DIY spectrometer

August 30, 2012 at 1:44 pm | | hardware, science@home, wild web

A Kickstarter project is aiming to make a kit for simple DIY spectroscopy. For spectra-nerds, this is pretty cool.

(Hat tip Austin.)

papers2 review

March 11, 2011 at 6:12 pm | | literature, software, wild web

Scientists have many options for organizing, reading, and syncing PDFs of articles: Papers, Mendeley, iPapers, Endnote, BibDesk, Zotero, and more.

My favorite is still Papers. It’s clean and simple and beautiful. It works awesome on my iPad: reading PDFs is more enjoyable on the Papers iPad app than on my laptop. Syncing to the iPad over wifi is simple and practically bug-free. Syncing libraries between my home and work computers is also possible by putting the Papers folder in Dropbox. (Although Dropbox syncing isn’t technically supported by Papers, many folks use it to sync across computers. I’ve been doing that for half a year without a problem.)

The major downside with Papers is that it works only on Mac OS. Papers2 is now on Windows, too. On my PC, I use Mendeley. Mendeley is nice because it is free and has native syncing to the web and between computers. The reason I’m not completely sold on Mendeley is that it’s just not as clean as Papers yet. Mendeley is not as buggy as it was a year ago, but it still doesn’t seem to find metadata as well as Papers. But, if you’re starting from scratch, Mendeley is a great option. (Edit: And I like the syncing to iPad/iPhone that Papers offers.)

And now Papers2 was just released! Honestly, Papers2 is a little disappointing, so far. But I suppose I was expecting a lot. But I still have high hopes for it. The support staff is working very hard to fix bugs and add functionality that users are screaming about on the discussion boards.

Some of the cool features of Papers2 include:

  • A quick way to add citations to Word (or any other application on your Mac) directly from Papers
  • Easier keyword tagging
  • Automatic metadata importing (although I haven’t seen this work, yet)
  • Linking supplemental info to the paper it corresponds to
  • Searching multiple databases (e.g. Pubmed and arXiv) simultaneously

The automatic metadata grabbing might be nice, if it ever works. Mendeley tries to do that, too, but I’ve never been impressed. I really liked that Papers1 made manual matching easy (by highlighting the DOI, for instance). The new interface and searching mechanism seems much clunkier in Papers2, and the support staff has already acknowledged as much.

There are several other issues, that make Papers2 feel very beta. Given that it’s brand-new, that’s not exactly surprising. But Papers1 was so refined, that Papers2 seems very clunky in comparison. But I think Papers2 does have a lot of potential.

For those worried about trying Papers2, have no fear: the new version doesn’t overwrite your Papers1 data and PDFs, so you can use both versions side-by-side until you’ve made up your mind. During the 30-day free trial, for instance.

For the Mac, Papers1 has been the cleanest, coolest, and bestest PDF organizer. Hopefully Papers2 cleans up nicely and becomes my new favorite. But right now, Papers2 is not clean enough for me to recommend anyone using Papers1 switch over to the new version.

UPDATE: In the last two weeks, Mekentosj has provided two updates to Papers2 that have made it significantly better. Papers2.0.2 has fixed a lot of the bugs and annoyances in the version I reviewed above. For instance matching is much much better. Like I expected, the folks behind the program are working really hard to make it the best program, evar!

UPDATE2: I use Papers2 daily and I love it. It still has some things on the wishlist that I look forward to, but I think it’s a great program. I guess it just had some bumps at the beginning.

UPDATE3: Papers2.1 is now out at better than ever. Definitely better than Papers1. I can recommend without hesitation that you get this software!

UPDATE4: A bookmarklet for JSTOR.


February 11, 2011 at 12:10 pm | | literature, science community, stupid technology, wild web

UPDATE2: OK, it turns out that the daily(ish) email isn’t too terrible. I now use it and I’m no longer upset that they don’t have an RSS feed. I correct myself and now fully endorse F1000!

Faculty of 1000 is extremely powerful with a lot of potential, but simultaneously completely worthless.

F1000 is like mini-peer-review post-publishing: it uses its “Faculty,” experts in various fields, to rate publications that those experts think are worth reading. It’s like … nay, it is … getting suggestions on what to read in the recent literature from a large group of experts. That is very cool. Of course, there are various databases like Cite-U-Like and Mendeley that are trying to mine their data to find interesting papers, but there’s something great about getting little mini-reviews from actual people.

OK, so why am I annoyed? F1000 doesn’t have an RSS feed! So I have to remember to go and check the website every week. Even if I happen to remember, there’s no way to mark which reviews I’ve already seen and the new ones. What is this, 2002?

UPDATE: rpg comments below with some good news: F1000 is actively trying to get RSS on the site. The comments also explain why it’s a challenge. I eagerly await RSS.

bouncing water droplets

October 19, 2010 at 8:32 am | | nerd, wild web

Fun video:

For your Tuesday.

acs feeds broken?

September 3, 2010 at 8:53 am | | literature, stupid technology, wild web

I was forced to update all my ACS feeds in my RSS reader (Google Reader). None of the ACS feeds I follow had updated for a couple days. I think ACS switched over to Feedburner and their old feeds stopped updating. Anyone else have this problem?

And TOC images seem brokenish with the new feeds

UPDATE: Alex updated us on the issues. I’m happy that ACS is migrating to a better system. They really tried to redirect, but there are some problems. I think the new feeds seem to be working well now!


August 23, 2010 at 8:50 am | | crazy figure contest, literature, nerd, science community, wild web

My (very nerdy) friends started a internetted-web-blog to celebrate/mock hilarious/terrible table-of-contents images: TOC ROFL. (In reference to NCBI ROFL.) I might even submit my own once in a while; you can too!

best spam comment ever

August 15, 2010 at 1:48 pm | | wild web

OK, this really cracked me up:

“I’m currently being held prisoner by the Russian mafia penis enlargement penis enlargement and being forced to post spam comments on blogs and forum! If you don’t approve this they will kill me. penis enlargement penis enlargementThey’re coming back now. vimax vimax Please send help! nitip penis enlargement penis enlargement.”

check out this cool link

December 19, 2009 at 11:29 pm | | nerd, science community, wild web

Check it out here. I promise you won’t be rickroll’d.

open letter to journals about RSS

November 25, 2009 at 9:14 am | | literature, open thread, science community, wild web

Dear all journal publishers,

If the RSS feed to your journal is missing a TOC image or a full list of the authors, you need to correct that.


Reading just titles can be hard, especially when you skim through many journals. TOC images make that much more enjoyable. It’s the way to go, and if your journal does not include TOC images, you’re behind the times.

Also, it’s very simple to include all authors in the RSS feed. First authors only is not helpful: it’s very helpful to be able to check who the corresponding author is on a paper you might be interested in. (I’m talking to you ACS.)

Mitch’s ChemFeeds is great, but I doubt it can add TOC artwork to journals that don’t request it from their authors!

Happy Thanksgiving, everybody!

that’s one way to get your message approved

November 17, 2009 at 1:22 pm | | science community, wild web

I received this email forward, BCC’d mistakenly (I presume) to ACS’s PHYS email list:

HI Anne,

I agree with all of you that we don’t want to do this direct e-mail stuff!

Cheers, Martin

On Tue, Nov 17, 2009 at 4:17 AM, Anne wrote:
> > Martin, Martin, Sharon and Mark,
> >
> > Please see the message from ACS – my inclination is negative regarding the
> > mailing, but don’t have a problem promoting the conf on the website and even
> > mentioning that conf are posted there in my next mailing.
> >
> > Before I reply, I’d be interested in your thoughts.
> > Thanks
> >
> > ANne
> > —– Original Message —–
> > From: Richard
> > To:
> > Cc: Division
> > Sent: Tuesday, November 17, 2009 7:14 AM
> > Subject: FW: Official RSC Request to Engage PHYS Division
> >
> > Laurie and Ann,
> >
> >
> >
> > I am forwarding you a request from the Royal Society of Chemistry to use the
> > PHYS mailing list to promote a new conference, Challenges in Physical
> > Chemistry and Nanoscience (ISACS2), July 13 – 16, 2010, Budapest, Hungary.
> >
> >
> >
> > Please read through the request below from Valerie with the RSC.
> >
> >
> >
> > If approved, I recommend sending the RSC the list as an Excel file with just
> > the email addresses and PHYS member names, not the entire eRoster list.
> >
> >
> >
> > Let me know if you need any additional information.
> >
> >
> >
> > Thanks,
> >
> >
> >
> > Richard


sorry IE users

September 25, 2009 at 4:57 pm | | wild web

Sorry to the 20% of folks who visit my site using Internet Explorer. I just noticed that the site is basically broken using that browser. Oops.

Unfortunately, I’m too lazy to fix it. Sorry.

The site does work with Firefox, Safari, Chrome, Opera, Camino, Netscape, Opera Mini….

protect the non-born-oppenheimer!

September 9, 2009 at 12:49 pm | | crazy figure contest, literature, wild web

This is how the table-of-contents artwork showed up in my RSS reader:


Oops. It turns out that the artwork was supposed to look like this:


It takes some balls to make your TOC “artwork” a big, complicated equation.

citeulike and mendeley collaborate

June 4, 2009 at 8:34 am | | literature, science community, wild web

It has begun: Mendeley is integrating CiteULike libraries.

CiteULike is an online program for extracting metadata (e.g. authors, titles, etc.) from webpages of journal articles, then storing and organizing that data. I use it to organize the citations and DOIs of all the articles I find interesting.

Mendeley is an online database for storing and sharing PDFs of papers (plus a desktop application). I still don’t find Mendeley to be very helpful yet: still too buggy, too slow, and missing some vital features (e.g. effective metadata extraction, searching for metadata, finding duplicates). But there’s a lot of potential: they’re still in beta!

I use Papers for organizing and reading PDFs, but it only exists on the Mac, and doesn’t have a simple way to share libraries of PDFs across computers. There are probably some serious copyright issues with PDF sharing, and it will be interesting to see how Mendeley and Papers adapts.

UPDATE: Mendeley is quickly getting better. Their metadata extraction is more accurate, there is a PDF viewer, and linking to CUL means tagging is simple. Duplicate finding and merging is still needed, but the software is much better than when I first wrote this. Although I’m still using Papers somewhat because of inertia, I might suggest a newcomer try Mendeley right-off-the-bat.

deja boo?

June 2, 2009 at 9:53 am | | everyday science, literature, open thread, science community, scientific integrity, wild web

I’d like to know everyone’s opinion about Deja Vu, the database of “duplicate” scientific articles. Most of the articles in the database are “unverified,” meaning that they could be entirely legitimate (e.g. a reprint). Some are instances of self-plagiarism: an author recycling his or her own abstract or intro for a new paper or review. A few instances are true plagiarism: one group of authors stealing the words (entire paragraphs or papers) of other authors. You can read more in Science.

I can imagine several possible responses (see the poll below):

  1. Great! Now there’s a way for authors, journals, and institutions to better root out plagiarism and unauthorized copying.
  2. Granted, this is information in the public domain, so authors should expect their work to be scrutinized. However, it’s worrisome to have a computer algorithm put red flags on articles that may be legitimate. Deja Vu is probably a good idea, but needs to be reworked.
  3. Careers will be unfairly destroyed by this approach. Labeling a paper as a “duplicate” sounds negative, even when listed as “sanctioned” or “unverified.” This database takes a guilty-until-proven-innocent approach that has the potential to sully the reputation of good scientists.
  4. Um, haven’t these people seen Terminator 2? What is Deja Vu becomes self-aware and starts killing plagiarists.

[poll id=”2″]

Fortunately, an author can check his or her work in the eTBLAST database before submission, to see if a coauthor copied a section, or if the text will unfairly put up red flags. But I found that the results were confusing (e.g. I can’t find the meaning of the “score” or the “z-score”) and unhelpful (of course papers in the same field will have the same keywords). And the results page was really buggy (maybe just in Firefox?).

Personally, I vote #2: Deja Vu is a good idea, but needs to be more careful about the papers it lists as “duplicates,” even “unverified” or “sanctioned.” When a junior faculty member  gets a hit in the database, his or her name will be associated with plagiarism. Some people will not bother to check if it was a legitimate copy, or even who copied whom. I think that the current approach that Deja Vu takes is reckless and unfair. Even lazy.

Moreover, self-plagiarism is not necessarily bad. Copying your own abstract is different than copying your entire paper. Obviously, at some point, self-plagiarism is unacceptable (e.g. submitting the same paper or review to two journals).

I think this topic deserves more nuance than Deja Vu offers.

(Deja Vu has it’s own survey here.)

looking forward to wolfram|alpha

May 15, 2009 at 12:35 pm | | news, science and the public, science@home, wild web

Wolfram|alpha search engine goes live on Monday. I can’t wait. Here’s a demo. I’m sure they selected the queries very carefully. But for the queries they ran, Wolfram|alpha looks awesome!

There will be a live broadcast of them trying to go online, starting at 8 PM EST (5 PM Pacific).

UPDATE: Try using the site for chemistry.

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