Wednesday, 6 November 2013

2012 Impact Factor Wars

It's that time of year again, when I post my list of selected impact factors. Controversial as impact factors are, they remain the main way in which journal quality is judged. The higher the impact factor, the more sought after the journal, as publishing in the top journals (especially Nature and Science) can make or break a scientist's career.

So how did the "competitors" do in this yearly war? I have selected a few journals that I find interesting personally, and are relevant to the research I am familiar with. This year, I decided to add some information about the open access policies of each journal, as I believe that more and more scientists might make their decision about where to publish based on the public availability of their work. Or maybe I am just hoping that they will! Here we go:

JournalImpact Factors 2012Impact Factors 20115-year Impact FactorsOpen Access?
Nature Biotechnology32.43823.26832.182NO
Cell31.95732.40334.366After 12 months
PLoS Biology12.69011.45213.447YES
Molecular Systems Biology11.3408.62612.392YES
PNAS USA9.7379.68110.583Public Access after 6 months
Nucleic Acids Research8.2787.4178.055YES
Metabolic Engineering6.8595.6146.696No, but supports OA option*
Bioinformatics5.3235.4686.911No, but supports OA option^
J of Proteome Research 5.0565.1135.223No, but supports OA option
PLoS Comput. Biology4.8675.2155.939YES
FEBS Journal4.2503.7903.600NO
PLoS ONE3.7304.0924.244YES
FEBS Letters3.5823.5383.478No, but supports OA option*
BMC Bioinformatics3.0242.7513.510YES
BMC Systems Biology2.9823.1483.300YES
J Mathematical Biology2.3662.9632.733No but supports OA option 
J Theoretical Biology2.3512.2082.496No, but supports OA option*
J Computational Biology1.5641.5461.722No, but supports OA option
IET Systems Biology1.5351.3491.783No, but supports OA option

The trend of "big journals getting bigger and small journals getting smaller" continued for another year. And it seems like almost every publishing house nowadays offers at least some open access option, if not having already fully embraced open access publishing.

Information about all journals can be accessed online on the ISI website, but a subscription is required. Accessing the website through a university IP address will usually do the trick.

* Elsevier journals that support Open Access publication of articles in subscription journals. 

^ Oxford University Press journals for which authors are given the option of paying a charge to make their paper OA (Oxford Open).

Have I left some interesting journals out of my table? Drop me a line and I will be happy to add any suggestions.

Monday, 4 November 2013

A vote for Enrico and for research against Alzheimer's Disease

The Geoffrey Beene Foundation Alzheimer’s Initiative is running their second online innovation challenge. The 2013 Geoffrey Beene Global NeuroDiscovery Challenge is a worldwide scientific competition to come up with new research ideas on the search for gender based differences In Alzheimer’s Disease. It is known that women develop Alzheimer's more often than men, but the underlying mechanisms are not known. If we would find out, we might be able to develop better drugs and therapies against this devastating disease. The winning submission will receive a $50,000 award for research.

My good colleague at the Luxembourg Centre for Systems Biomedicine (LCSB), Enrico Glaab, is not only participating in the challenge, but has made it into the final round of the competition, and has a good chance of winning it. This is me trying to muster the power of social networking to support Enrico: If you have a few seconds, please go to the Geoffrey Been Challenge website ( and show your support for Enrico Glaab. Just follow the links for "Scientific Community" or "Citizen Scientists" and vote for the project entitled: Male/Female Differences in Aging Brains in a Gene For Ubiquitin-Specific Peptidase 9 (USP9) as a Possible Cause for Increased Incidence of Alzheimer’s Disease in Older Women.

Everyone gets one vote every day until the 5th of November, so it would be great of you to come back and vote again, if you agree that Enrico deserves to win. 

 If you need further encouragement, here is the video summary that Enrico and his collaborators put together:

Tuesday, 16 April 2013


How would people react if Starbucks bought their favorite local coffee shop? Or if Halliburton bought Greenpeace? Or if the Rebel Alliance... allied itself with the Galactic Empire? Judging by the outburst of the online scientific community one would think all three happened at once when, on April 8th 2013, Mendeley and its popular research paper management and sharing program was sold to scientific publishing giant Elsevier, for an amount that is reported to be somewhere between 69 and 100 million dollars.

The backlash from the scientific community, especially from proponents of the Open Access movement who had largely adopted Mendeley as their preferred platform was immediate. A grassroots campaign was started on twitter under the hash tags #mendelete and #mendelsevier and has picked up a small following, pushing for researchers to abandon the application and delete all their data from Mendeley's databanks. Prominent blogs have weighed in on the matter (examples here and here). Good friend Duncan Hull has posted on his blog a step-by-step guide on how to delete your Mendeley account, which seems to be making the rounds on the blogosphere and the twitterverse.
Mendeley officials have gone on the offensive on social media (see in particular the comments of that Danah Boyd post), trying to convince their users and the community of their continuing good intentions and their commitment to the integrity of their product. While there have also been voices pointing out that Elsevier's move shows that even a publisher known for its corporate ugliness and greed is willing to expand its open data efforts and promote easier access to its content, disgruntled scientists are not buying it. This is partly because the glass between the scientific community and Elsevier had already been broken. Last year, another grassroots movement was started against Elsevier by mathematician Timothy Gowers to protest their support of SOPA and their business model. The protest has so far managed to convince more than 13,000 scientists to promise not to support Elsevier journals until they change their practices.

Users retain the right to chose their own platform. Even if Mendeley provides a good product, and proves eventually that their new affiliation will not fundamentally change their practices, the fact remains that they are now part of Elsevier and therefore, for many, on the wrong side of the fence. Scientists are free to abandon the software if they still have strong enough feelings about this.

Among them, myself. I pledged last year to avoid supporting Elsevier in any capacity if I can help it, and I feel that now this extends to Mendeley. Yesterday, I jumped on the bandwagon and #mendeleted, moving all my literature database to zotero.

Tuesday, 12 March 2013

Systems Biology Conferences 2013

Time for my annual post on systems biology conferences. This is becoming a bit of a tradition, after my corresponding posts in 2012 and 2011.

As always, I am not claiming that this list is comprehensive, but I do make an effort to add here all relevant conferences that come to my attention, and I expand it with newer information as it comes along. If you see any obvious, or not so obvious, omissions, please let me know and I will make sure to update the list.

 I followed Mike Hucka's advice and removed conferences organised by either WASET or WORLDCOMP (3 in total). Apparently, these are dubious and not even worth mentioning in passing.

I also added several conferences and workshops, courtesy of COMBINE's event calendar "Meetings relevant to Computational Biology", which I can only assume is maintained by Nicolas Le Novère

21 - 23 January 2013

24 - 25 February 2013

4 - 6 March 2013

4 - 6 March 2013

13 - 16 March 2013
Systems Biology: Networks (Cold Spring Harbor, NY, USA)

18 - 20 March 2013
9th International Symposium on Integrative Bioinformatics 2013 (Gatersleben, Germany)

19 - 22 March 2013
Computational Cell Biology: The Interplay between Models and Experimentation (Cold Spring Harbor, NY, USA)

20 - 22 March 2013

25 - 26 March 2013
7th International CellML Workshop (Waiheke Island, New Zealand)

7 - 10 April 2013
BioCuration 2013 (Cambridge, United Kingdom)

7 - 10 April 2013

9 - 11 April 2013
BioITWorld Conference and Expo 2013 (Boston, MA, USA)

14 - 15 April 2013
24 - 28 April 2013
14 - 16 May 2013

19 - 21 May 2013
CBSB13: From Computational Biophysics to Systems Biology (Norman, OK, USA)

20 - 23 May 2013

22-24 May 2013

5 - 7 June 2013
ICCS 2013: International Conference on Computational Science (Barcelona, Spain)

9 - 11 June 2013
Systems Biology of Stem Cells (Irvine, CA, USA)

10 - 12 June 2013

12 - 14 June 2013

13 - 14 June 2013

17 - 22 June 2013
PRIB-CIBB 2013: 8th IAPR International Conference on Pattern Recognition in Bioinformatics & 10th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (Nice, France)

23 - 27 June 2013

26 - 29 June 2013

25 - 28 July 2013

7 - 10 August 2013

14 - 16 August 2013

27 - 29 August 2013
NeuroInformatics 2013 (Stockholm, Sweden)

29 August - 4 September 2013

11 - 13 September 2013
ICCB 2013: 5th International Conference on Computational Bioengineering (Leuven, Belgium)

16 - 20 September 2013
Metabolic Pathway Analysis 2013 (Oxford, United Kingdom)

17 - 20 September 2013
COMBINE 2013: 4th Annual Forum (Paris, France)

23 - 25 September 2013

Monday, 14 May 2012

As much as you can

My favourite Cavafy poem is a slightly obscure one. It has always spoken to me on a deeply spiritual level.

As much as you can
by C. P. Cavafy

Even if you cannot shape your life as you want it,
at least try this
as much as you can; do not debase it
in excessive contact with the world,
in excessive movement and talk.
Do not debase it by taking it,
dragging it often and exposing it
to the daily folly
of relationships and associations,
until it becomes burdensome as an alien life.

 You can find the Greek original below.

'Οσο μπορείς

Κι αν δεν μπορείς να κάμεις την ζωή σου όπως την θέλεις,
τούτο προσπάθησε τουλάχιστον
όσο μπορείς: μην την εξευτελίζεις
μες στην πολλή συνάφεια του κόσμου,
μες στες πολλές κινήσεις κι ομιλίες.
Μην την εξευτελίζεις πηαίνοντάς την,
γυρίζοντας συχνά κ' εκθέτοντάς την
στων σχέσεων και των συναναστροφών
την καθημερινήν ανοησία,
ως που να γίνει σα μια ξένη φορτική.

Κωνσταντίνος Π. Καβάφης 

Sunday, 15 April 2012

More of Mr Miyagi's pearls of wisdom

 As I might have mentioned before in my posts, I am Greek. Today is Easter Saturday for the Greek (and generally, Eastern) Orthodox Church, which includes the Easter Vigil, the most important service of the year, and an event every Greek, and I mean everyone irrespective of religiousness, strength of faith, or even religion sometimes, attends. This is often hard to explain to non-Orthodox people, but attending mass for Easter, is not a religious event in our culture; it is more of a social event. Even if you have no interest in the spiritual side of things and you could not care less for celebrating the resurrection of Jesus Christ, you still go to church for at least an hour or so, because it is the thing to do, and it kicks off the festivities for Easter Sunday. And trust me when I say, you definitely want to kick off the festivities for Easter Sunday.

Small Easter feast.
Except, I am sitting at home writing this post instead of going to church, as every other Greek person would do. The truth is, I don't know any Greeks in Seattle and, as I have just explained, this is supposed to be a social event (at least for me). There doesn't seem to be a point in making the effort when there is no prospect of social interaction, is there? 

I am therefore skipping the visit to the beautiful Greek Orthodox church of Saint Demetrios in Seattle. It's moments like these, on traditional holidays steeped with family memories, that the distance from family and friends weighs one down the most. What is a man supposed to do when he finds himself alone on Easter Sunday (with every single one of his alternative plans having fallen through, no less)?

Why, turn to the wisdom of Mr Miyagi of course! Here it is, from the sequel to Karate Kid, the sequel to my original post of Mr Miyagi's wise words. Enjoy:

"For person with no forgiveness in heart, living even worse punishment than death."

"When you feel life out of focus, always return to basic of life: breathing. No breath, no life."

"This [points to heart] say you brave, this [points to medal] say you lucky."

"Daniel-san, never put passion before principal. Even if win, you lose."

"Daniel-san, nobody perfect."

"This rules to karate. Rule number 1: Karate for defense only. Rule number 2: First, learn rule number 1."

"Sometime what heart know, head forget."

"Never stop war by taking part in one."

"Best way to avoid punch, no be there."

"Lie become truth only if person want to believe it."

Not surprisingly, Mr Miyagi has words to comfort any soul, even some pertaining to my current mood. And, watching Karate Kid II, it is easy to see where Mr Miyagi gets his propensity for wise one-liners. When Miyagi's father, now near death, sees his son for the first time in more than 50 years, he has this gem to offer:

"If I am dreaming, let me never awake. If I am awake, let me never sleep."

Not only that, but it is clear that the Miyagi family wisdom is rubbing off on Daniel-san as well. As Mr Miyagi is despairing over the death of his father, guilt-ridden over his long absence and his inability to change the fate of his village and his loved ones, Daniel-san succeeds in comforting him with this little speech:

"When my father died, I spent a lot of time thinking I wasn't such a great son. Like maybe I could have listened a little more, spent some more time with him, together. I felt so guilty, like he did everything for me, and I didn't do anything for him. Then one day I realized, I did the greatest thing for him before he died. I was there with him, and I held his hand, and I said goodbye."

Karate Kid II is a decent film; unfortunately not as strong as the first one because of a weaker script and slower pacing, but with better character development, and with deep narratives about the meaning of family and tradition. Overall, a good choice for a night like this one.

Stay tuned for the next installment!

Wednesday, 28 March 2012

What's in a name?

Voilà! In view, a humble vaudevillian veteran, cast vicariously as both victim and villain by the vicissitudes of Fate. This visage, no mere veneer of vanity, is a vestige of the vox populi, now vacant, vanished. However, this valorous visitation of a by-gone vexation, stands vivified and has vowed to vanquish these venal and virulent vermin vanguarding vice and vouchsafing the violently vicious and voracious violation of volition. The only verdict is vengeance; a vendetta, held as a votive, not in vain, for the value and veracity of such shall one day vindicate the vigilant and the virtuous. Verily, this vichyssoise of verbiage veers most verbose, so let me simply add that it is my very good honour to meet you and you may call me V.

Hi. My name is also V.

It's not really. That's not even a real name! My name is Vangelis. Unless you actually check my ID, which says that my name is Evangelos. It is about at this point that people either think I am pulling their leg, or just give up completely. 

But no more! It is time to once and for all answer all questions regarding my name! Dispel all confusion, bring light to the darkness! But first, some background. My proper name is Evangelos, but a very common nickname for "Evangelos" is "Vangelis". Greek is funny like that with names, just take my word for it. If this is not short enough for you, you can also go with Vangos, another common nickname in Greek. 

The Annunciation, by El Greco. See what I did there?
My name means messenger of good news, or good angel if you will, since angel (angelos) means messenger. It is a reference to Lady Day, otherwise known as the Annunciation of the Blessed Virgin Mary: the announcement by archangel Gabriel to Mary that she would become the mother of Jesus. By parthenogenesis. If you are not Christian, or you were not paying attention in Sunday School, you are probably really confused by this point, but roll with the punches here, it gets easier. The Annunciation in Greek is called Evangelism (literally, "spreading of good news"), thus the derivation of my name.

Generally speaking, I never really minded which name people use, "Evangelos" or "Vangelis". I am also not particularly bothered by pronunciation: even though in modern Greek the g is hard, I really don't care if people use a soft g. English is full of Greek words, and there are widely accepted rules on how these words are transliterated. As I said, angel is a Greek word, and it is pronounced with a soft g, so why not my name?

In the end though, I need to have a preference. For anything that an ID would be required (banking, travelling, dealings with the government), it is just convenient to use my full name. Once upon a time, I made the decision to stay with the full version for academic and research purposes as well, and now that I have a published record I am stuck with "Evangelos", for better or worse. "Vangelis" is more familiar, so I've always gone with that for social interactions. It wasn't long before people started looking for shortcuts though, and, especially in basketball circles, I became known simply as V. At some point I decided that embracing it was much easier than fighting it. After all, "V" is a pretty cool nickname. There are worst things a man can be called. Trust me, I've been there.

For bonus points, you can even 
learn to spell my name correctly!
So if you need to call me anything, go with V or Vangelis, both are perfectly fine with me. And now for the difficult part: how do I explain in a written piece what the correct pronunciation of my name is? Obviously, I don't need to explain "V", but how about "Vangelis"?

As is often the case, Google has the answer. Google Translate recently added word pronunciation for Greek, including most common names. All you have to do is follow this link, then click on "Listen" on the right. Problem solved. 

Hi, my name is Vangelis, but you can call me V. Very nice to meet you.