Archive for January, 2013


I find figshare a great idea for using and sharing results and data that do not fit the “system”. These can be of great use by others. I use figshare and have already posted some forgotten files from the past (see These files are results that were not published in a journal before. I discovered full papers that were included in project reports, conference contributions that were not published, nice posters and presentations that can be useful to others preparing teaching material. These results and scientific products are not leftovers or rubbish of lower quality. They just did not fit in some publications prepared.

Let me use an example. My PhD (1995) produced 4 research papers and several conference contributions. I extracted results and prepared papers that the journals usually publish: target oriented, focused and brief. A whole part of the PhD research output was never published. Why? If it would be merged with other results it would produce too heavy and loaded manuscripts. Alone, these results would be too isolated and specific. The central idea of the PhD was already published as a conclusion of other papers. These results do not fit the “system”, thus they cannot produce something that the standard journals would prefer. However, these are nice results. based on good sampling and analysis techniques, they give clear and sound conclusions. I was always thinking of publishing them, but I never had time or courage to find a way to produce a “compatible” manuscript. After discovering figshare, I just put the results together and prepared a manuscript that explains why and how this research is done, presents all data in long boring tables and lists the major conclusions of the research. This was done in a few hours and the manuscript had a place on the net, a DOI and a dissemination mechanism that would never enjoy if published in any other mainstream journal. I am as proud for this paper as much as I am for the ones published in mainstream journals.

I encourage colleagues to dig in their computers and publish all their results through figshare. Publish posters and presentations from conferences. Publish initial manuscripts that you have submitted and then had to change severely to satisfy reviewers and editors. Publish the theoretical background of your work or some thoughts you may have about your field. Use your raw data to connect with others and why not prepare joint new analysis!

figshare can become a teaching tool as well. I encourage students to publish their essays, posters, reviews and other things they prepare for courses. They can also publish initial results from their diploma or MSc theses. This will give them an initial publishing experience and the satisfaction that their work is read, used and cited.

Also read: Figshare – A New Way to Share Your Research

by Ben Mudrak (

In today’s scientific realm, a large amount of the research being conducted is never published in any way. Unpublished research could include negative data, unexplained observations, or simply data that are not deemed “interesting” enough to any journal. Given the continued reduction in research funding in many areas around the world, should investigators waste their time on research that may have already been done (but not published)? What if researchers could easily publish data that would otherwise be simply left alone and never shared? And what if those data could be accessed, reused, and cited by others?

Figshare offers an effective solution to the issue of the incredible amounts of unpublished data sitting on researchers’ computers around the world. At figshare, researchers can sign up for free accounts and upload data in any file format (common uploads include figures, posters, full manuscripts, raw data sets, and videos). All data are published immediately under a Creative Commons license, allowing for instantaneous discovery by anyone around the world. Perhaps more importantly, each contribution is given its own digital object identifier (DOI), a unique identifying code that provides a permanent link to the file in question. DOIs are found with increasing frequency in reference lists, meaning that items on figshare can be cited easily in peer-reviewed literature if desired.

The next time you have data to share but do not want to expend the effort of writing a manuscript and fighting through the publication process, consider alternative options like figshare. Remember that other scientists may take your smaller contribution and use it for something much greater, and they’ll be able to cite you if they do!



Παναγούσης Χ, Τριγκίδου Α, 2013Image

Παρουσίαση στο πλαίσιο του μαθήματος “Πληθυσμιακή και Εξελικτική Γενετική” του ΜΠΣ του Τμήματος Δασολογίας & Διαχείρισης Περιβαλλοντος & Φυσικών Πόρων του ΔΠΘ.

Click to access cebbceb7ceb8ceb1cf81ceb3cebfcf83-cf83cf80cebfcf81cf89cebd.pdf

Fagaceae Genomics Web

Posted: 27/01/2013 by arilab in General
Tags: , , ,

The Fagaceae Genomics Web is the web front-end for a multi-institutional NSF-funded project dedicated to the development of genomic resources for the Fagaceae. This site disseminates data and analyses by providing genetic and physical maps, transcriptomic data, functional analyses, a listing of available resources and data mining tools. Additionally, background and progress information is available.


Ιωαννίδου Μ, Μιχαήλ Μ, 2013Image

Παρουσίαση στο πλαίσιο του μαθήματος “Πληθυσμιακή και Εξελικτική Γενετική” του ΜΠΣ του Τμήματος Δασολογίας & Διαχείρισης Περιβαλλοντος & Φυσικών Πόρων του ΔΠΘ

Click to access cebcceb5ceb9cf89cf84ceb9cebaceb7-ceb5cebacf84cf81cebfcf80ceb7-cf84ceb5cebbceb9cebacebf.pdf

ImageΒιδάκης Κ, Στόικου Μ, 2013

Παρουσίαση στο πλαίσιο του μαθήματος “Πληθυσμιακή και Εξελικτική Γενετική” του ΜΠΣ του Τμήματος Δασολογίας & Διαχείρισης Περιβαλλοντος & Φυσικών Πόρων του ΔΠΘ

Click to access cf83cf84cebfcf87ceb5cf85cebcceadcebdceb7-ceb1cebdceb1cf80ceb1cf81ceb1ceb3cf89ceb3ceae-2013.pdf

Poster presented during the Systematics Conference 2008, Göttingen, Germany. Download from figshare:


The taxonomic classification of European beech has been lately subject of long scientific discussions. Genetic variation at AFLPs, chloroplast microsatellites and variation in leaf morphology have been analysed in four populations of F. sylvatica in the greek Rodopi Mountains. The analysis of morphological traits reveals differences between the western and the eastern part of the Rodopi Mountains. Moreover, high levels of haplotype diversity were observed within populations, while in central and western Europe no variation at cpDNA markers was detected. Clinal variation patterns have occurred at both morphological and molecular markers, with the variation increasing from the west to the east. Differentiation among populations was found, as expected, stronger at maternaly inherited cpDNA. The results obtained in this study, can be explained either by considering the greek Rodopi an introgression zone between subspecies sylvatica and subspecies orientalis or by the existance of a main glacial refugial area. These scenarios are not mutually exclusive.

Hardy Weinberg Problems

Posted: 26/01/2013 by arilab in General
Tags: ,

Nice tutorial about HW law and problems based on this law.

Επειδή στις εξετάσεις έκλαψαν μάνες με το θέμα του Hardy-Weiberg, δείτε πόσο απλό ήταν τελικά!

journal.pgen.1003234.g003Read in PLOS Genetics

Coring a tree_Dan GriffinPromitheus tree, the oldest individual on earth

After a nearly 5,000-year vigil upon a Nevada mountaintop, an ancient tree now finds its home in the UA Laboratory of Tree-Ring Research. A member of the long-lived Bristlecone pine species, the tree called Prometheus is the oldest individual ever known to have lived. Its age was not accurately known until a few years ago.

Is climate change happening?

Posted: 24/01/2013 by arilab in General

Is climate change happening?

Alternative scenarions for global change

A useful quick guide for R

Posted: 23/01/2013 by arilab in General
Tags: , ,

The fate of a presentation: by PhD comics

Brilliant. This will boost the morale of all of you presenting today in the graduate class…

By PhD comics

Το mRNA προκύπτει από το DNA αρχικά και έχει να κάνει με τη μεταγραφή των πληροφοριών του (m=metagrafi)

Posted: 21/01/2013 by arilab in General

by Theodoros Mouratidis, Seraphim Hatziskakis, Nicolas George Eliades, Ioannis Tsiripidis, Reiner Finkeldey, Aristotelis C. Papageorgiou

This study aims at the description of beech postglacial movement within a mountain. The selected mountain Paggeo is isolated, while beech forms an altitudinal continuum for more than 1000m. Previous genetic studies have indicated the possible presence of a glacial refugium in the broader region. Seven sub-populations were sampled, in order to describe the structure of this refugial population. Three cpDNA microsatellite primer pairs were used. A high variety of haplotypes and a significant differentiation among sub-populations was detected. The results indicate that besides the refugial lineage on the north side of the mountain, two additional beech lineages have arrived from other refugia and occupied specific locations.

Poster presented at the International Conference “Hot Spots of Ancient and Present genetic Diversity”, 17 – 20 June 2009, Sofia Bulgaria.

Uploaded in figshare

(Submitted on 16 Jan 2013)

Much has been said about the increasing bureaucracy in science, stifling innovation, hampering the creativity of researchers and incentivizing misconduct, even outright fraud. Many anecdotes have been recounted, observations described and conclusions drawn about the negative impact of impact assessment on scientists and science. However, few of these accounts have drawn their conclusions from data, and those that have typically relied on a few studies. In this review, we present the most recent and pertinent data on the consequences that our current scholarly communication system has had on various measures of scientific quality (such as utility/citations, methodological soundness, expert ratings and retractions). These data confirm previous suspicions: using journal rank as an assessment tool is bad scientific practice. Moreover, the data lead us to argue that any journal rank (not only the currently-favored Impact Factor) would have this negative impact. Therefore, we suggest that abandoning journals altogether, in favor of a library-based scholarly communication system, will ultimately be necessary. This new system will use modern information technology to vastly improve the filter, sort and discovery function of the current journal system.

Comments: 5244 words, 120 references, one figure, one table and one supplemental figure (the raw data for table 1)
Subjects: Digital Libraries (cs.DL); Physics and Society (physics.soc-ph); Other Statistics (stat.OT)
Cite as: arXiv:1301.3748 [cs.DL]

(or arXiv:1301.3748v1 [cs.DL] for this version)



Posted: 20/01/2013 by arilab in Opinions

A nice small survey showing that we can upload and maintain our own versions of our published papers without braking the law.


Edit: As was pointed out in the comments, you can find self-archiving info for most journals at [h/t Laurent]

I have been a bit frustrated about scientific publishing, as you might have been able to tell if you read some of my earlierposts on open access in academia.  I posted earlier this week about Aaron Swartz and the legal predicament in which he found himself when he downloaded huge numbers of scientific papers.  I was frustrated at the lack of access that most people experience to academic publishing, but didn’t want to resort to breaking the law to remedy the situation.  However, a certain amount of that frustration could have been relieved had I just taken the time to figure out where the boundaries lie in the copyright documents that I sign when I publish papers.  I decided to have a look to see how many of my rights remain…

View original post 1,188 more words

the impact factor game

Posted: 19/01/2013 by arilab in General, Opinions

A critical view on impact factor as a sole measure of scientific quality. From PLOS blog…

Different ways of assessing papers tell you different things. Isn’t it better to have a diversity of measures rather than rely on a single, over-used and over-interpreted metric?

Open access explained

Posted: 19/01/2013 by arilab in General, Opinions

by PhD comics

Βελούχι από το Μαυρίλλο

Posted: 18/01/2013 by arilab in General

Βελούχι από το Μαυρίλλο

A nice view from this great mountain…