May23

A wonderful example of Open Science

In: own data • Tags: , , , , , ,

In our new lab here in Regensburg, we are currently re-establishing the method of confocal microscopy. To start with, we used the fly lines which show a defect in the temporal structure of their spontaneous behavior (a project of one of our graduate students). this fly line uses two transgenic constructs (c105 and c232) to drive expression in specified neurons in the fly brain, i.e., the merged expression patterns of c105 and c232. In this case, the transgenes drive expression of green fluorescent protein (GFP). Around 7pm on the evening right after the dissections and the confocal imaging, I reconstructed the image stacks as a 3D video of the expression pattern in the brain and uploaded it to my YouTube channel:

Only an hour or so after I posted the video, Douglas Armstrong sent me an email:

Are you sure c232 is in there? most of its neurons are missing, looks like c105 though

Cheers,

D

https://flytrap.inf.ed.ac.uk/html/enhancer/c105/
https://www.fly-trap.org/html/enhancer/c232/

And sure enough, upon closer inspection and comparison with the data displayed in the two links Douglas sent along, it seemed as if only the c105 expression pattern is visible. So as we are establishing the technique here, we need to pay extra attention to threshold effects, preparation and the imaging settings at the two different confocal microscopes we have here. In addition, we need to image flies with the individual drivers, to make sure nothing is wrong with the fly strain that should contain both drivers.

All of these things are important and we probably would have not paid special attention to them as we thought the double driver line was simply a good line to start optimizing the method.

In other words, if I had never published the data online right after we got them, I probably might have spent quite some time not being aware of potential problems with this fly strain.

Thanks so much, Douglas!

Posted on May 23, 2013 at 10:54 2 Comments
May21

PostDoc opportunity in our lab now advertized

In: news • Tags: , ,

I have now posted the job ads for the PostDoc position in our lab at Nature, Science, SfN and FENS. If you’re interested in the neurobiology of spontaneous behavior and are into open science, have a look at the job ad and send your application to me at bjoern.brembs@ur.de.

Below is the text of the advertisement:

Universität Regensburg with its over 20,000 students is an innovative and interdisciplinary working university which provides a broad variety of research projects and disciplines for German and foreign students. The laboratory of Prof. Björn Brembs (see https://lab.brembs.net) in the Institute of Zoology at Universität Regensburg, Germany, is offering a position as

Postdoctoral fellow (m/f) – neurobiology of spontaneous behavior and operant learning in Drosophila

The full time position is initially limited to two years (with possible extension). The position is paid according to the German pay scale 13 TV-L.

Job description:

Our lab focuses on the neurobiology of spontaneous behavior and operant learning using Drosophila as a neurogenetic model organism. Methods include computer-controlled behavioral experiments with wildtype, mutant and transgenic flies, neuroanatomy using standard and confocal microscopy as well as some molecular biology such as qPCR to determine the effectiveness of RNAi-mediated gene knock-down.

Selected references:

  • Maye, A.; Hsieh, C.; Sugihara, G.; Brembs, B. (2007): PLoS ONE 2(5): e443

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  • Brembs, B.; Plendl, W. (2008): Curr. Biol. 18(15):1168-1171

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  • Brembs, B. (2009): Curr. Biol. 19(16): 1351-1355

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  • Brembs, B. (2011): Proc. Roy. Soc. B. 278(1707), 930-939

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Requirements:

Outstanding candidates (m/f) holding a PhD in a relevant field and interested in this topic as well as being enthusiastic about working in an open science lab are encouraged to apply. The position is fully funded for 2 years, with possible extension. Nonetheless, ideal candidates are expected to have or develop a publication record allowing them to apply for competitive external funding. Candidates with a background in Drosophila biology, coding experience, (R, MatLab, Python, LabView et al.) or psychology will be given priority; proficiency in all three areas is an advantage, but not required. Comprehensive oral and written communication skills in English are also important.

Employment:

The fulltime position is a university-paid, fixed-term position along the funding scale outlined by the TV-L E13, according to seniority and including medical and social benefits, as well as a retirement plan. The position includes a teaching requirement of 5 SWS which can be fulfilled in either English or German.

Universität Regensburg is committed to the compatibility of family and career (for more informa­tion, please visit https://www.uni-regensburg.de/equal-opportunities). Severely disabled applicants are given preference in instances where applicants demonstrate an equal level of qualification. Please mention any severe disabilities, if applicable, in the application.

Applications:

Starting date for the position is October 1, 2013 and applications before July 1, 2013 will receive preferred treatment, but applications will be considered until the position is filled. Applications including a short statement of research objectives, a CV, as well as the names and coordinates of three references should be sent in a single PDF file to: bjoern.brembs@ur.de

Posted on May 21, 2013 at 13:00 Comments Off on PostDoc opportunity in our lab now advertized
May17

Official call for an end to journal rank

In: science politics • Tags: , , ,

While our own manuscript on journal rank is almost through the peer-review process, this morning I received several messages announcing the DORA (San Francisco declaration on research Assessment), which I signed immediately. Echoing some of the sentiments we also refer to in our article, part of the declaration reads:

The Journal Impact Factor is frequently used as the primary parameter with which to compare the scientific output of individuals and institutions. The Journal Impact Factor, as calculated by Thomson Reuters, was originally created as a tool to help librarians identify journals to purchase, not as a measure of the scientific quality of research in an article. With that in mind, it is critical to understand that the Journal Impact Factor has a number of well-documented deficiencies as a tool for research assessment. These limitations include: A) citation distributions within journals are highly skewed [1–3]; B) the properties of the Journal Impact Factor are field-specific: it is a composite of multiple, highly diverse article types, including primary research papers and reviews [1, 4]; C) Journal Impact Factors can be manipulated (or “gamed”) by editorial policy [5]; and D) data used to calculate the Journal Impact Factors are neither transparent nor openly available to the public [4, 6, 7].

Of course I wholeheartedly agree with this declaration and with all the recommendations mentioned in it (which is why I signed it). However, while the recommendations are great, they merely echo what people have been editorializing about for at least a decade, some even longer. I also fail to see any clear vision as to how publication reform is supposed to happen. Finally, since our paper isn’t out, yet, (other than on arxiv) they cannot include in their statement that there is absolutely no evidence that research published in high-IF journals are in any way better than those in journals with a lower IF: there is not a single study that I know of where there is a positive correlation of anything that could be construed as a direct measure of any aspect of scientific quality with Impact Factor.

In the absence of such evidence, the appeal in the declaration to drop journal rank as an evaluation signal is just that: an appeal – it lacks evidence-based reasoning and substance, as one could simply argue that the flaws of the IF just need to be fixed.

Nevertheless, such a public and widespread declaration is justified, comes at the right time and carries the right message, so it deserves our full support, even if it may not go quite far enough in its demands for reform. Clearly, being a platform seeking the most widespread support, some compromises have to be made.

Now go and sign the declaration already, what are you waiting for?

Posted on May 17, 2013 at 18:30 Comments Off on Official call for an end to journal rank
May11

A new home for bjoern.brembs.blog

In: server • Tags: , ,

After Mike Taylor kept complaining about how horrible my old e107 platform was (which obviously it isn’t: I love this CMS), I finally gave in and moved everything over to a new home. The entire brembs.net domain with all its subdomains is no longer hosted in the good old US of A, where its home was since about 2000, when I moved there myself. After almost ten years back in Germany, I’ve now brought my online presence back home as well. As of this post, all my blogging will be done on WordPress.

The 912 old posts from the last ten years are still accessible, of course, at blogarchive.brembs.net. I should have everything set up in a way that even all the original links should be redirected to the archive, such that nobody should really notice much more than a slight difference in appearance.

I’ll now slowly adjust all the content and design on this place, until the required functionality and look-and-feel is in place. Let me know if there is anything you’d like to see here in terms of plug-ins or other functionality, or if any of the design is off-putting. Also, if you will, could you test the commenting system and let me know if anything, what needs to be modified/adjusted?

Posted on May 11, 2013 at 07:42 3 Comments