Comments for bioinfoblog.it

Comment on a script to fetch images from the UCSC browser by brentp

brentp — Fri, 03 Feb 2012 23:41:41 +0000

Thanks, This is very cool.
It would be a nice option if the regions file could be a BED file with the 4th column being the label and description and the up/downstream set from a kwarg on the command-line.

Comment on The analogy between Blast and Google by Giovanni Marco Dall'Olio

Giovanni Marco Dall'Olio — Fri, 03 Feb 2012 10:20:37 +0000

Hello Jessica,
thank you very much for your feedback!! I have added your comments to the post.

I don’t have many tips to explain Blast to new users, apart from the google analogy.. but I think that showing some examples of usage can be very useful to make it easier to understand!

Comment on The analogy between Blast and Google by Jessica

Jessica — Fri, 13 Jan 2012 21:18:16 +0000

Dear Giovianni,
I like your Google analogy in terms of explaining that BLAST is a search program–it makes a nice thought exercise. Here are some additional points I thought of…
Pro: Google and BLAST are both used as verbs, because they are such widely used search programs.
Pro: Google is not the Internet, and BLAST is not a database.
Pro: You can set limits for both kinds of searches, i.e. Google to “site:edu,” and BLAST to “organism=Rat”
Con: BLAST searches very specific, curated, selectable online databases, while Google searches the Internet. You can (and should) control what BLAST searches, but you can not control what Google searches. I don’t think many new users understand that, and I think it is important.
Con: Google comes in one-size-fits-all, but there are several BLAST algorithm options which accomplish different things. I think this is another point of confusion for new users.
I am a science librarian and am creating a drop in workshop on the (very) basics of BLAST searching. I would love any tips you have on presenting BLAST in a simple, easy to understand way to beginning users.
Librarians love instructional analogies
Thank you,
Jessica

Comment on The analogy between Blast and Google by Giovanni Marco Dall'Olio

Giovanni Marco Dall'Olio — Fri, 16 Dec 2011 10:13:46 +0000

Hello Yannick, thank you very much for the feedback! I have been lucky to never had to install a blast database by myself, but I imagine it must be quite a pain. However, your tool seems to be a good way to do it easily. Thank you for sharing it.

Comment on The analogy between Blast and Google by Yannick Wurm

Yannick Wurm — Fri, 16 Dec 2011 09:25:20 +0000

An additional con:
* Google is easy to use.
* Whereas NCBI’s BLAST interface is super confusing, and locally installing BLAST, setting up databases, performing searches and understanding what the different result elements mean is quite challenging!

Cheers,
yannick

Comment on About me by Francis Nunes

Francis Nunes — Tue, 29 Nov 2011 11:57:35 +0000

Dear Dall’Oliothe, congrats on the blog and recent PLoS Comp Biol papers. I study genetics and bioinformatics, and honeybee is my biological model. I appreciate your initiative in coordinate collaborative efforts of writing articles. Please, call me in a future endeavor.

Comment on Ten Simple Rules paper published! by ygc

ygc — Fri, 25 Nov 2011 02:22:31 +0000

cong!

Comment on Scifund projects online by Daniel

Daniel — Sat, 19 Nov 2011 00:28:36 +0000

I’d like to announce a new crowdfunding platform expressly for scientific research and technology: http://www.fundageek.com We have a unique place in the crowdfunding ecosystem since unlike most of the other crowdfunding sites that have a creative focus (art, film, music, etc.) all we do is science and technology. We’re seeking project in the physical and life sciences, engineering and education. Please check out FundaGeek!
Cheers,

Daniel

Comment on New ways to explore your academic impact by JB

JB — Thu, 17 Nov 2011 22:31:01 +0000

it’s a great move from Google Scholar to release their citation data and I am looking forward to further developments. However, citations from Google should be used with care when it comes to evaluations of researchers etc. As we showed in some papers, Google Scholar counts self citations and it is even possible to manipulate citation counts on Google Scholar.

“Google Scholar’s Ranking Algorithm: An Introductory Overview” http://www.sciplore.org/publications/2009-Google_Scholar's_Ranking_Algorithm_–_An_Introductory_Overview_–_preprint.pdf

“Academic search engine spam and google scholar’s resilience against it” http://www.sciplore.org/publications/2010-Academic_search_engine_spam_and_Google_Scholars_resilience_against_it_-_preprint.pdf

Comment on New ways to explore your academic impact by Martin B.

Martin B. — Thu, 17 Nov 2011 17:27:21 +0000

PPS. Just submitted a feature request for Mendeley so that emails would get extracted from PDFs etc. – that would be a first step towards introducing more direct communication with authors via platforms such as PaperCritic. Vote here http://feedback.mendeley.com/forums/4941-mendeley-feedback/suggestions/2395696-extract-author-email-from-uploaded-pdf