Tag Archives: research

[update]Tip of the Week: A Lapse in Appropriations, Some Affects on Research

nsfclosed[to keep abreast of the effect on research, this from is a good article from Science Careers, see below for more links and information]. Forgive me as I create a lapse in our weekly tips and instead give one ‘insider’s’ view of the shutdown (or lapse in appropriations in official parlance). This most definitely not a full understanding of how the government shutdown will effect you as a researcher, educator or student, but hopefully will give you an idea.

As many readers know, I am currently on a temporary leave from OpenHelix to work at the National Science Foundation. Though on leave, I still write Tips (among other activities) for the blog. My turn was today. Unfortunately, yesterday the government shut down and though it did, it took a lot of the day to prepare for an ‘orderly shutdown.’  We were given a large portion of the day to shut down operations. That was an intense time of emails, calls and preparations. We had to leave the office by 1:30pm. (unfortunately for me my home computer seized up in it’s own version of a shutdown the day before). So that you, our readers, may get an idea of the affect of the shutdown on NSF and research in general, allow me to relate my experience and some of the affects the shutdown will have on research and possibly you.

My work at NSF (and AAAS), for the most part, entails working on programs to broaden participation in science education. Among other activities, I organize working meetings to explore the research in the topic and develop and run a science engagement project for refugee youth.

As part of the shutdown, NSF shut it’s doors. This is pretty much a complete shut down. All NSF employees were told they had till 1:30pm to complete an “orderly shutdown” of all activities. For me this included emailing all the PIs and educators attending a meeting next week here at NSF about computer science education for those with disabilities and others that I am working with on other projects. By federal rules, no NSF employee, fellow or other staff is allowed to access email, respond to communications, work on any and all NSF-related activities, travel to conferences or meetings or otherwise conduct any business. The violation of this is a large fine.

What does that mean for those who have funding or dealings with NSF? If you have no immediate work or need to contact an NSF employee, than the effect will be minimal if the shutdown is short. If you need to submit a grant proposal, talk to a grant officer or have an NSF meeting to attend or any other business with NSF within the next few days (or as long as the shutdown lasts) you will be unable to do so. All activities have ceased. If there is an NSF meeting that takes place during the shutdown, it is canceled.

For example, I have been planning and organizing a meeting here at NSF for educators in computer science for persons with disabilities. It has entailed everything from getting rooms settled to setting agendas to choosing reviewers to procuring ASL interpreters and translating documents into Braille. If the shutdown continues into next week, that meeting will be canceled  and all attendees will be unable to come. So, in my case, if the shutdown lasted into the next week, this even would be canceled, the researchers and educators (about 20) attending will have to cancel their flights and plans and all arrangements will be for naught. Obviously this will have some costs from lost flights and plans, but it will also mean that hundreds of man hours of past work will be wasted.

If you have a current award, there should be little impact in the short term, but no new solicitations will be made, grants will not be allowed to be submitted, etc. As the homepage now says:

No new funding opportunities (program descriptions, announcements or solicitations) will be issuedFastLane proposal preparation and submission will be unavailable.Grants.gov may be up and running, however, since FastLane will not be operating, proposal downloads from Grants.govwill not take place. Therefore proposals will not be checked for compliance with NSF proposal preparation requirements or processed until normal operations are allowed to resume.”

The National Institutes of Health will also shutdown though the impact will be somewhat different. Since NIH is a research institution in addition to be a granting one (NSF is a granting institution), all research at NIH will cease. Universities will feel little short term affect as one of the three granting cycles just completed. That said, October 5th is the next round of deadlines and if the shut down continues past that date, no grant applications will be accepted. A short shutdown will only delay the processing of those grants for up to a month, the longer the delay the more exponentially delayed the process will become because of backlogs.

There are other effects on the shutdown on researchers also. Visa sponsorships or requests from visiting scientists will not be issued during the shutdown and some activities will be postponed or cease. Another example from my own work is the science engagement program I run for refugee youth. Though not funded through NSF, it is something I do under my fellowship and thus I am not allowed to work on it. THis means the program will be halted until further notice and the students will not be able to participate in the activities they’ve been very excited to do.

So, let’s reiterate the top 10 effects on research the shutdown will have:

10. NSF, NIH and other agency websites and information will be unavailable or affected. Many databases such as PubMed will not be updated or maintained.
9. Visas for visiting scientists to the US or scientists collaborating overseas will not be processed.
8. Payments of student loans and stipends might be slowed or otherwise affected in the long term.
7. NIH, NSF and other agency-hosted meetings and discussions will cease.
6. New grants proposals will not be accepted, processed or reviewed.
5. Contractors and businesses that rely on NSF, NIH and other research and granting institutions will receive no business and payments will be delayed.
4. Government employed researchers, grant officers and staff (at NIH and NSF among other agencies) will not be paid.
3. Government employed researchers, grant officers and staff will not be allowed to work or contribute to any and all meetings, work-related activities or communications.
2. Research at NIH (and some other agencies such as Energy’s ARPA-E) will cease.

and the number one affect (at least in the sadness factor)
1. Children with cancer will be turn away at NIH.

Do you know of an effect missed here? Comment!

An article from ThinkProgress about some other effects on science and research including other agencies such as NOAA, etc.

A long Reddit discussion from scientists  (with some good pointers and not-so-good stories) about the effects.

Don’t worry, the lapse in a video tip will not be long as the shutdown. I have a lot of time today :D , so will be doing one for later.

There’s a database for everything, even uber-operons

I was playing around with Google Scholar’s new citation feature that allowed me to collect my papers in one place easily (worked pretty well, btw, save a few glitches, see below) when I noticed it missed a paper of mine from 2000: “Gene context conservation of a higher order than operons.” The abstract:

Operons, co-transcribed and co-regulated contiguous sets of genes, are poorly conserved over short periods of evolutionary time. The gene order, gene content and regulatory mechanisms of operons can be very different, even in closely related species. Here, we present several lines of evidence which suggest that, although an operon and its individual genes and regulatory structures are rearranged when comparing the genomes of different species, this rearrangement is a conservative process. Genomic rearrangements invariably maintain individual genes in very specific functional and regulatory contexts. We call this conserved context an uber-operon.

The uber-operon. It was my PI’s suggested term. Living and working in Germany at the time, I thought it was kind of funny. Anyway, I never really expanded more than another paper or so on that research and kind of lost track whether that paper resulted in much. I typed in ‘uber-operon’ in google today and found that it’s been cited a few times (88) and, I found this interesting: there have been a few databases built of “uber-operons.”

A Chinese research group created the Uber-Operon Database. The paper looks interesting, but unfortunately the server is down (whether this is temporary or permanent, I do not know), the ODB (Operon Database) uses uber-operons (which they call reference operons) to predict operons in the database , Nebulon is another, HUGO is another. Read the chapter on computational methods for predicting uber-operons :)

Just goes to show you, there’s a database for everything.

Oh, and back to Google Scholar citation. It did find nearly every paper I’ve published, though it missed two (including the one above) and had two false positives. Additionally, many citations are missing (like the 88 for this paper, and many others from other papers). That’s not to say it’s not useful, I find it a nice tool but it’s not perfect. You can find out more about google scholar citation here, and about Microsoft’s similar feature here.

Oh, and does this post put me in the HumbleBrag Hall of Fame? If that’s reserved for twitter, than maybe I should twitter this so I can get there :). (though I’m not sure pointing out relatively small databases based a relatively minor paper constitutes bragging, humbly or not LOL).

New feature, research articles, on OpenHelix site

If you go over to the OpenHelix home page, you’ll start to notice some differences. Our tutorial landing pages have an added new feature. We now have a section on each landing page that shows the most recent research in the BioMed Central journals. For example, the screenshot here is for our GeneMANIA tutorial suite. At the bottom left corner you’ll see the 5 most recent research articles that have used GeneMANIA from the BioMed Central catalog of research journals. This will be useful to users to get an idea of what kind of data  a resource has and research that is done using the resource. This will also be helpful to find other resources that might be of use (often a related-resource will be mentioned in conjunction with the resource of interest).

This is the beginning of a series of new features we hope to add to the landing pages that will enhance the ability of researchers to learn all they can about the data and tools available to them. We will be adding a “recent video tips” section and more.

And, if you are a publisher of research literature and would like to get a ‘recent research list’ like this on our landing pages for your journals (will need access to full text of articles), please contact us and we’d love to work with you to do so for the benefit of your journals, the resources, the researchers and yes, OpenHelix :).

In our continuing effort to maintain and expand our search database and engine, our tutorials, our blog and more, you will also notice we have added advertising to our site. The ads are a top banner ad, a side skyscraper ad and a small ad on tutorial landing pages. Please consider viewing these sponsors if they interest you. Ads will not be on sponsored tutorials such as UCSC Genome Browser and PDB, and others, nor will they be visible for any subscribers to the catalog of tutorials.

If you would like to sponsor a tutorial so that it is publicly available, whether you are the developer of the tool or a company, please contact us about the opportunity to get training and outreach to a large number of researchers.

Also, though we have a dozen sponsored tutorials that are publicly available, we do have a large catalog of over 90 additional tutorials available for subscription. You can subscribe to access these as an individual, department or institution.


Tip of the Week: SciVee, the YouTube of science

Every week we do a video tip of the week. Every week we use SciVee to upload and share that video (our account here). We now have nearly 50 tips and videos residing at SciVee. SciVee has been called the YouTube of science. Like YouTube, it allows you to upload videos, though in this case exclusively related to science. Additionally though, SciVee allows you to do some ‘science-specific’ actions you wouldn’t be able to do with YouTube or Vimeo. PubCasts and PosterCasts are two of several such features (Papercasts are similar to Pubcasts, only non-published papers). These features allow you to upload a video describing your research and then upload a paper and poster and sync the paper or poster to the video. This allows the author to describe the paper (or poster) and the research while the viewer can see the relevant sections of the paper or poster. There is more about how to do this here. A virtual poster session, or a virtual talk. Once you do that, you can embed your video on another web site (as we do here!) to share and allow others to share. It’s an excellent tool to share your research and get it to a wider audience.

Today’s tip of the week is a short intro to SciVee and a quick tutorial on uploading your own videos.

At the end you’ll see we have a community at SciVee called “Genomics Resource Training.” There you will see all the tips of the week we’ve done. In addition, we add other genomics and biological data resource tools and databases to the community when we find them. Check out and join the community:

Visit Genomics Resource Training Community

A new BioMed Central feature

Brought to you by OpenHelix and BioMed Central :D. We really like the feature and idea (of course) and thought we’d pass it on.

BioMed Central (BMC) is an open access publisher. BMC along with OpenHelix launched a new feature recently to give readers of BMC journals timely access to relevant genomic resource tutorials. When reading a research article at BMC, researchers are now provided links to online tutorials of many of the genomics resources and tools used or cited in the article. The link takes the reader directly to the training landing page on the OpenHelix site. BMC has a large selection of open access high quality peer-reviewed research journals and much of the research reported today uses and cites many of the resources OpenHelix trains on. Researchers can now quickly find training on the databases and tools used in the research. For example, this recent article Genomewide Characterization of non-polyadenylated RNAs, in BMC’s Genome Biology cites several tools used in their research including GEO, MEME and others. The new feature finds these citations in the article and lists links to the OpenHelix tutorials on those resources as seen in the image.

It can be hard to find a quick link to a relevant resource in papers–the citations are sometimes incomplete, or not linked to the site.

We have plans to expand this feature in several ways to make training on relevant and important genomics resources simpler and quicker for researchers.

We’ve already gotten some great feedback on this–Great idea!

@jytricker Great idea! @BioMedCentral/OpenHelix jv will coach scientists on genomics/bioinformatics tools mentioned in papers http://ow.ly/4eQbG


iPad app for moving molecules

Found this from Wired on Friday, iPad Lets Scientists Drag, Pinch and Swipe Real Molecules . It’s an app that allows scientists to manipulate molecules with an optical tweezer using the iPad as an interface. Quite a fascinating app and the video is interesting.

Got me to thinking, how is and could a tablet computer be used in biological science (bench or otherwise)? I wrote about iPhone apps before.

I have an iPad, and I use it a lot for reading news, reading books, catching up on email, watching movies. I find it’s potential though much more intriguing than what I’m using it for.

There are some great biology research-related apps I use. I use Papers (opens iTunes) to read and annotate research papers, and I have the Nature and PLoS reader apps, but it feels to me that developers have only mined the surface of what one could do with a handheld touch-screen tablet (be it iPad or Slate or…). Or at least what it seems you should able to do based on Star Trek movies :D.

I can see an app for keeping a lab book (there are notebook apps, but I want something geared towards lab notes. I can see an app for manipulating multiple sequence alignments (kind of like JalView) or even a game like Fold It on the iPad for multiple sequence aligns. In fact, why not Fold it on the iPad or tablet. Thought he UCSC Genome Browser can be viewed using the browser on the iPad, I can see a suped up GenomePad for the tablet. How about a personal genomics app?

Have any ideas or apps that you use for research or would like to see?

Peer review again…

Just a quick comment gathered from a link Mary showed me. I have had my run ins with reviewers of papers and grants. Some reviewers definitely have an agenda and, as humans, all reviews have subjective biases. I could tell you stories. But, for the most part, even given the few huge frustrations, the review process have made my research and papers better and tighter science.

Peer review is not without it’s problems, there are entire blogs (like Peer-to-Peer) and communities discussing it. And of course, a lot of substandard research is published, as possiblty evidenced by the recent discussion of the arsenic-eating bacteria paper. I’ve read my quota of really bad research and spurious conclusions from peer-reviewed journals. But again, it’s the sum-total of the peer review system (and the subsequent discussion, more research, rebuttal publications) that has obviously created excellent science and the advancement of our understanding of biology heretofore.

Nature Precedings is not an alternative peer-review, it’s a place to put research before peer-reviewed publication to invite discussion, spur further research and claim priority. But I’ve seen it pointed to as the part of an alternative. Yet, it’s papers like this (and two others by the same author) that make me realize that peer-review is a necessary purgatory. I won’t spend the time eviscerating the issues of this research, they are legion and it’s not worth my time. I can imagine the casual reader of Nature Precedings might come across it and see all the biolingo and think it’s legitimate research, but really that doesn’t concern me. But, the author of these articles uses them to lend legitimacy to his main thesis: “genome data proves false the theory of evolution.” He does this in a press release (http: //www.prweb.com/releases/theory/genome/prweb4896744.htm .. I won’t link so as not to give this any more web legitimacy, but you can take the space out if you want to see it) where he links to all three “publications”:

Using modern genomics, Dr. Senapathy and his team’s work, showed how the abundance and diversity of life on earth originated directly in the prebiotic environment. They have presented the results in three scientific publications in Nature Precedings: publication 1publication 2publication 3.

Research shows that modern genome data completely uproots the evolution model.

He uses the well-deserved respect of the brand “Nature” and the sleight of hand to call them “publications” (when all they are pre-prints with no peer review or review of the science) to lend legitimacy to a counterfeit conclusion.

With all the ‘woo’ in this world, I would suspect that peer-review or some other rigorous solution (which I haven’t yet seen) is more necessary than ever to move science forward.

Edit by Mary: I was just watching some journalists discover this story on MuckRack (http://muckrack.com/sci ) and here’s what they said:

Tip of the Week: BioExtract Server

The BioExtract Server is a tool that allows the researcher to search and access data, analyze that data and then store the data and create workflows from the analysis. In that respect it’s very similar to Galaxy. BioExtract was developed by two groups (Brendel and Lushbough) at Iowa State and University of South Dakota, respectively.

Today’s tip in a quick introduction to BioExtract. If you have used Galaxy before*, you will immediately notice differences in execution, usability and community. Both have workflows. I like Galaxy’s implementation of histories better and Bioextract does seem to focus on comparative genomics more. Both BioExtract and Galaxy are (or will be) part of MyExperiment, a site to find, use and share workflows and other “research objects.”

In today’s tip I am giving a basic intro, they have a good tip on how to do workflows, which I don’t go into, here (more help here).

*(Disclosure: OpenHelix does training and outreach for Galaxy)

Tip of the Week: Galaxy Pages

This week’s tip is a brief introduction to Galaxy Pages. These are special pages that users can create within the Galaxy system to annotate, describe and explain various analyses done using Galaxy. The user has many abilities to link to and embed histories, workflows and datasets along with using text and images and more to fully annotate analyses. As described last week, this is one of the many additions Galaxy has added to increase reproducibility and transparency of genomics research.

Moroccan Science

Al Akhawayn University, Ifrane Morocco

Last week I attended and taught a workshop for the Moroccan American Society for Life Sciences (Biomatec-US) at their 2nd International Workshop and 9th Annual Meeting, in Ifrane Morocco.

I was thoroughly impressed. Impressed with Morocco, Moroccan Scientists and Moroccan students. I had the opportunity to interact with all three. First this students. I taught three workshops, including a tour of genomic resources and two how-to’s for the UCSC Genome Browser and Table Browser. All were enthusiastically received. But more than that I was impressed by the enthusiasm these students showed for genomics and bioinformatic research. After each talk and later in the day, I was barraged with questions and requests (which I love). Their enthusiasm for science matches or surpasses any other group of science students I’ve met in my 20+ year career in biology. In addition to that, I met several students who I was able to discuss their research with a bit.

Also, I was able to discuss research in Morocco with several Moroccan scientists informally and attend a roundtable discussion about advancing Moroccan science, specifically biological and bioinformatics research. Moroccan scientists, both within and outside of Morocco, are doing worldclass research, including my host of course. The research done within Morocco and by the Moroccan ‘diaspora’ of scientists (there were Moroccan scientists from the US, Europe and the Middle East there), seems to be a ripe network that, together with the enthusiasm of the students, is a great resource for that nation.

If the level of research and enthusiasm of the researchers and students are any indication, Moroccan science will be making great strides in the years to come. Of course, this isn’t anything new I’m sure, just new to me :D.

I learned (relearned) two things on this trip. The world is very small, and very big. I met several people who with whom I had crossed paths with before or who we had mutual friends. There was the Moroccan scientist who I briefly met in Germany while doing a postdoc there and the Moroccan student who knew someone I knew from Qatar. I was asked to talk briefly and the roundtable discussion and I mentioned a virtual African conference I had given a workshop at, and that I thought there was a Moroccan hub at that conference. Sure enough, one of the scientists at the discussion had attended my workshop (and had good words for it :D). Ok, you might say, that’s the ‘world’ of science. Well, it got down to even the woman I met in the hotel who was a Fulbright scholar doing research on Berber and Arabic music… and the man who gave me a ride from the conference the last evening, who just happened to be her Moroccan supervisor.

And it’s a huge world with a lot to discover and awe my sometimes jaded self (rarely, but I can be there). I never had heard of Argan oil before,

Street & shops in the medina of Fes, Morocco

traditionally produced from seeds collected from the feces of goats (today it’s more likely collected and processed by more modern methods :), or even considered touring the magical medina of Fes (to which I MUST return). I had no inkling of the existence of Al Akhawayn University in Ifrane, a small liberal arts school in the cool (it snows) mountains of Morocco in Ifrane (why do I want to keep writing that as iFrane :D? ). Beautiful campus.

The other thing that came to mind while attending this conference and speaking with Moroccan scientists is the potential (and unnoticed reality) of the research possibilities outside of the US-European-Japanese triangle. Of course India and China are producing great research more and more over the years, but there are another 100 or so countries out there with another few billion people with huge potentials. Of course these smaller countries have always produced great scientists, but I was beginning to think that genomics and bioinformatics is beginning to assist smaller countries ‘leapfrog’ biological research much as cell phone technology allowed some developing countries to ‘leapfrog’ from traditional telephone lines (expensive, hard to do) to wireless (less expensive). Biological research has traditionally be resource intensive: labs, larger universities, equipment. Bioinformatics and genomics research, though still requiring infrastructure, has a lower barrier of entry I believe. I made a comment in my talk, “There is no lack of data,” and it’s true. The amount of data available for analysis is staggering. The number of publicly available tools and databases is overwhelming. One doesn’t have to do “big science” in genomics (though there sure is that) to do world-class research. Thar’s research gold in them thar data hills (sorry for the reference to the California gold rush, I _do_ live in what was the center of it all). Gold that can be mined by any individual, lab or nation with a bit of education and enthusiasm.

I hope to return next year to Morocco and next years conference. I have a lot more to learn :D. And maybe I can teach a bit too.