::Blogs #8
population, and the population dynamics of the
gorilla population. I am sure there are many
other factors involved. The kind of data here
remind me of the kinds of challenges facing the
field of biomedical informatics, which seeks to
combine classic bioinformatics with healthcare
and clinical information. In fact, the challenges
are probably far greater, since the data are not
as well understood, and the uncertainties are
significantly more. Reading the paper, one gets
a much better understanding of the challenges
that the field faces. What makes the entire
subject so fascinating in the end is the fact that
ecological information is only really useful if it
can be used predictively.
Right of the bat the heterogeneity and nature of
ecological data would present the informatician
with significant challenges, and that’s just in
data management. Ecological information is
also temporal, often over long time lines, which
adds further complexity to the available
information. However being able to mine
diverse studies is critical to the success of
ecological studies and hypothesis generation.
Multiple studies over different temporal points
not only lead to better results, but re-using the
8

data in combination with different studies at
the later date can help ecologists gain better
insight. For the uninitiated, i.e. yours truly, this
screams for some data standards at the
minimum and the development of an ecological
ontology in a perfect world.
Currently ecological data is spreadsheet based,
i.e. it is still document centric. A number of
ecologists also use packages such as R and SAS,
since most ecological hypotheses are generated
via statistical modeling. Most people will tell
you that this is a recipe for data disaster. There
is a need for quality databases, and a data
centric approach. Regardless of integrative
analysis or synthetic analysis, having data in
well-designed databases will only help
ecologists in the long run. The authors spend
some time talking about metadata. In a field like
ecology, metadata is critical, especially in cases
when studies are re-used at a later point in time
in conjunction with newer studies. The authors
seem to talk about metadata driven data
collections as being separate from vertical
databases (data warehouses). That seems to be
too simplistic a view. Combining the two
paradigms is probably a more powerful
approach, one that has been discussed here in
the past. There is a role for core databases in
the mode of Genbank, which can be combined
with data on the edges. While the data on the
edges might lack the structure of a
comprehensive databases, but by building
semantic intelligence and developing
appropriate standards/ontologies, one can
combine the knowledge in metadata driven
datasets with the core knowledge housed in
structured data warehouses. Ecological projects
are very diverse, crossing species, societies,
data types, data volume and data quality. All of
Reference: M.B. Jones, Schildhauer, M.P., Reichman,O.J., and Bowers, S. The New Bioinformatics: Integrating Ecological Data
from the Gene to the Biosphere, Annual Review of Ecology, Evolution, and Systematics, 37: 519-544 (2006). Picture: Via bprm2
Bio::Blogs #8
this makes the nature of metadata rather
complex and will require ecologists to spend a
considerable amount of time developing data
standards and better still, ontologies to come
up with ways to enable the interoperability of
the datasets so that high quality data analysis
becomes possible.
The good news for the field is that there are a
number of existing resources, e.g. The
Knowledge Network for Biocomplexity which
seems to be a fairly modern resource for
ecological data. There are attempts to provided
a unified interface to many ecological data
sources, but one could argue that their time is
better spent enabling the creation of search
engines and interfaces to any resources of
ecological information since information will be
generated by a variety of sources. The dynamic
nature of ecological data will be a significant
challenge for data integration, especially since a
lot of continuous modeling and re-modeling.
There needs to be a way to store and version
different studies, to make sure people are not
making incorrect decisions.
For someone with only a peripheral knowledge
of ecology, but a good understanding of
bioinformatics, the review by Jones et al is a
very useful and interesting read. Ecologists are
trying to understand several critical problems
facing our society and planet. How they access
data, interpret it, and publish their results
should be a problem with more eyeballs on it.
Given the very public interest in sustainable
development and the environment these days,
hopefully there will be more informatics-savvy
people working in the field to develop high
quality databases, data standards and
ontologies.
9

The Future of Evolution
This post was originally posted by Phil B. at:
http://bellsouthpwp2.net/b/e/benichou//The_Future_of_Evolution.html
Compared with the progress of modern science,
evolution is too slow and error prone. We are
entering a period of time when scientists will be
able to greatly surpass natural evolution.
First, genetic engineering will allow doctors to
modify existing genes or entirely replace genes
to remove genetic defects, treat diseases, and
augment natural abilities. For instance, plants
and animals could be modified to yield better,
healthier, and more food. What if your eyesight
could be fixed without surgery? What if all your
future children would be guaranteed not to get
your original bad genes of poor vision or a
genetic disease? What if people choose to have
their vision enhanced to be far greater than the
natural human range, such as a bird’s vision?
How about people with the reflexes and speed
of a cat? Now imagine if a large number of our
children had perfect memory thanks to genetic
modification. These children would find school
very easy and would most likely be far more
successful than their parents.
Second, cybernetics could artificially replace
human body parts. People could replace limbs
with fully functional machines that would
seamlessly be directly connected to the human
brain. The human brain could be enhanced too.
Imagine if people could immediately look up
information just by thinking about it. For
example, people would instantly know what to
do in medical emergencies or how to solve
complex problems that they never encountered
Bio::Blogs #8
before, by relying on the knowledge and
experience of other people. Eventually, people
could become far more intelligent,
knowledgeable, and capable than anybody who
has ever lived before. Eventually this could lead
to completely artificial and intelligent life forms
that are not limited to evolution at all, since
they would not have any organic parts. Instead,
they could just upgrade themselves.
We already discussed forced evolution of plants
and animals for the sake of humanity, such as
better sources of food. Now consider modifying
non-intelligence and non-sentient (sentient
means self aware or self conscious) animals into
becoming an intelligent and sentient species
through the methods described above. This
very possible idea is called "uplifting". Humanity
could artificially uplift lowly species to the ranks
of civilized and productive people, for better or
worse. Imagine the philosophy, music, and
literature that intelligent animals, such as cats
and dolphins, would invent. I am sure they
would be creative in ways that humans are
not… yet.
These methods of leapfrogging evolution will
ultimately create hyper-intelligent super beings
that are far more capable than human beings.
Hopefully these future people will care more for
humanity than we do for less fortunate people.
Maybe these super beings will be able to solve
some of the world’s greatest problems, such as
10

global warming, pollution free energy, diseases,
etc.
The only problem that I see with these methods
of artificial evolution is that the variety or
diversity of people would lessen. The more
people become alike, then the less likely we
would have another Mozart or Einstein if we
Bio::Blogs #8
start restricting variation in our children before
they are even born. As a result, our children will
be geniuses but not unique.
Whatever methods that humanity will use to go
beyond natural evolution, the purpose should
always be to better humanity, our children, and
ourselves.
11

Organising yourself as a dry lab scientist
This post was originally posted by Mike on the 16th of February 2007 at:
http://www.bioinformaticszen.com/2007/02/organising-yourself-as-a-dry-lab-scientist/
Browsing wikiomics, I found this small section
on keeping organised as a practising
bioinformatician. In particular these lines
contain gems of information.
Use text files/plain e-mail whenever
possible
Give meaningful names to your files
Create separate folders/directories for
each project with meaningful names
I find keeping my work organised one of the
most frustrating but necessary tasks of being a
bioinformatician. Also this subject seems to
recieve little attention in the bioinformatics
community.
Wet scientists are expected to keep laboratory
books. Where not doing so considered very bad
practice. I am jealous when I see these books
filled with pictures of gels and printed tables of
results. I’ve tried using a lab book, but I didn’t
find it applicable for the many different types of
scripts and results I was producing.
Here are some tips I find useful for organising
myself.
I couldn’t agree more with the above tips. Give
directories and files the most verbose names as
possible. This helps when trying to find a
specific file. Being verbose as possible in naming
your files is useful because often sets of files are
all related to a similar subject. Take the
following example.
Bio::Blogs #8
ancova_sequence_hydrophobicity.R
ancova_sequence_hydrophobicity_inter
action_term.R
ancova_sequence_hydrophobicity_resi
duals.R
All three files contain a script fitting an ancova
model, but all differ slighty in focusing on
different parts of the model. Finding the one
you need is still simple for you, but perhaps not
so in a few months time when you return to the
results to write a paper.
Consider this example
ancova_sequence_hydrophobicity.R
ancova_sequence_hydrophobicity.csv
ancova_sequence_hydrophobicity.tiff
ancova_sequence_hydrophobicity_inter
action_term.R
ancova_sequence_hydrophobicity_inter
action_term.csv
ancova_sequence_hydrophobicity_inter
action_term.tiff
ancova_sequence_hydrophobicity_resi
duals.R
ancova_sequence_hydrophobicity_resi
duals.csv
ancova_sequence_hydrophobicity_resi
duals.tiff
Here, there are files for the results of each
model (csv) and a plot of the results (tiff). This
illustrates how quickly things can expand.
12

Making it more difficult to understand what
each file refers to.
Here’s one way that this could be organised
1.ancova_sequence_hydrophobicity
o scripts
 model.R
 model_interaction_ter
m.R
 model_residuals.R
o results
 model.csv
 model_interaction_ter
m.csv
 model_residuals.csv
o pictures
 model.tiff
 model_interaction_ter
m.tiff
 model_residuals.tiff
Each sub directory names describes its
contents, which keeps things verbose.
Furthermore the directory path contributes to
Bio::Blogs #8
describing each file, e.g.
1.ancova_sequence_hydrophobicity/results/mo
del_residuals.csv. This helpful if you are
referencing the file else where and want to
know what the file contains.
Since the files are related, they each have an
identically named counterpart in the other
directories. This is useful for determining which
script produced which result.
Finally the top level directory has a number.
Often projects and experiments are carried out
linearly, one being done after another. Keeping
the directories numbered can help to trace the
thought process at a later date.
There’s an interesting post at LifeHacker about
organising file structure. The comments also
have a lot of useful ideas too.
There are an infinite number of ways to
organise. Probably the best way to do this is to
use the system that suits you best. Experiment,
you’re a scientist.
13
 Bio::Blogs #8

My first “AJAX for bioinformatics” page

This post was originally posted by Neil Saunders on the 20th of February 2007 at:
http://nsaunders.wordpress.com/2007/02/20/my-first-ajax-for-bioinformatics-page/

So you’ve heard about this wondrous thing for bioinformatics, but it should give you an
called AJAX. You’re dimly aware that it can idea.
generate interactive, user-friendly and dynamic
websites without the usual cycle of reloading 1. Getting set up
the page after submitting a request to the First, I went to the place where I do my web
server. You know that Google Maps and Flickr testing (e.g. /var/www/testing/) and created 3
are two excellent examples. You’re keen to directories: php for the PHP, js for the javascript
explore the possibilities for your bioinformatics and xml for - you guessed right. In fact no XML
web applications. What you need is a “minimal files were saved in this example but I like to be
example”. Where do you start? organised. The HTML files just go in the /testing
root, right above these 3 directories.
That’s the situation that I was in last weekend
and here’s what I did. 2. The HTML form
There’s nothing special about the form. I named
I’ll start by making it clear that much of what the file form.html and it goes like this:
follows is lifted from the W3Schools AJAX
tutorial, with minimal adaptation to make it 1. <html>
relevant for bioinformaticians. Please go there 2. <head>
3. <script>script
and read their excellent work. src="js/ncbi.js"</script>
4. </head>
When I figured out how AJAX works my 5. <body>
6. <h3>Get protein name from NCBI
response was: “Oh. Is that all it is?” AJAX, you Gene DB ID</h3>
see, is nothing new. In fact if you’re familiar 7. <form>
with web programming and know a little about 8. <b>Select a Gene ID:<b>
9. <select name="geneID"
HTML, server-side scripting, javascript and XML onchange="showName(this.value)">
- well, that’s all it is. It’s just combined in a 10. <option value="none"
clever way to produce a pleasing result. selected="selected">-----</option>
11. <option
value="54123">54123</option>
Here’s what we’re going to do. We’re going to 12. <option
construct a simple form with a drop-down list of value="21354">21354</option>
13. <option
options. The options will be UIDs from the NCBI value="11988">11988</option>
Gene database. When we select an option, our 14. </select>
form will display the protein name associated 15. </form>
16. <p>
with the UID - without the need to reload the 17. <div id="geneName"><b>Gene info
page. It’s the AJAX equivalent of “Hello World” will be listed here.</b></div>

14
 Bio::Blogs #8

18. </p> 23. if (!response) {

19. </body> 24.
20. </html> document.getElementById("geneName").
innerHTML="No data returned!"
25. }
Nothing complicated about that. Our select list
26. else {
has 3 values which correspond to NCBI Gene 27.
UIDs. When we choose one (onchange, line 9), document.getElementById("geneName").
innerHTML=response
we fire the javascript code in js/ncbi.js. At the
28. }
bottom of the form is a DIV element with the 29. }
name geneName. Initially it displays “Gene info 30. }
will be listed here”; later on we’ll see the
31. function GetXmlHttpObject()
javascript alter it to something different. 32. {
33. var xmlHttp=null;
OK, how about that javascript? 34. try
35. {
36. // Firefox, Opera 8.0+, Safari
3. The javascript 37. xmlHttp=new XMLHttpRequest();
38. }
39. catch (e)
Once again, nothing to be scared of. The file
40. {
ncbi.js reads like this: 41. // Internet Explorer
42. try
1. var xmlHttp 43. {
44. xmlHttp=new
2. function showName(str) ActiveXObject("Msxml2.XMLHTTP");
3. { 45. }
4. xmlHttp=GetXmlHttpObject() 46. catch (e)
5. if (xmlHttp==null) 47. {
6. { 48. xmlHttp=new
7. alert ("Browser does not ActiveXObject("Microsoft.XMLHTTP");
support HTTP Request") 49. }
8. return 50. }
9. } 51. return xmlHttp;
10. var url="php/ncbi.php" 52. }
11. url=url+"?q="+str
12. url=url+"&sid="+Math.random() I’m not a strong javascript programmer - truth
13.
xmlHttp.onreadystatechange=stateChan
be told, I don’t like the language much, but
ged even I can follow this one. We’ve got 3
14. xmlHttp.open("GET",url,true) functions: showName() on lines 2-16,
15. xmlHttp.send(null)
16. } stateChanged(), lines 17-30 and
GetXmlHttpObject(), lines 31-52. showName()
17. function stateChanged() first calls GetXmlHttpObject(), assigning the
18. {
19. returned value to the variable xmlHttp. All you
document.getElementById("geneName"). need to know about lines 31-52 is that they test
innerHTML = "Fetching XML file..." whether your browser supports AJAX and if so,
20. if (xmlHttp.readyState==4 ||
xmlHttp.readyState=="complete") return a special object, the xmlHttp request
21. { object. This object is what “does” AJAX. As you
22. var response = can see from the code it has a number of
xmlHttp.responseText

15

methods that send, listen to and act on HTTP
requests.
In fact, the main reason why many of us are
only now hearing about AJAX is - you guessed it
- browser standards. See if you can guess which
browser is being difficult from the code.
Assuming that all is well, we move to lines 10-
16. Here, the javascript is calling a server-side
PHP script named php/ncbi.php. It appends a
couple of things to the URL query string. The
first, “q”, is the value that we get from the
select list in our form. The second is a random
number (which W3Schools assures us is to
prevent server caching). The PHP script is going
to get the value of “q”, use it to make a request
to the NCBI and return some data. The
javascript is going to grab that data and display
it. This happens in lines 13-15.
We know when our data comes back thanks to
the function stateChanged(). When the request
is sent, the text of the “geneName” element
(formerly, you recall, “Gene info will be
displayed here”) is altered to “Fetching XML
file…”, line 19. When the request is complete
(line 20), we check the variable named response
to see what came back. If nothing, we display
“No data returned!”, line 24. Otherwise, we set
“geneName” to the value of response.
For me, the javascript is the trickiest part of the
whole thing. If you’re like me, read the code
through a few times and you’ll soon have it. OK
- the last part is the server-side PHP script,
ncbi.php.
4. The PHP
The PHP isn’t much more complex than the
HTML:
Bio::Blogs #8
<?php
1. $val = $_GET['q'];
2. $baseURL =
"http://eutils.ncbi.nlm.nih.gov/entr
ez/eutils/efetch.fcgi?db=gene&id=";
3. $urlSUFF = "&retmode=xml";
4. $url =
$baseURL.$val.$urlSUFF;
5. $xmlDoc = new DOMDocument();
6. $xmlDoc->load($url);
7. $titles = $xmlDoc-
>getElementsByTagName("Prot-
ref_name");
8. foreach($titles as $node) {
9. echo "<b>" . $node->nodeName
. ": </b>".
10. $node-
>textContent . "<br />";
11. }
?>
First, you should be aware that this code is PHP
5. PHP 5 has some new functions to make
handling XML files quite easy, even for people
like me who don’t much care for XML. There’s a
good introduction to XML in PHP 4 and 5 at this
Zend page.
Off we go. In line 1-4 we grab the value “q”
which, you recall, is sent from ncbi.js and
corresponds to a gene UID from form.html. We
then construct a URL to the Efetch component
of NCBI EUtils, to return our record as XML.
We can read the XML stream straight into the
variable $xmlDoc and parse the XML for the
element “Prot-ref_name” (lines 5-7). This
contains the official protein name for the gene
UID. We then loop through the stored XML
object, retrieving the node name (”Protein-
ref_name”) and its value ($node->textContent).
Purists will frown at the use of textContent, by
the way. These values are what the script
returns to ncbi.js and are displayed as the value
of the “geneName” element in form.html.
16

To recap then:
We select a gene UID from a drop-down
list in a normal HTML form
Javascript and PHP interact to perform
an EUtils query at the NCBI and return
an XML file
The XML is parsed and appropriate
values retrieved
Using asynchronous requests to the
server (that’s the first ‘A’ in AJAX),
javascript updates the page with
progress and displays the result
All without reloading the page
That’s it. That’s AJAX. It’s a particularly stupid
example - fetching a huge XML file to parse out
Bio::Blogs #8
one element, but hopefully you get the idea.
You can imagine all sorts of uses for this in
bioinformatics applications: fetching the most
recent data rather than local storage, XML-SQL
interconversions, real-time BLAST results and so
on. As ever, the only limits are your creativity
and requirements.
You can see it in action for a short time at this
location. Feel free to grab the files and/or copy-
paste from here to try it on your own server. I
added a little extra to the javascript at that
location to display a “spinning disk” progress
indicator - see if you can figure out where the
addition goes. Finally this is all new and exciting
to me so if you spot any shocking errors, do let
me know.
17