Phil Jones holds himself defensively, his arms crossed tightly in front of his chest as if shielding himself from attack. Little wonder: Jones has spent the past three months being vilified for his central role in what is now called ‘climategate’ (sic, arch).

and

“I don’t think we should be taking much notice of what’s on blogs because they seem to be hijacking the peer-review process.”

and concluding

It is now essential for climate researchers to stand up for their science, he says. “[I'd] like to see the climate science community supporting the climate science more. Lots of them are trying but they’re being drowned out.”

Some points:

1- He was and still is vilified, not because we (the public) think he is a villain, but his actions made him one (in the public’s eye). As a scientist, I understand the process and understand what he might be going through, what takes us to the next point …

2- Open your data, let it be scrutinized, dissected, explored. I’m not the greatest supporter of Open Science/Research, but if you’re feeling this way, open up, show the methods, don’t go crawling into a cocoon with you fellow vil … climate scientists. I don’t trust bloggers too (including myself) but I have seen some wonderful science or science related material in blogs and by bloggers. Send us the data and we will publish some peer reviewed climate research. Want to bet?

3- You can only abstract from the concluding phrase the fact that climate researchers need is more support (go figure!) and maybe to become a tighter group. Summarizing, they need more money.

This only reminds me more and more about some scientists websites that first mention their awards, prizes and interviews before any scientific content. You know who you are.

We will come to your lab with a TV crew, a interior designer and a high level authority in your field of research and we are going to stop to nothing to make your lab the best research space on earth. You won’t need to pay a dime for the makeover/walkover/takeover, on the contrary we will give you $5000 for consumables and a new PCR machine (if applicable).

I’m already looking for sponsors and channels, and if you want your lab o qualify for the walkover, send me a picture.

Yesterday somebody posted at HN, an article about open access to publications: Open Access to Scientific Publications The good, the bad, and the ugly. It’s a so-so read, but gives some information on the current scenario of open and closed access publishers. But what really caught my eye (thanks initially to a comment on HN) is this passage:

But how much are authors ready to pay to publish an article? A few hundred dollars? The most prominent Open Access publisher, the Public Library of Science (PLOS), is a nonprofit organization that has received several million dollars in donations. Yet it charges between $1,350 and $2,900 per paper, depending on the journal.d In fact, many in the profession estimate that to be sustainable, the author-pay model will need to charge up to $5,000–$8,000 per publication.

There are seven journals on PLoS, with an average publication fee of $2125. In average each journal publishes around 310 papers per year [I took Computational Biology (388 pubs) and Neglected Tropical Diseases (236 pubs) for 2009]. With the fees and number of publications in each journal being quite similar, that the total revenue for one year is around $4,000,000. From the article we have the idea that these fees should be (and will be) higher in the future, from double to quadruple of what we see now. This, of course, will double or quadruple the revenue. The comment on HN that made me read the article is this:

WTF? $8000 per article would pay for each article to have its own EC2 instance for >10 years, including bandwidth costs. Something not right there…

Indeed, something is not right here. With the costs of hardware infrastructure going down every day, nothing justifies these fees (or a bit of them) to “host it [publication] on a server that is accessible around the clock.” I really like PLoS, but in almost no time is becoming another publishing company. I don’t know if PLoS financial books are open, and if not, don’t you think they should be open too?

Ok, let me explain then. But before that, a disclaimer: I own Windows 95, 98, XP and Vista, and this represents only my opinion, not the opinion of my employers, co-workers and family.

And why is MSFT more detrimental to Science than anything else? It’s simple: the openness of their system. Maybe open is not the right word, transparency might better to explain it. As MSFT has the leadership on the OS market, vendors tend to attach their products (in this case laboratory equipments, analysis software, etc) to the OS. And how that is bad? Because when it works, it works fine, but when it doesn’t work, it’s a nightmare. Software registry that fails, legacy software that doesn’t work even when compatibility mode, no control over installation protocols. Most of the time you also don’t have free/open source tools that help you solver the problem.

After all this, you have to throw in license costs, expensive certification for sys admin in order to manage the machines, time wasted troubleshooting applications, OS, updates, etc. All of this drag all the way up and all the way down the Scientific ladder, increasing costs all over the board, and man-months of work that could be used in different aspects of research.

I’m not advocating either OS X, Linux, BSD or Solaris, I’m just saying that these systems are easier to use, cheaper (maybe not OS X) and provide a better experience to the users. And I’m not advocating that “regular” users should migrate to these systems, I’m just saying that if you are cost conscious scientist, they are a better alternative. Maybe if every university had an introduction to Linux/Unix course, maybe we would be able to cut costs every where, have better scientists and work more efficiently with our computers.

Do you think universities would have a course like this? I don’t think so, but it would be nice to see.

(I’m really behind on my promise to post 365 in 365, four to keep the average on 1, three to go after this one)

In mid-October I went to Brazil, first to attend the 2009 X-Meeting in Angra dos Reis and for a first vacation period since 2005. When I moved to Canada, I wasn’t able to bring all the scientific literature I had amassed over the years, mostly stuff about frogs, evolution and phylogenetics. Nowadays printed or copied papers and out-of-date, PDF is the new in, so I decided to throw away most of the things I would be able to recover online later, but still keep some copies of rare stuff and original copies of papers.

Some of the original copies I saved where from the 50’s, 60’s and 70’s, and some of these contained the stamp that they belonged to Dr Crodowaldo Pavan (you can know more about his distinguished career on his Wikipedia entry). Dr Pavan died early in 2009, so these papers with his stamp now have more than its scientific merits, they have some sentimental value (for me at least). I got them when he was cleaning his office at the Biosciences Institute at USP, where he worked good part of his life.

I never had a lot of personal interaction with Dr Pavan, but I always read and learned about his work. But the strongest impact that I have from one of his presentations ( I think it was a round table) was in fact what I heard after it: Dr Pavan was an old fool and shouldn’t be invited to any other conference because his ideas were idiotic. This happened at one of the Brazilian Meeting of Genetics (mid/late 90’s), the most important genetics conference in Brazil, organized by the society that Dr Pavan helped creating and managing.

Don’t be surprised, that’s the way Brazil and Brazilians really treat the ones that accomplished something, the ones the opened the paths. Very typical, but I’m quite sure that Dr Pavan’s obituary(ies) was(ere) poetic and well-written, praising (deservedly) his career and work. I guess it was to late then to pay some respect while he was still alive.

A quick challenge, mainly because I’m lazy as hell to do these kind of things: if you advocate Open Science or Open Access, please leave a comment with your list of publications on PubMed or your own website/repository.

The paper of this week touches a subject that I have been involved in the past: sequence simulation. INDELible, by Fletcher and Yang, is a program that is capable of simulating both DNA and amino acid sequences, and it seems to be the complete package to do so. It contains several substitution models and it can even simulate codon substitutions.

As the article mentions, the closest comparison to INDELible is DAWG, developed by Reed Cartwright, that seems to be faster. DAWG is a nice program and generates good simulations and has a very well designed code with strong models and quite reliable results. And that’s what you want on a simulation program. You really want is a good implementation of the amino acid/nucleotide substitution pattern and a good model of indel simulation. It seems that INDELible has all of that, based on the publication (I haven’t tested yet).

Sequence simulation is usually a fringe field (if there is such field) in bioinformatics and phylogenetics/evolution. We usually forget that the best alignment and phylogenetic reconstruction is basically the best estimate with the methods we have. There’s no way to prove or test different alignment methods and programs without a solid in silico simulation or a hand curated alignment. And I think the simulation is better and can generate much more input than meticulously curating a sequence alignment. Also, there is the need to test for phylogenetic reconstruction methods, and nothing better than good simulation packages that can mimic perfectly evolutionary phenomena.

I’m really looking forward to test INDELible and see what it is capable of. The only complaint that I have is that it uses yet another markup language as the control file. Why not use YAML or some other markup language? That would make usage more straightforward, but at least the authors provided a tutorial section on their website.

Fletcher, W., & Yang, Z. (2009). INDELible: A Flexible Simulator of Biological Sequence Evolution Molecular Biology and Evolution, 26 (8), 1879-1888 DOI: 10.1093/molbev/msp098

This is a new series here at the Blind.Scientist headquarters. My team and I will try to feature one scientific publication a week, it might not be hot from the presses or it might not be only about biology and/or bioinformatics. We (my team and I) will try to be eclectic and cover different areas. Alternatively you will find these posts on Research Blogging too.

This week we start with a recent publication that appeared on PLoS Computational Biology, titled A Quick Guide to Organizing Computational Biology Projects, by William Stafford Noble (reference and link are on the bottom of the post). It’s a well written publication, that falls under the Education scope of this PLoS, understandably by its title. Mainly it tries to teach some tips and tricks on how to organize your files in a directories (folders) and subdirectories (subfolders). Believe me, all advices in the paper are sound, but only if you know nothing about computers or you’re just starting using them.

Apparently the author focused on newcomers to the bioinformatics field, mainly biologists learning the skills and not computer scientists making the jump. In my opinion this is the wrong focus. Hardly these days you find some summer student, even the ones that go directly to the wet-lab, with no computer skills. The kids come to the lab these days knowing how to program, or at least with good notion of scripting and they have used computers basically their whole lives. This paper should have been focused on old timers, like myself, and go deeper into the subject. We, old timers, already have a lot of baggage and a lot of bad habits on daily work, and we read this with a scorn on our faces. We read this and say (or think) “why do I need to do things this way?”. We need this kind of advice, but I don’t know if this is something that should be granted a scientific publication. Any computer scientist fresh from graduation and starting at some multi-national company would laugh at this and maybe think why do biologists need to put this on paper, or PDF files and even have it on a scientific journal.

Most of the tips presented in the paper, at least for me, are a mere declaration of what common sense should be applied to manage digital files. I’ve been in the trenches, I suffered with my own disorganization, and I learned from it and from a myriad of blogs and websites devoted to software design and development. These references not only give you a perspective on what the real world of software and project development looks like (or should be) but they teach you how to survive in the jungle of “databases” stored in Excel files.

It’s really sad that in 2009 we need to read these kind of papers, or even a paper with this subject is published. I know dozens of bioinformaticians that would be able write an identical or better publication, but decide not to write it because this is basically common sense, or maybe they wrote the same thing in their blog. Some of them will scratch their heads and think this was a sure thing, an easy publication where they just needed to write about what they do daily. Just browse some Bioinformatics and Computational Biology blogs and you will get more and better advice than you get from PLoS and this paper.

We need more papers like my friend Jan Aerts and his colleague published on Ruby and Bioinformatics. That’s a paper that makes you want more and gives you a primer to do more. It’s not a paper about common sense. But, hey, not everyone has it.

Noble, W. (2009). A Quick Guide to Organizing Computational Biology Projects PLoS Computational Biology, 5 (7) DOI: 10.1371/journal.pcbi.1000424