Nature Reviews Genetics 9, 678-688 (September 2008) | doi:10.1038/nrg2414

Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges

Lincoln D. Stein

there's even a companion wiki page for an article in Nature Reviews Genetics by Lincoln Stein:

Cool part is that it’s free to read for a month for logged in nature.com users (you can use your Nature Network credentials).

I think he definitely hit it on the nail when he said "Much of the data is 'out there', but it can be difficult to find and challenging to use effectively once found."

Google has recently released knol, which most people are calling Google's version of Wikipedia. The main difference between a knol and a wikipedia article is that a knol has associated authorship or ownership against an article. This factor has caused some issues an outcries focusing on the merits of the wisdom of crowds verses the merits of single individuals and the whole ethos if information dissemination on the Web. (There are too many to cite but some discussion can be found on FriendFeed+knol)

However, on looking at knol and having a snoop around I was not drawn into thinking about competing with Wikipedia or advertising revenue, rather what struck me is that a knol, with owner authorship looks incredibly like a scientific journal publication platform...

According to the Introduction to knol (or instructions for authors)  you to can write about anything you like, so disseminiation of science must fall under that. You can collaborate on a unit of knowledge (or manuscript) with other authors and they are listed - I assume the contribution to the text will also be stored in the revision history, makes the authors contribution section a little easier to write. It is not limited to one article per subject, so this allows all manner of opinions or scientific findings to be reported contrasted and compared with each other. You can select your copyright and license for your article (rather than handing it over). You can request a (peer-) review of the article, However more important the article is available for continuous peer-review in the form of comments on the article.

So is a knol a Google Wikipedia or is it a scientific publishing platform? What would prevent publishiing a knol and getting credit (hyperlinks), citations (analytics) impact factors (page ranks) in the same way you do for the traditional scientific publishers? You would of course not have to pay for the privilage of trying to diseminate your findings, loosing copyright and then asking your institution to pay for a subscription so you and your lab members can read your own articles. In fact you, as an author (lab, institution) can even share revenue for your article via adsense.

Some traditional publishers are trying to embrace new mechanisms of disseminating scientific knowledge. Only today Nature Reviews Genetics (as described by Nacsent) published the paper Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges by Lincoln Stein and published the supplementary material as a community editable wiki.

With knol as a scientific publishing platform, what can the traditional scientific publishing houses now offer for the publishing fees? Faster turn around? revenue sharing? Are they really still the gatekeepers of scientific knowledge? Or in the Web 2.0 era has that mantle passed to Google? Certainly, in the first instance it would make a nice preceedings platform.

Let's take for example stem cell research. Say you are working on a groundbreaking research that requires some kind of secrecy, because some guy in another lab is trying the same thing. If you decide to open your notebook the guy-next-door can check it and maybe have an insight and modify his approach and find the desired result before you do. If the guy-next-door is a "nice" guy you will share the discovery, if not you will end up with crumbs. In this case Open Science is only good if it is a two way street, as everyone is sharing data, results and publications freely.

On to the a bioinformatics example. Say you are working on a software the would allow analysis to be more elaborate and exact to some kind of biological problem. Your notebook is open, you software is on Github (or any other repository), so anyone can see it, especially the guys (non bioinformaticians) which analysis will be improved. You are the only one that knows the code and most of the algorithms in it, and you test, release and publish. Great ... but wait: the analysis is wrong and there are some major errors on the results. You look, search, dissect your code and cannot find the bug or error. You, frustrated, mentions it in your notebook. Some guy from the internet notices it and decides to check the code and in 10 minutes finds the error/bug. Everything solved and marvelous results are expected.

As anything there are many sides, many different angles that Open Science can be viewed, and it might not serve everyone at first, but it is clearly a great start. The only question is where it is going to take us. What is it good for?

The MIAPE: Gel Informatics module formalised by the Proteomics Standards Initiative (PSI) now available for Public Comment on the PSI Web site. Typically alot of this information will be contained in the image analysis software, so we would especially encourage software vendors to review the document. The public
comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process.

This message is to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal.

If you do not feel well placed to comment on this document, but know someone who may be, please consider forwarding this request. There is no requirement that people commenting should have had any prior contact with the PSI.

If you have comments that you would like to make but would prefer not to make public, please email the PSI editor Norman Paton.

Being a bioinformatician, I tend to ignore the GUI in favour of the input -> script -> output approach, as I'm mostly interested in batch processing. Documentation describing this operation for CCP4 programs is strangely lacking on the web. The best that I can find is the CCP4 wiki; if you know the package well, please contribute to it.

I eventually dug up what I was looking for in:

/opt/ccp4/ccp4-6.0.2/examples/unix/runnable/

or the equivalent on your system. Here, you'll find a collection of shell scripts, confusingly named with the suffix ".exam". As an example, here's how you might run the program "contact":

[sourcecode language='python']
#!/bin/sh
set -e
contact XYZIN $1 << eof > $1.contact
MODE ALL
ATYPE ALL
eof
[/sourcecode]

You might run that on a bunch of files using e.g. "find ./ -name "*.pdb" -exec contact.sh {} \;".

Other mysteries: many CCP4 programs are quite happy to take gzipped files as input (such as you might download from the PDB FTP archive), but may choke if unzipped filenames don't contain ".ent" or ".pdb".

Special thanks to Dr. Kevin Karplus, professor of Bioinformatics at University of California, Santa Cruz, for his useful and detailed responses.

So I do a lot of file processing in my bioinformatics work and I've always really liked the perl function chomp.

I wanted to implement something in python to do this and something, that like the perl one, is able to handle multiple line endings (that is, Linux, Windows, and Mac line endings).

So this is chomp in python , in a sense a def chomp, but I rename it.

IMPORTANT: I am not guaranteeing in any way that this completely replicates chomp behavior. And, of course, this won't work on more unusual systems that have different line ending conventions. In my work, I use UNIX/Linux, windows, and older mac stuff - so this works for those. And it handles ugly cases well, as you can see.

Enjoy! and comments welcome.

Also, this is not beautiful code! I threw this together because I was frustrated.

NOTE: you will have to adjust the tab spacing for the function to work; but you already know this... copying to HTML can be a pain...

>>> def chomppy(k):
    if k=="": return ""
    if k=="\n" or k=="\r\n" or k=="\r": return ""
    if len(k)==1: return k #depends on above case being not true
    if len(k)==2 and (k[-1]=='\n' or k[-1]=='\r'): return k[0]
    #done with weird cases, now deal with average case
    lastend=k[-2:] #get last two pieces
    if lastend=='\r\n':
        outstr=k[:-2]
        return outstr
    elif (lastend[1]=="\n" or lastend[1]=="\r"):
        outstr=k[:-1]
        return outstr
    return k

>>> chomppy('cow\n')
'cow'
>>> chomppy('')
''
>>> chomppy('hat')
'hat'
>>> chomppy('cat\r\n')
'cat'
>>> chomppy('\n')
''
>>> chomppy('\r\n')
''
>>> chomppy('cat\r')
'cat'
>>> chomppy('\r')
''

I am Oommen. A Graduate in Computer Applications & Master’s Degree in Bioinformatics with Specialization in Open Source programming. Currently I am a python software developer. Presently working as a senior software analyst, for rKc Technology Solutions, philadelphia, at their Kochi development center.

I was previously a lecturer in Bioinformatics at Mar Athanasios College for Advanced Studies, Tiruvalla, Kerala.

My Passions are

• Python
• Bioinformatics

Now I am working on a projects in the telecome domain.

My Publications:-

1. Protein * Quest :- Web based cross-reference protein information resource
   Shameer P. K, Oommen K. M, Sam C. Thomas and Prof. Ignatius Kunjumon (2004) PROTEIN * QUEST: - A Web Based Cross-Reference Protein Information Resource. Bioinformatics India Journal, Vol-2 Iss-3 P 47 - 52.

2. Hypothetical FANC core complex formation based on motif analysis
   Shameer P. K, Oommen K. M and Prof. Ignatius Kunjumon (2007), Hypothetical FANC core complex formation based on motif analysis

3. Gene^Scape :- A web based tool for gene mapping
   Shameer P. K, Oommen K. M and Prof. Ignatius Kunjumon (2007) GeneScape:- A web based tool for gene mapping.

Projects I have Completed so far:-

1. Computational Systems Biology Resources – Database of tools and resources for Systems Biology: Available at: http://www.macfast.org/csbr Technical Details: PostgreSQL based database, PERL, HTML, CSS and CGI based interface.

2. Gene ^ Scape – Software for multiple gene mapping: Web based gene mapping tool implemented for immediate mapping of large number of genes from microarray experiments. Available online at: http://bio.macfast.org/genescape Technical Details: CGI, PostgreSQL, HTML, PERL, PERLMagick/ImageMagick.

3. DDTdb – Drug, Disease & Target database: A database which provides information about disease, drugs and the possible drug targets developed for internal use of a Medical College. Technical Details: PERL, PostgreSQL, HTML, CSS and CGI technology.

4. Protein * Quest – Web based Cross-reference protein information resource: P*Q is a derived database from PDB an NCBI Taxonomy data to explore maximum information about the biological macromolecules from the organism of interest in easy steps. Available at: http://bio.macfast.org/proteinquest Technical Details: PERL, BIO-PERL, PostgreSQL, HTML, CSS and CGI

5. Hypothetical FANC Core Complex Pathway Based On Computational Sequence Analysis – An Integrated sequence and structural motif based Sequence Analysis Approach is implemented for reconstruction of the Pathway prediction. (Communicated for Publication)

6. MacPDB – MACFAST version of PDB Available at: http://bio.macfast.org/macpdb Technical Details: PERL, BIO-PERL, Postgres, HTML, CSS and CGI

7. PROTEIN VIZ – MACFAST PDB IMAGE BANK & Visualization tool Available at: http://bio.macfast.org/images Technical Details: Raster_3D and PERL Image Magick modules.

Skill Set :-

1. Strong Command in Python Programming.
2. Experienced in developing softwares, in Python, interacting with telecommunication switches.
3. Experienced in SOAP and Socket Programming.
4. Strong command in MySQL.
5. Strong command in PERL/PERL-CGI/SQL on LINUX/UNIX platform.

6. Professional experience in Database development using PgSQL / PLSQL for academic / research projects.

7. Involved in establishing a computational biology lab, Systems Bio Lab for MBCBG.

8. Installed a Bioinformatics Server at Systems Bio Lab, MACFAST – Affiliated to Mahatma Gandhi University

9. Initiated the formation of a creative and dynamic Bioinformatics group, MBCBG – MACFAST Biological and Computational Biology Group.

10. Currently managing local copies of largest bioinformatics database: Protein Data Bank, NCBI-nr / Taxonomy / Protein Database for academic activities.

11. Excellent working knowledge with important Bioinformatics software, database and prediction servers.

12. Familiar with Chemoinformatics, Molecular modeling, drug designing and systems biology approaches.

Modularity is one of the most interesting features of the trimeric autotransporter adhesins, and probably one of the most frustrating. As I wrote before, domain annotation is quite difficult, especially that these proteins can have often few thousands residues in length.

BadA, the major adhesin of Bartonella henselae, is probably the best known large TAA out there. Its sequence served us as a unofficial benchmark for domain annotation tool. Its head consist of three domains, one resembling head of YadA and two others which we claimed are similar to Hia head domains. The claim at the moment of starting this project wasn't supported very well - Evalues of HHpred alignments were around 1 (of course all less sensitive tools didn't see anything), but we knew they must be similar (because that two,three conserved residues were at exactly where we expected). Crystal structure of these two domains from BadA couldn't be solved directly, so we've attempted molecular replacement and that worked. On the picture above you can see three known head structures for TAAs, BadA (ours), Hia and YadA (full BadA head model in on the right) and arrangement of corresponding domains in all three proteins. The whole story and lots of pretty pictures (you must see EM figures) was published today yesterday in PLoS Pathogens (OA).

Today the story isn't so exciting as it was at the beginning. Currently HHpred easily finds domains from Hia and BadA similar with high probability - it's an advantage of bigger database size and more mediating sequences. But I'm still pretty happy about how it went - such projects build confidence in one's analysis skills.

Related articles by Zemanta

• Domain annotation in trimeric autotransporter adhesins

Erle Frayne Argonza

Good afternoon from Manila!

Controlling or regulating biopiracy is among the toughest tasks regarding intellectual property. Currently, there is an ongoing research by a corporate group to map the genome of Indigenous Peoples or IPs in the Philippines, the results of which will redound to improving the survival chances of the human species in general. The research is so surreptitious, however, that nobody knows who are the data gatherers and how is data collected.

That behavior is tantamount to biopiracy. Incidentally, the United Nations released a roadmap recently, which has direct implications on improving regulatory aspects of biopiracy. The news is contained below.

Enjoy your read.

UN roadmap paves way for curbing biopiracy

Hepeng Jia

13 June 2008 | EN | 中文

Yading Nature Reserve, China

USDA/pirateparrot

[BEIJING] Countries have agreed a roadmap for negotiating an agreement for the sharing of genetic resources, following a UN biodiversity conference.

The two-week conference in Bonn, Germany, ended last month (30 May) with renewed promises from countries to substantially reduce the rate of biodiversity loss by 2010.

The conference set out a roadmap for negotiations on access and benefit sharing (ABS) of genetic resources to help curb biopiracy. Delegates discussed and tentatively agreed a variety of options on elements for the future agreement that could be legally binding, non-binding or a combination of the two.

Participants hope to reach a global agreement on ABS at the next UN biodiversity conference in Nagoya, Japan, in 2010.

Xue Dayuan, director of the China Institute of Environment and Resources Protection for Minority Areas and a member of China's delegation to the conference, says the roadmap anchors the diverse debates over the issues and narrows down action to a set of suitable options that could be further explored.

But environmental groups have expressed scepticism, saying developed nations have failed to offer enough financial aid to developing countries for biodiversity protection.

Xue says previous efforts for biodiversity protection focused too much on funding from the developed world, and that countries should develop their economy first in order to fund their own, more sustainable, protection measures. 

"China, together with other fast-developing countries like India, could offer an exemplar in realising economic growth with relatively less destruction of biodiversity."

According to the Chinese Ministry of Environmental Protection, China had established 2,531 natural reserves by the end of 2007, covering more than 15 per cent of its land.

China's vice environment minister Wu Xiaoqing pledged a "strong commitment" at the conference to participating in global biodiversity protection.

Delegates at the conference also agreed action plans to expand nature reserves and launch the 'Life Web Initiative,' a network that aims to enhance partnerships to support the preserves. For example, an online database will help global funders match nature reserves to finance.

Germany pledged €500 million (US$775 million) over the next four years to aid global forest protection, particularly those in developing countries, and another €500 million each year after that.

Norway also announced plans to spend €600 million (US$936 million) on global forest conservation annually over the next three years.

Further information is at the BioBarCamp wiki and Deepak has a nice summary of the back-channels and other, similar events.

Congratulations to all involved - sounded like an excellent event.

The first is a letter advertising the PSI's MIAPE Guidelines for reporting the use of gel electrophoresis in proteomics. This letter is also accompanied by letters referring to the  MIAPE guidelines for Mass Spectrometry, Mass Spectrometry Informatics and protein modification data.

The second is a paper on the Minimum Information about a Biomedical or Biological Investigations (MIBBI) registry entitled Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.

The following press release describes this paper in more detail.

More than 20 grass-roots standardisation groups, led by scientists at the European Bioinformatics Institute (EMBL-EBI) and the Centre for Ecology & Hydrology (CEH), have combined forces to form the “Minimum Information about a Biomedical or Biological Investigation” (MIBBI) initiative. Their aim is to harmonise standards for high-throughput biology, and their methodology is described in a Commentary article, published today in the journal Nature Biotechnology.

Data standards are increasingly vital to scientific progress, as groups from around the world look to share their data and mine it more effectively. But the proliferation of projects to build “Minimum Information” checklists that describe experimental procedures was beginning to create problems. “There was no way of even finding all the current checklist projects without days of googling,” says the EMBL-EBI’s Chris Taylor, who shares first authorship of the paper with Dawn Field (CEH) and Susanna-Assunta Sansone (EMBL-EBI). “As a result, much of the great work that’s going into developing community standards was being overlooked, and different communities were at risk of developing mutually incompatible standards. MIBBI will help to prevent them from reinventing the wheel.

The MIBBI Portal already offers a one-stop shop for researchers, funders, journals and reviewers searching for a comprehensive list of minimum information checklists. The next step will be to build the MIBBI Foundry, which will bring together diverse communities to rationalise and streamline standardisation efforts. “Communities working together through MIBBI will produce non-overlapping minimal information modules,” says CEH’s Dawn Field. “The idea is that each checklist will fit neatly into a jigsaw, with each community being able to take the pieces that are relevant to them.” Some, such as checklists describing the nature of a biological sample used for an experiment, will be relevant to many communities, whereas others, such as standards for describing a flow cytometry experiment, may be developed and used by a subset of communities.

"MIBBI represents the first new effort taking the Open Biomedical Ontologies (OBO) as its role model", says Susanna-Assunta Sansone. “The MIBBI Portal operates in a manner analogous to OBO as an open information resource, while the MIBBI Foundry fosters collaborative development and integration of checklists into self-contained modules just like the OBO Foundry does for the ontologies".

There is a growing understanding of the value of such minimal information standards among biologists and an increased willingness to work together across disciplinary boundaries. The benefits include making experimental data more reproducible and allowing more powerful analyses over diverse sets of data. New checklist communities are encouraged to register with MIBBI and consider joining the MIBBI Foundry.

Mike presents the paper above.

Slides (PPT)
Paper (PDF)
Supplementary Info (PDF)

• Circos: This is a tool from Martin Krzywinski who described this as: Circos is a Perl application for the generation of publication-quality, circularly composited renditions of genomic data and related annotations. Circos is particularly suited for visualizing alignments, conservation and intra and inter-chromosomal relationships.

• Genome coverage simulator: This script simulates the manner in which a genome would be covered by the process of mapping or sequencing. In both cases, elements much smaller than the genome size are used to successively cover parts of the genome until (ideally) every area of the genome has been sampled. (Again from Martin Krzywinski)

• Genomic sequences in colour: visualization of genomic sequence assemblies. (And again from Martin Krzywinski)

• Integrative Genomics Viewer: "This new tool offers a Google Maps-like view of integrative genomic data..."

If you know any more, don't hesitate to share those with us.

is a set of tools aiming at connecting biomedical researchers together helping them to find informations about their previous works, collaborators and affiliations. The remarkable fact is that no information is required! Our intelligent software knows how to combine information already available on the web, specially on the Pubmed database, to provide meaningful information.

Now they have:

• Single Search: Based on co-authoring of Pubmed publications, find someone's collaborators, publications, affiliations.
• Fight: Who's got more publications? Whos got more collaborators? When did this fight reach its climax?
• Get in touch: Whos's between you and someone else?

Unique idea on the life science market. You should definitely check it out.

We have recently released a new biomedical image search engine we call YIF. You can access it at:

http://krauthammerlab.med.yale.edu/imagefinder

You can search the actual image content of over 34,000 Open Access articles from PubMed Central. We use OCR with different levels of image correction (article and corpus) for highly accurate image text extraction.

For more details about our algorithms, we have a paper in Bioinformatics titled “Yale Image Finder (YIF): a new search engine for retrieving biomedical images“.

[sourcecode language="python"]count += 1
mean += (x - mean) / count
[/sourcecode]

I remembered that I had come up with a similar thing for standard deviation back when I was developing clustering algorithms that could use that value. It uses a power sum average, where you track the power sum as an average (divide the power sum by n) in a similar way.

[sourcecode language="python"]n=0
mean=0
pwrSumAvg=0
stdDev=0

def update(x):
n += 1
mean += (x - mean) / n
pwrSumAvg += ( x * x - pwrSumAvg) / n
stdDev = sqrt( (pwrSumAvg - n * mean * mean) / (n - 1) )
[/sourcecode]

We get this using the running sum formula for standard deviation and essentially simplifying away the sum by removing n:

In this formula, the core values for the standard deviation is the sum of the squares minus the square of the sum, which we can recreate from the mean and power sum average, respectively:

p: power sum average
m: mean
n: elements

$latex s=\sqrt{\frac{pn - (mn)^2}{n(n-1)}}$
$latex s=\sqrt{\frac{pn - m^2n^2}{n(n-1)}}$
$latex s=\sqrt{\frac{n(p - nm^2)}{n(n - 1)}}$
$latex s=\sqrt{\frac{p - nm^2}{n - 1}}$

Sorry for all the math, but I wanted to make sure I got it right, and that I can prove this later. I've already had to reconstruct it once, so I don't want to do it again. Also, I just figured out how to embed $latex \LaTeX$ equations in WordPress, which is pretty damn cool.

Another neat thing to do with this has to do with manipulating centroids of vectors. That is, dealing with lists of values that correspond to the same datum. For instance, a row of data can be considered an n-dimensional vector, where each value in the row is a value along that dimension of the vector. The traditional data mining definition of a centroid usually deals with only the mean, but I like to refer to centroid clouds when adding in standard deviations, because rather than a point in the n-dimensional space, we refer to a diffuse cloud of probability when adding in the standard deviation value.

To find a centroid of two value vectors, it is a simple matter to apply the formulas above to create the mean and standard deviations of the centroid by applying them to each value along the vector. Combining a centroid with a value works the same way, where the centroid is a vector of mean and power sum averages, and the count appies to the entire centroid.

A neat part comes in when you try to combine two centroids. The equations and code from before become  more symmetrical than when only adding in one value at a time. A given value, $latex x$, can be generalized into a mean of $latex m=x$ and a count of $latex c=1$. By doing this, we can change our code to be:

[sourcecode language="python"]class value:
_init_(self, x=0):
self.n=1
self.mean=x
self.pwrSumAvg=x*x
self.stdDev=0

def merge(self, val):
self.mean = (val.mean*val.n + self.mean*self.n)
 / (self.n + val.n)
pwrSumAvg = ( val.pwrSumAvg * val.n + self.pwrSumAvg * self.n)
/ (self.n + val.n)
self.n += val.n
stdDev = sqrt( (pwrSumAvg - n * mean * mean) / (n - 1) )
[/sourcecode]

We lose our nice calculation of the mean, but we gain the ability to merge these two centroids together. Note that the calculation for the standard deviation is the same as before, but we change the way the power sum average and the mean are calculated.

Why go through all this trouble? You can now use this for data clustering and also to potentially visualize the centroid clouds with their data scattered through them. In bioinformatics, for example, data is often summarized at many levels. Gene expression probes are grouped into probe sets, and probe sets are often clustered or combined into functional units, or gene sets. Preserving standard deviation at these levels allows for greater clarity into the data.

There are twenty-three chapters called chromosomes.
Each chapter contains several thousand stories called genes.
Each story is made up of paragraphs called exons,
which are interrupted by advertisements called introns.
Each paragraph is made up of words called codons.
Each word is written in letters called bases.

There are 1 billion words in the human "book."

That's what I'm feeling about GeneWiki.

Last year as part of my comparative genomics project, I went through a very rough self guided crash course in bioinformatics. Having to navigate through competing and partially overlapping databases that use different sequence formats was a big frustration.

There is a whole lot of freely accessible genetic sequence data out there. And the best thing is that you do not need a heavy duty wet lab to do any work with it. It's all bits and bytes. All you need is a computer. You might need a heavy duty supercomputer to do complex high throughput similarity screening - but to do simple analysis and comparisons - a standard desktop should be plenty - as free online access to supercomputers that do the hard processing for you is also readily available.

The worst thing is it is very clogged up. Over catalogued and under-connected. For a web-savvy post-Y-gen-er like me - it is very annoying to find linkable content unlinked.

Wiki-technology to me seems and obvious way to bring everything together

The simple nature of wiki does make it easy for anyone to create links without any real programming language. If you can write an email, you can write a wiki.

The nature of multi-user editing also facilitates the creation of a wide network by allowing new links to be inserted or old links to be updated - and even future links can be  predicted, suggested or even demanded.

Content can also be layered and catalogued. Forums are in-built. Best of all external software can be developed to aggregate and process information contained in the wiki.

My biggest concern here isn't so much accuracy. One would expect GeneWiki to have at least the same level of peer review that Wikipedia does (which works rather well) if not more - such as verifying registration, or non-immediate publishing. I'd be more concerned about maintaining user interest and capacity to create cooperation to release what might otherwise be sensitive data in a free-to-access form.

Another part of me also cries that so much more is feasible with online technology. Why limit to just human genes? A database that provides referencing to homologues and orthologues in non-human species would be great. And are we also going to limit ourselves to outmodable concepts like "gene" and "species". Summary data on mammalian, reptilian or avian gene groups, their transcription factors, chromosomes, and even whole genomes now - the information is all there - a lot of it already online - it just needs to get connected.

Erle Frayne Argonza

Magandang araw! Good day!

From the Land of the Pharoahs comes a welcome news about genetically-modified crops. It has got to do with the commercialization of a Bt maize variety, a pattern that has already taken off in the Philippines.

The contentious issue here concerns the entry of Monsanto, the agri giant, in the control over the patent of the food variety. Let the Eqyptians deal with the matter themselves, but for now I am of the opinion that the corn variety is a good news altogether for our fellows in the great Land of the Pharoahs.

Let Isis make us dance with delight over this welcome news!

[22 July 2008, Quezon City, MetroManila. Thanks to the SciDev news summaries.]

================================================

Egypt approves commercialisation of first GM crop

Wagdy Sawahel

13 May 2008 | EN

Flickr/simpologist

[CAIRO] Egypt has approved the cultivation and commercialisation of a Bt maize variety, marking the first legal introduction of genetically modified (GM) crops into the country.

A report last month (16 April) from the US Department of Agriculture, noted that the Egyptian Ministry of Agriculture had "approved decisions made by the National Biosafety Committee and Seed Registration Committee to allow for commercialisation of a genetically modified Bt corn variety".

The endorsement was based on a series of field trials conducted between 2002 and 2007 for the variety MON 810, produced by biotechnology company Monsanto. Bt crops produce a toxin that guards against pests.

The variety to be distributed, Ajeeb-YG, is a cross between MON 810 and an Egyptian maize variety with resistance to three corn borer pests, developed by Monsanto scientists in South Africa — currently the only African country planting GM crops commercially.

Cairo-based company Fine Seeds International is partnering with Monsanto to distribute the variety in Egypt.

Ahmad Yaseen, an agricultural engineer at Fine Seeds, says the seeds will be available this month to farmers in ten Egyptian governorates.

Yaseen said the seeds will initially be imported from South Africa, but "starting from next year, Ajeeb-YG will be produced in Egypt".

Amr Farouk Abdelkhalik, an Egyptian biotechnologist and regional coordinator of the Agricultural Biotechnology Network in Africa, says the new variety "points to the potential agronomic and environmental benefits of Bt maize in Egyptian cropping systems and accordingly the reduction of the massive use of pesticides".

"We should develop our own GM plants using our genes and technology to protect small-scale farmers," he added.

Magdi Tawfik Abdelhamid, a plant biotechnologist at the National Research Centre in Cairo, expressed concerns about the long-term effects of the crop.

He says research on the issues surrounding GM crops "must be conducted in Egypt, and an in-depth assessment must be carried out to examine the impact of GM plants on small-scale farmers".

Egypt currently has no official biosafety legislation, though a regulatory framework exists. Hisham El-Shishtawy from the National Biosafety Committee secretariat told SciDev.Net that the existing framework follows the Cartagena Protocol on Biosafety and encompasses ministerial decrees regulating the registration of GM seeds. 

Hiring and Firing Scientists

Ultimately, funding agencies like the BBSRC get to "hire and fire" scientists and the laboratories they work in, based on their own selection and rejection criteria. Although they don't have the power to make established Scientists redundant, they can squeeze their funding. So, here is who I would be hiring and firing if, in my fantasy world, I was responsible for the budget:

You're Fired!

Just like Sir Alan Sugar on the UK television show The Apprentice, we should be "firing" weaker candidates and giving them less BBSRC funding. Here is who I would be firing:

1. Molecular Biology, 1953 to 2008, Rest In Peace At the top of my 'fired' list is molecular biology. Once upon a time, molecular biology was at the frontier of human knowledge, but its time has come and gone. While the techniques it has produced are invaluable and here to stay, PCR and blotting etc, the reductionist DNA mania mindset has been harmful to longer term advances in Biology and Biotechnology generally. We need more big-picture quantitative Science (call it systems biology if you like), not qualitative "study one gene or one protein" nonsense. It is time to take Molecular Biology into the back garden, strap on a blindfold, give it a last cigarette and put a bullet in its head. Molecular Biology, you are fired! (in more ways than one)
2. Unrepeatable experiments. This shouldn't be allowed, whether they are wet lab or dry lab experiments, it shouldn't be acceptable to publish unrepeatable experiments. How you actually stop people doing this is a challenging problem. The same goes for disposable software [2,3]. Biology and Biotechnology needs sustainable long-term infrastructure that is solid and dependable, not flaky custom half-baked experiments and solutions that come and go like teenage fashion fads. Dodgy experiments, you are fired.
3. Closed Access publishing. That £400 million pot of money has come directly from the hard earned wages in the British taxpayers pocket. The general public, having paid for all that research, should have access to ALL the primary data, not just the second-hand press releases and mainstream media reports. Primary data and journal publications shouldn't disappear behind some Scientific publishers pay-wall. Closed Access publishing, you are fired.

You're Hired!

When we've finished firing, we should be "hiring" and giving more BBSRC funding to...

1. Young scientists. I would say that wouldn't I? I am a young scientist. But seriously, todays young scientists, before and after their PhDs, are tomorrows leaders and Professors. Currently the BBSRC offers up to 10 David Phillips fellowships, which are a bit of a golden handshake for "World class early career scientists". These prestigious fellowships are obviously important, because they are over-subscribed with around twenty applicants for each single award available, according to Joshua Knowles. So why are there only ten awarded each year? If talented young scientists fail to get these fellowships, they will move abroad. How will Britain be competitive in Global Science in twenty or thirty years time if all its young Scientists have permanently moved abroad to pursue their careers? The BBSRC should be awarding hundreds not tens of these fellowships, to encourage home grown talent to develop their careers close to their families and friends in the UK. Ambitious young Scientist with fresh ideas? You're Hired.
2. BIO- and CHEM- informatics research and development. By which I mean cheminformatics, bioinformatics and whatever-o-informatics (this is a fantasy remember, in my own selfish self-interest). I'm not talking about the the kind of "my algorithm is 2% better / cheaper / faster than yours" but the kind of bold and innovative information management, that makes new biological and chemical insights into massive data sets. Informatics needs to be tightly integrated with wet lab experiments because "dry" laboratory informatics in silico can be pretty pointless when it gets divorced from biological problems in vivo and in vitro. Likewise, wet laboratory work has much to learn from dry lab insights. Better integrated informatics, with emphasis on the BIO and CHEM? You are hired.
3. The Web of Science. It is deeply ironic that the Web was invented by a Scientist, for use by Scientists in a laboratory, yet 18 years later, we're not even close to exploiting the full power of the Web to organise, share, manage, communicate and discuss scientific experiments and their results. Blogs, wikis, Web 2.0, Web Ontologies, Web services, Workflows on the Web, Web accessible citation and publication databases, let us boldly experiment with and build the future of the Web. As a founding father of the internet, Vint Cerf, puts it "It's easy to forget just how far the internet still has to go". In many ways the Web embodies what Science is all about, why are scientists so slow to adopt this (cough) "new" technology? The Web of Science? You are hired.
4. Databases and Ontologies. We don't need more of these (thank you very much), we need less but they need to be much better integrated, so that we can understand what the hell all the bloody data actually mean. Less is definitely more in this case, that sounds easy, but it is mind-bendingly hard and challenging problem which we need to work on and invest in. Peer-reviewed knowledge-bases and ontologies are big part of the solution, see the OBO Foundry for a leading example. More work on fewer, but much better, databases and ontologies is what I would fund. High quality digital knowledge-bases? You are hired.
5. Open Access Publishing. I don't care too much if it is green or gold. We need Open Access publishing NOW! (Bangs the table, Bob-Geldof-at-Live-Aid style). Well actually we needed Open Access fifty years ago before all these scientific publishers started taking control. Free access, via authors depositing their articles in PubMedCentral, is a good step forward, but ultimately, I want urgently need FULL Open Access so that unrestricted text-mining can take place on large public repositories. While the BBSRC encourages its funded scientists to publish in Open Access journals and self-archive papers in PubMedCentral, at the time of writing it does not currently enforce this enough, as far as I know. The BBSRC should follow the NIH, and actually enforce open access publishing. Open Access? You are hired.

There I think I'm done self-indulgently fantasising now, back to reality. It's a good job important decisions about science funding are taken by experienced people, rather than humble postdocs like me. Now where did I put those grant application forms? Of course, your mileage may vary, so if YOU controlled a £400 million Science budget, how would YOU spend the money?

References

1. John Denham MP has announced the appointment of Professor Douglas Kell as the next Chief Executive of the Biotechnology and Biological Sciences Research Council (BBSRC), Biochemist e-volution, Society news, 2008-07-08
2. Stella Veretnik, J. Lynn Fink and Philip E. Bourne [2008] Computational biology resources lack persistence and usability. PLoS Computational Biology, 4(7). pubmed/18636105, DOI:10.1371/journal.pcbi.1000136
3. Jonathan D. Wren [2008] URL decay in MEDLINE - a 4-year follow-up study. Bioinformatics 24(11): 1381-1385, DOI:10.1093/bioinformatics/btn127, pubmed/18413326
4. The Stranglers [1982] Gordon Golden Brown, texture like sun
5. Rage Against The Machine [1992] Bullet in the Head

CC-licensed picture of Queen Elizabeth's head on a £20 bank note from canonsnapper , picture of Alan Sugar's firing finger from jovike

This work is licensed under a

Creative Commons Attribution-Noncommercial-Share Alike 3.0 License.

- It was great to meet so many of my online friends for the first time. I've "known" some of you for years, others for a few months and really enjoyed catching up with you all in person.

- Thanks to all who contributed to the coverage in the ISMB 2008 FriendFeed room. It was quite an experiment and I think we were all pleasantly surprised by how well it worked out. Looks like this could lead to some form of semi-official live blogging next year too, which would be excellent.

Tomorrow takes me through Chicago to Manchester, UK, then north to a little place called Carlisle - which happens to be where I was born. It's not the most wired town in the world, so networking could be sporadic until I get back to Brissie on August 5th.

1. install alien
2. download EMBOSS RPM file: ftp://emboss.open-bio.org/pub/EMBOSS/contrib/RHEL/RPM/EMBOSS-5.0.0-1.i386.rpm
3. install libgd2-xpm
4. convert the .rpm to .deb
5. install the .deb

This blahg {wink to Dharam} is my experiment in self propelled expression.

I am hoping it will serve as an outlet for the ideas that have been percolating in my brain lately. You see, every day I participate in the culture, if not the activity of skateboarding, and I bro-down with skateboarders, as kind of a pseudo-savvy fan. You may ask, and it is a fair question, how or why have I become so entrenched in the past time of rolling around on wooden planks without ever risking my own pretty skin? Well, that's an easy one. My boyfriend, s.b., "skates". And when I say he "skates", I mean he skates like a shark swims. So it's totally fitting that he and his twin brother decided to open a skate shop with another skater friend a little more than year ago.

So for the past year or so, I have been working and hanging out in a skate shop. Kind of trippy, considering I spent the preceding eight and a half years pursuing a meandering but ultimately very technical degree in computational biology. Now days, relieved to have graduated from college, and newly baptised by fire into the world of parenting twins, I am discovering the joys of being stoked out by pure awesomeness on a daily basis in a place called No-Comply.

For instance, just yesterday, this blog was just kind of a joke I was making about how frustrating it can be to have a conversation with the boyfriend while he constantly assess the skateability of the landscape just over and beyond my shoulder. I wondered aloud how other so-called 'skate-widows' deal with this phenomenon. I laughed and said I would like to blahg about it, if only i could come up with a clever name for my page.

About a half a second later this dude William spits out, "the Professional Betty Chronicles", and I recognized my new muse immediately. William gets hella cool points for christening my new blog, not that he gives a rats ass about much, if anything, I'll ever write here. Still, it's pretty sick that he threw me a bone, and got this whole thing up and moving.
He kind of challenged me in that moment, as I admittedly whined about what it can sometimes feel like, being left at home while the boyfriend looses all track of time with a handful of scro's in some ditch i've heard way to much about. "Well, first of all, you should have your own thing going on, while he's out skating and doing his [thing]."

At first I thought, "Oh god! This dude is so right. I DO need my own thing. And, how embarrasing to be called out in front of my other bro's for not having any 'thing' to speak of." Then I thought, "Hold it right there. Let me just catch up with reality. I do have a 'thing'. As a matter of fact, I have several very sick and mega-awesome things popping off right about now.

In addition to raising two little kick ass baby girls, I rep a skateboard clothing line that is currently on course to save the planet (righteous!). I just scored a sweet pair of Ltd. Ed. Seiben high tops from Adidas (finally). And I'm organizing a pretty biggish skate demo/ fashion show at a Whole Foods here in Austin (stressful). Oh yeah---and my picture is in this month's Thrasher magazine (insane).

All at once I realize that I am, in fact, a Professional Skate Betty.

And it's a good thing, too. Since I'm pretty sure that in the biology lab, they frown on skirts as short as the one I'm wearing.