a new PALM software package

February 13, 2015 at 2:11 pm | | nerd, software

2015-02-13 13.56.48

on the importance of hardware syncing

June 10, 2014 at 9:42 pm | | hardware, software

Before hardware syncing:


For more details: https://micro-manager.org/wiki/Hardware-based_synchronization

EDIT: And now incorporating a Sutter TLED transmitted light:

am i finished using Papers?

April 4, 2014 at 1:39 pm | | literature, software

I’ve been using Papers for years. When Papers2 came out, I was quick (too quick) to jump in and start using it. It’s worst bugs got ironed out within a couple months, and I used it happily for a while. Papers2 would let you sync PDFs to your iPad for offline reading, but it was slow and a little clunky. Papers3 library syncing is not for offline reading and it is VERY slow and VERY clunky. And it relies on Dropbox for storage. The plus of this is that storage is free (as long as you have space in Dropbox); the downside is that they syncing isn’t clean and often fails.

Mendeley has proven itself the best at syncing your library and actual PDFs to the cloud (you have to pre-download individual files for offline reading you can sync all PDFs in iOS in settings). Papers PDF viewer is still better, but it’s not worth the hassle: Mendeley syncs cleanly and the reader is fine. Not only that, but Mendeley has sharing options that make managing citations possible when writing a manuscript with co-authors (as long as they’ll use Mendeley).

Mendeley is also better than Papers at automatically finding the metadata for the paper (authors, title, abstract, etc.). The program simply works (most of the time), so I’ve given up and finally started using it. Almost exclusively.

PubChase syncs with Mendeley and recommends related papers weekly. (Update: the recommendations update daily, and they send out a weekly email with updates from that week.) They also have some pretty nice features, like a beautiful viewer for some journals and alerts when papers in your library are retracted.

Readcube still has the best recommendations. And they update daily, unlike PubChase’s weekly. And you can tell which recommendations you’ve marked as read, so it’s very quick to scan the list. But that’s really where Readcube’s benefits end. The enhanced PDF viewing feature is nice (it shows all the reference in the sidebar), but not really worth the slow-down in scrolling performance. The program is just clunky still. (I thought Adobe was slow!) And there’s no iOS/Android app yet. It’s on its way, allegedly, but I need it now! Readcube is really taking off, so maybe in a year it will be perfect. But not yet.

Edit: Readcube has a new version of their desktop application. Maybe it’s faster? Wait, did the references sidebar disappear? No, wait, it’s there. Just not on by default.

readcube and deepdyve update

June 6, 2013 at 7:48 am | | literature, science community, software

I just wanted to reiterate how great the ReadCube recommendations are. I imported all my PDFs and now check the recommendations every day. I often find great papers (and then later find them popping up in my RSS feeds).

Also, I wanted to let folks know that DeepDyve, the article rental site, is now allowing free 5-min rental of journal articles. Try it out!

PubReader review

April 14, 2013 at 7:52 pm | | literature, software

I’ve reviewed several PDF reader/organizers, like ReadCube, Papers, and Mendeley. Currently, I use Papers for organizing my PDF library on my computer. I also like Papers a lot for reading PDFs, because it displays in full screen so well. But I’ve started using Mendeley for adding citations to Word documents, because it makes it really easy to collaborate with other people who have Mendeley.

Now check out PubReader! It’s really cool. Pubmed has the advantage that it requires all research publications resulting from NIH funding to be uploaded to their depository. And they don’t just grab a PDF; they get the raw text and figures and they format it their own way. I used to think that was silly and overkill, but now I see that that approach was genius: it now allows Pubmed to reformat the papers into more readable shapes and sizes … and they can reformat in the future when the old format becomes antiquated. You can’t really do that with a PDF.

It’s always been nearly impossible to read PDFs on a phone or an e-ink tablet like the basic Kindle. Now, with PubReader and the beta option to download the article in an ePub format (for reading in iBooks or Kindle or something), that option is here. Or on its way, at least.

PubReader on a computer:


PubReader on iPad:

pubreader on ipad

ePub in iBooks:

ebook epub

Now PubReader just needs to display the references in an elegant way like ReadCube, and it will be the best!

It makes me think the future of reading and storing scientific papers is not the hard drive, but simply reading on online depositories. Pubmed allows you to create collection and star favorites, so you can just use Pubmed to store your collection of papers and never have to download a PDF again in your life!

readcube review

April 10, 2013 at 11:45 am | | literature, software

I recently tried Readcube, which is a PDF reader and organizer. I did so because Nature has been using it built into their site, and I like how it displaying PDFs. The article data downloads seamlessly for most papers, and  interface is quite beautiful:


The really cool feature is that Readcube automatically downloads the references and the supporting information documents and can display them at a click of a button. More importantly, it displays the references in the sidebar. It makes an excellent reading experience!

readcube2 readcube3

The final interesting feature is that Readcube offers recommendations based on your library. From my quick scan, the recommendations seem pretty good.

Other than that, Readcube is quite feature poor. It doesn’t have a way to insert citations into a Word document, like Papers and Mendeley does, although you can export to Endnote. I don’t see a way to read in full screen nor does it let you view two pages simultaneously, like Papers does.

papers fullscreen

The screenshot above is from Papers fullscreen view, which is how I really like to read PDFs.

But Readcube is still in beta, and they’re starting from a really nice starting point. I’m not ready to give up on Papers for reading (and I’ve been using Mendeley for Word citations, because it has really nice collaborative features). But I might try Readcube some more, mainly because of the awesome ability to see all the references and the paper simultaneously. I really wish I could mash Papers, Mendeley, and Readcube all together into one feature-rich program…

google reader alternatives

April 3, 2013 at 8:12 am | | everyday science, literature, science community, software

Now that Google Reader is going the way of the dodo Google Gears, how am I going to keep up with the literature?!? I read RSS feeds of many journal table of contents, because it’s one of the best ways to keep up with all the articles out there (and see the awesome TOC art). So what am I to do?

There are many RSS readers out there (one of my favorites was Feeddler for iOS), but the real problem is syncing! Google servers took care of all the syncing when I read RSS feeds on my phone and then want to continue reading at home on my computer. The RSS readers out there are simply pretty faces on top of Google Reader’s guts.

But now those RSS programs are scrambling to build their own syncing databases. Feedly, one of the frontrunners to come out of the Google Reader retirement, claims that their project Normandy will take care of everything seamlessly. Reeder, another very popular reader, also claims that syncing will continue, probably using Feedbin. Feeddler also says they’re not going away, but with no details. After July 1, we’ll see how many of these programs actually work!

So what am I doing? I’ve tried Feedly and really like how pretty it is and easy it is to use. The real problem with Feedly is that its designed for beauty, not necessarily utility. For instance look how pretty it displays on my iPad:


But note that its hard to distinguish the journal from the authors and the abstract. And it doesn’t show the full TOC image. Feedly might be faster (you can swipe to move to the next articles), but you may not get as much full information in your brain and might miss articles that might actually interest you.

Here’s Reeder, which displays the title, journal, authors, and TOC art all differently, making it easy to quickly scan each  article:



And Feeddler:


I love that Feeddler lets me put the navigation arrow on the bottom right or left, and that it displays a lot of information in nice formatting for each entry. That way, I can quickly flip through many articles and get the full information. The major problem is that it doesn’t have a Mac or PC version, so you’ll be stuck on your phone.

I think I’ll drop Feeddler and keep demoing Reedler and Feedly until July 1 rolls around.

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.

new chemistry dictionary for Word and OO.o

January 20, 2011 at 9:40 am | | science community, software

Check it out: azmanam has a new version of the chemistry dictionary for Word:


Now you can eliminate all those red squiggly lines under half the words in your document.


how do you read PDFs?

July 28, 2010 at 8:59 am | | everyday science, help me, literature, open thread, software, stupid technology

I now have a longer commute, with at least 30 minutes of quality reading time. I don’t really want to carry my laptop everyday, so I’m seeking a better way to read journal articles. I’m not going to print them out, so don’t suggest reading them on paper. :)

[poll id=”3″]

Of course, cost is a factor, but I don’t want to go for the cheapest option if I end up never using it! My guess is that the Kindle DX is the best for reading PDFs, but loses on other fronts (e.g. large, expensive, limited, only grayscale). The iPad is a versatile color reader and I can sync with programs such as Papers or Mendeley (soon for the latter), but it is very expensive. Also, the screen isn’t as nice for reading print. The iPhone is way too small to read PDFs.

Man, I need to test-drive these devices for a month!

Other options?

why are email clients dumb?

March 2, 2009 at 11:06 am | | software, stupid technology, wild web

Why does Thunderbird not recognize the word “inbox”?


It seems to me that it should.

chemistry dictionary for Word

December 17, 2008 at 9:32 am | | science community, software

This is pretty cool. Check out this chemistry dictionary for Word that contains thousands of chemistry words for the spell checker. That should reduce the little red squiggles all over the documents! Thanks azmanam over at Chemistry-Blog.


I’m using it. It knows what an azepine is!

It’s very easy to install and it doesn’t overwrite your own custom dictionary. The README file is helpful, but I suggest you store the chemistry.dic file here instead of My Documents:
C:\Documents and Settings\USER\Application Data\Microsoft\Proof

Gaming for Science: Fold.it goes public!

May 9, 2008 at 11:47 am | | science and the public, science@home, software, wild web

I just saw a remarkable take on an age-old problem: Protein Folding. David Baker at the University of Washington converted the problem of protein folding into an interactive game that we can play. Check it out at Fold.it (currently beeing /. to death)

Details about the science are sparse, but my undestanding is that they’re trying to train us like a neural network of sorts- first we learn to fold known protein structures, and then the group will release new “puzzles” of unknown or unreleased structures and see how the the borg collective does against other folding projects .

Oh yea, I made an “Everyday Scientists”mebeli group! Can’t wait to play when I get home

filter your RSS feeds using Pipes

March 20, 2008 at 10:51 am | | great finds, science community, software, wild web

I read all my TOCs via RSS in Google Reader. Normally, this is just marvelous. However, some journals (e.g. Science and Nature) include a lot of junk along with the real science articles: news and whatnot. Also, PNAS has so many articles, it’s really hard to get through them all.

So I’ve started filtering some of those TOC RSS feeds using Yahoo! Pipes. (Click the image above for an example—the filter function is found under “Operators.”) So PNAS was easy, because they include the subject category in the title of each feed item. For Nature and Science, I need to find a way to filter out the news and fluff pieces somehow. Maybe there’s a keyword in those entries I can find.

Anyway, I just wanted to pass this along, because it’s really helpful. I know there are other RSS filters, but I like the versatility and ease of Yahoo! Pipes. Lemme know if you find any cool tricks!

Here’s a library of my edited feeds.

think gum

March 11, 2008 at 8:32 am | | lab safety, pseudoscience, software, stupid technology

Finally, a gum that will clean my teeth and my synapses! My PI found this wonderful product:


This gum must have brain-boosting powe, with all its “proven” ingredients (including rosemary and peppermint). It does have 20 mg of caffeine (which is a little less than a cup of green tea of a Coke), which I’ve found does help concentration; but coffee makes my breath smell so much better! This caffeine is “natural,” which is nice because I’m sick of getting my caffeine the only other way possible: via that intravenous injections of SynthCaffTM eight times a day.

You know, at first, I was just going to make fun of this product. But then I read the story. Hey! This kid went to Cal and now he’s a PhD student here at Stanford. I’m quite impressed with his entrepreneurial spirit. I’m really happy that this gum isn’t secretly made by Clorox or ExxonMobil or something.1

OK, back to making fun of it. I still think the gum is bunk: it uses the label “science” to sell a product to the gullible public, like my mom. (Just kidding, Mom.) But I’ll try it…

Well, the flavor is really good: a nice mixture of herbs and it has a green taste that transforms to an almost spicy pleasant-bitter, with a hint of spruce; the flavor lasts longer than some brand-name gums. Is my writing getting any better? I can see the fourth dimension and smell “yellow.” Is that normal? I feel like taking the rest of the day off and watch each blade of grass discover its little world. Seriously, though, I do feel a little light-headed.2

Well, I guess this product is no worse than all the other “mind-boosting” drinks and pills out there; and it tastes good! I did feel a little different after chewing it for 15 minutes, but no different than after half a cup of coffee, wondrous coffee.

Jeez, I almost recommend it. (That’s embarrassing.) But I recommend it if you want a nice flavored gum with some caffeine that will make you light-headed and feel happy … and your French press is broken.


1 Great stocks to own, terrible companies to make you gum.
2 My spelling got a lost wose [that was supposed to be “worse,” for instance] after chewing the gum, for some strange reason. And my HTML editing just got an order of magnitude more destructive

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