Mendeley groups on environmental PCR, metagenomics, and microbial eukaryotes

As part of my NSF Research Coordination Network grant (RCN EukHiTS), I am currently managing a number of Mendeley groups that amalgamate relevant journal articles on different topics related to environmental PCR, metagenomics, and microbial eukaryotes. These groups are open (anyone can join with a Mendeley account), and I’m trying to keep them regularly updated with new articles (Mendeley members can also add articles, which I strongly encourage!):

  • Eukaryotic HTP Studies – Publications relevant to high-throughput environmental sequencing approaches focused on microbial eukaryotes. Articles will include any type of -Omic methods (marker gene amplicons, metagenomics, metatranscriptomics, etc.), eukaryote-focused tools/pipelines, and review/opinion pieces.
  • rRNA in Eukaryotes – Literature related to the ribosomal repeat array in eukaryotic genomes – variation in rRNA gene copy number, intragenomic polymorphisms, concerted evolution, transposable elements and their evolutionary and ecological implications.
  • Environmental PCRs – primer sets and bias – Literature related to primer set usage and bias across all taxonomic groups (bacteria, archaea, fungi and microbial eukaryotes) – includes primer sets and methods focused on 16S, 18S, ITS, other rRNA, COI, and other marker genes used for environmental sequencing.
  • eDNA in aquatic ecosystems – This group focuses on environmental DNA (eDNA) applications in aquatic ecosystems, include use of eDNA in bioassessment and environmental monitoring. Literature collection covers methods, analytical tools, and empirical studies (both basic and applied science).

The kitten microbiome – new related paper and Mendeley collection

Saw this new paper today: Dietary format alters fecal bacterial populations in the domestic cat (Felis catus) – Bermingham – 2013 – MicrobiologyOpen – Wiley Online Library

And was reminded on the Kitten Microbiome project. It was conceived as a (sort of) joke but studying the microbes in our domestic companion animals is a good thing and could be very interesting in many ways.

So I created a Mendeley group on cat / kitten microbiome studies:

Oh, and while I was at it I created a group for the Dog Microbiome.

Not sure these should really be completely separate (i.e., there could be a collection on the domestic animal microbiome) but am keeping them separate for now.

Social Networks and Scientists: Chronicle for Higher Education Article

Quick post here.

There is a new article in the Chronicle for Higher Education in which I am quoted: Social Networks for Academics Proliferate, Despite Some Scholars’ Doubts

The article discusses many connected topics relating to the use of social media by scientists – though it does not make clear how everything is connected perhaps.  Anyway the author talked to me about Mendeley and various uses of Mendeley and I told her about an effort to create a Mendeley collection of my father’s papers.  The article also discussed LinkedIn, Academia.Edu, Twitter and other social media systems.

Some quotes

Jonathan A. Eisen, a professor of medical microbiology and immunology at the University of California at Davis, used Mendeley to distribute the research papers that his father, Howard J. Eisen, a researcher at the National Institutes of Health, published before he died, in 1987. After struggling to free papers locked behind pay walls, Jonathan Eisen compiled the articles and posted nearly all of them on a Mendeley page he had created for his father. 

Mr. Eisen, a self-described “obsessed open-access advocate,” described the impact in a blog post last year: “Thanks to the social features of Mendeley, more and more people will see and have access to those papers, thus ensuring that they do not wallow in never-never land but continue to have some potential impact on science and society.”

Perhaps most important from my point of view – I love the picture of me taken by Max Whittaker.

Phylogenetic analysis of metagenomic data – Mendeley group …

Just a little plug for a Mendeley reference collection I have been helping make on “Phylogenetic and related analyses of metagenomic data.” If you want to know more about such studies you can find a growing list of publications at they group collection.

Phylogenetic and related analyses of metagenomic data is a group in Biological Sciences on Mendeley.

More fun with Mendeley plug ins for reference management #thingsIshouldhaveknownabout

OK – so I am a bit slow. I have been using Mendeley a lot recently. It has all sorts of nice “Social Networking” features for sharing reference lists and publications. I have for example used it as part of my push to free up papers by my father: Freeing my father’s publications part 5: near completion of PDF collection at Mendeley (h/t @David_Dobbs). And I have created some groups on Mendeley for sharing publications relating to various topics in which I am interested including: Microbial Forensics, Microbiology of the Built Environment and Phylogenetic and related analyses of metagenomic data. I have experimented with other online reference management systems like CiteULike, Connotea, Zotero, etc and each have some nice features. I have even written up some more detail on how to use citeulike for one project: Introducing citeulike group on microbiology of the built environment ….

 But it is the more elaborate social networking features that drew me to Mendeley and why I am using it more than the other online system.  And I have focused for example on getting all my personal publication in there to share them with others. And I confess I did not pay attention to many of the other features.

Yesterday however I discovered that Mendeley has plug-ins for generating bibliographies in various word processing programs: Reference Manager | Mendeley. Obviously I probably should have known this. But I have been using EndNote forever and had not experimented with anything new in a while. But I tried out the Mendeley Plugin for MS Word and it is OK. Not perfect. Still needs some work. But it is another factor in why I will likely shift even more to using Mendeley over other system. Still will play with the other ones out there … so if people have comments or suggestions please post.

Plus see below for an example of some of the Mendeley embed widgets one can make

Freeing my father’s publications part 5: near completion of PDF collection at Mendeley (h/t @David_Dobbs)

Well, the story continues.  Yesterday marked a major achievement in my goal to free up the scientific publications of my father Howard J. Eisen, who passed away in 1987 when I was in college.  I have been working for the last 3+ years or so on collecting and sharing as much of his scientific work as possible.  I have documented this effort on a page on this blog: Freeing dads pubs.  That page contains links to various details about my effort here.

I have been doing this for many reasons.  And I could detail them all here.  But instead I point you to the amazing story written by David Dobbs that relates to this effort: Free Science, One Paper at a Time | Wired Science |  David is a science writer/blogger/scientist/journalist and about a year ago he was interviewing me for a story that he was working on about Mendeley.  It was good timing as right around then I was trying all sorts of different tools for sharing his publications, from Academia.Edu to web pages and so on.  And I had been looking at Mendeley too.  When Academia.Edu did not pan out, Mr. Gunn suggested in a comment on one of my posts that this might work in Mendeley.  So I set up a Mendeley page for my father which I diddled around with for a bit.  But inspired by the discussions with David I tried to beef up the Mendeley page and try to learn how to use the system.  And I managed to post many of my dad’s papers there and on my blog.  And I ended up telling David about the whole saga of trying to free up my dad’s papers.  David, being an insightful journalist, realized that this saga was a good story and he asked a lot of questions about it.

But then I got caught up in life and the effort to free my dad’s publications slowed down.  That was, until David’s blog post came out: Free Science, One Paper at a Time | Wired Science |  The piece moved me.  It scared me a bit at first, since there are some really personal details in there, but I realized when reading it why he had focused in on this story.  So, with his post out there – for all to read.  I realized, I had to get my shit together and redouble my efforts to free up my father’s publications.  So over the last week or so I have been scavenging around (with some help from people around the web) trying to dig up PDFs of as many of my father’s papers as possible.  Note – I generally would like to obtain these papers without having to pay for them but I am trying to not break any laws either.

I am writing today because I have nearly completed the task of getting PDFs of all of his papers.  And I have discovered that Mendeley is really a great way to share them.  So now on the Howard Eisen Mendeley page almost all of his papers are there for anyone to obtain.  And thanks to the social features of Mendeley, more and more people will see and have access to those papers, thus ensuring that they do not wallow in never never land but continue to have some potential impact on science and society.  Anyway – thanks David, for a wonderful article and for inspiring me to get moving on the “Freeing My Father’s Publications” effort.  And thanks to all the people who have supported me along the way including Linda Avey, Mr. Gunn, David Williams, and more.  It has been a slog but we are getting there.

Afterthought: some additional discussions of David’s story include: