It's like citrus on a porcelain, maybe?

It looks like blogger's updated their interface again -- this time into something that resembles, for better or worse, Google Docs. It's very clean though, and given that one of my favorite decor themes is the modern-minimalist style (the others are garden cottage and this wood/glass/ceramic mix that I still haven't quite figured out how to describe yet) I have, as of now, decided that I like it.

Whether or not the interface functions well, however... ask me in a month.

(Though there is this odd thing: why is the "compose" tab's textbox around....hmm...700 x 300pixels? Especially when  the "html" tab can take up all the grey space between the post settings in the right hand column and the toolbars on top?)

(Also: augh, I'd forgotten why I don't switch between the two more frequently -- the compose tab adds needless tags. It's like trying to make a webpage using solely Dreamweaver and looking at the HTML after you're done with the design -- the code's just so ...bulky and ugly.)

In the meantime, the sudden distraction provided by a GUI change (really, what else does grey/white/orange theme makes you think of, besides tangerines on a plate?), I am going to do my software review post now while I still remember. As everyone knows, I work in a laboratory and am listed as a graduate researcher. In the current day laboratory, computer is an absolute necessity, and efficient research means ways to organize, process, and manage a ton of data / material of all kinds. Here are, my composite list of things that I found indispensable, composed during the past few months.  

Libre Office - as compared to Open Office and MS Office on PC and Mac. People tend to prefer MS for a variety of reasons, but the more recent versions that laptops in my (and my classmate's) experiences ship with is only the trial version. If the deadline doesn't get to you, the advertisement well. And all of us being poor grad students, I've been introducing people to the free, open source alternative that at this point pretty much does everything that I need MS for (yes, including the custom error bars that, as far as I was concerned, was the only blemish with the new spreadsheet program). I originally used Open Office even while I had MS Word because depending on the version of computer, the version of MS would be different and the old MS Office cannot open the new MS Office files, while Open Office opened...everything. This was key to me and many of my co-workers because in science there's a lot of collaboration between researchers and labs, and so a lot of files get shared and it's really frustrating to try to contact a collaborator who's terrible about answering his emails for a different format of data that you can actually read. The interface is set up the same way as MS, for PC and Macs the installation is very simple and both Fedora and Ubuntu (Ivy's been doing fine, thanks) comes with, so I get cross platform compatibility. Libre Office is what I'm using now since Open Office got forked. While Open Office may die a slow death as the company shut down its development, Libre Office, as the forked version, will live on in the open source community, or so is the impression I'm given. Libre Office / Open Office do have their own file format, but everything exports to MS compatible files. The newer, full version of MS Office that one of my co-workers have (we're mostly a mac-dominated lab), at least, can open the Libre Office / Open Office files as well. The only downside is that the embedded images in presentations and word documents will...ah...experience a shift in their formatting...but as this is also a major issue between Mac and PC versions, I don't really see it as a major problem.

Evernote - as compared to gnote, nevernote, tomboy, Yes, yes, Microsoft has OneNote and Apple has Simplenote (and possibly something else that's like an integrated calendar + note taking + I don't know what all in one that's all very shiny but unnecessary for what I need), but again: grad students. Evernote is free, though you can pay for larger upload space I found that the monthly allowance of space of 60MB is more than enough for my labnotes, complete with the images and tables. Yes, I keep eNotes, and have convinced Wendy to do likewise. Know why? Otherwise handwriting our notes each week, printing and pasting our figures and images into a hardcopy notebook? Takes about 2.5hrs. That's how much stuff I generate in terms of experiments. Those 2.5 hrs? Enough to run more experiments or actually finish analyzing my data before lab meeting. My PI is the sort who doesn't care if the note's in a bound notebook or not (mileage may vary, some professors are VERY strict about this), so I'm taking full advantage of this. I have to confess though, the main reason why I was won over completely was that I can generate separate notes that can organized by notebooks, then by stacks, and I can tag every single note by experiment in addition to doing keyword search on all my notes. Need to find the exact protocol that gave me the results for that blog two months ago? No problem, select "blot" for experiment tag, and then key word search in those entries for my sample names. Beats flipping through stacks of physical notebook every time. (It's just so...efficient.) Evernote also runs on both Mac and PC, with Nevernote being the Linux version of it. Nevernote can be synced with your Evernote files, though I don't think the reverse is true, which is one downside. But yes -- syncing. It allows you to create "local" notebooks that exist only on that computer, or "global" notebooks that can be loaded on any computer that runs Evernote or, in my case one sad Friday night when I realized I forgot my laptop charger in lab -- it allows me to access all my synced notes online, without downloading any program onto the computer. Gnote and Tomboy are also note taking applications I've tried on Linux, but they just don't have as many features and formatting options and I can't attach spreadsheets, pdfs, what-have-you, or clip an entire email or segment of website with the click of a button. Evernote may well be the best discovery I found since the days when I discovered CutePDF, back before printing to PDF was an option browsers came with. All the notes can be exported as database (keeping the tag organization) or as html (which I then promptly convert to PDF, so I can print them out for a hardcopy as needed without worrying whether or not moving my gel image will upset the img src tag).

Xournal - vs. acrobat reader vs. jarnote I'll confess that I have acrobat reader right now on my computer, because it shipped with Kerral and handy enough that I didn't bother installing anything else. The function of Xournal and Acrobat are a little different though. Where Acrobat gives you more room to maneuver in terms of forms, Xournal is meant to be a program that's compatible with a tablet. For someone who used to like to print out notes to scribble on them because typing up notes in Notepad is Just Not The Same? I have a tablet, and Xournal was my reader of choice before my new laptop arrived. Only issue is that if you export your scribbles to PDF, the people after you can no longer change that scribbling. If you use the default format you can ...but that Acrobat doesn't support that format. Jarnote just doesn't have the interface.

GIMP vs Photoshop vs Seashore I love Photoshop, I really do. In fact when I get my next round of training grant allowance I will probably buy it. However, that is the issue: Photoshop is sooo freakin' expensive, and GIMP is free. For the manuscripts they often prefer files generated from Name Brand programs, but for my drawings and editings for fun and for lab, I use GIMP. It has everything I need, essentially. Though Photoshop will have some fancier manipulation tools, I don't normally use them, and GIMP does filters, layers, transformation, and can complete very well with Photoshop in the sense of image conversion and the number of files it can open. In the meanwhile, for all the students who come into our lab who doesn't have an image editing program (I'm sorry, but Paint just doesn't cut it). I've also tried Seashore because as I've said, I'm in a Mac-dominated lab, but it doesn't quite have the same level of sophistication / number of functions. I have GIMP on all my PCs, so yes it's for Linux and Windows. My only issue with it is that it doesn't have a very pretty name.... (Yes, I like it that much. I'm not even bothering to install my old version of Photoshop right now.)
 
Mendeley vs Zotero vs Endnote Ah the life of a researcher. Where would we be without something to manage our hundreds of reference papers and generate our bibliographies? Do it by hand? I think not. That would mean every time you change and add / delete a reference you have to click through your entire paper to remove references AND editing the Works Cited portion at the end, and given the average number of citations is anywhere between 35 to over 100...it can be painful. Not to mention different publishers have different formats for bibliography. Imaging retyping ALL 100 of the citations by hand because the citation you used for your research proposal does not match that of your journal of submission. No. We'd be even crazier than we are if we did that. Instead most of the people I know uses Endnote. And then I, being the nerdy open-source girl that I am, went and found both Zotero and Mendeley, both of which are free and does essentially the same thing as Endnote (yes they include the citation styles for over 100 journals -- both of them). Both have limited storage space online so you can sync your articles, and both come with built in networking function that makes it simple to share references between collaborators. Zotero is cleaner in terms of interface, does not require a desktop download, and runs integrated to Firefox. I am currently running Mendeley because it has a lot more resources for life sciences (Zotero seems to aim more toward the social sciences) and has a slightly larger size limit. It does require a desktop download, which is a benefit in my case because I have crashed browsers and sometimes Zotero has trouble restarting along with the crashed Firefox. While both Zotero and Mendeley allows you to retrieve citation information for any paper before and after you installed their program from the internet, as well as download citation directly with a click of the button, Mendeley also comes with a cool integrated pdf viewer / editor. The functions there are a little limited for my taste (see: Xournal), Mendeley has a much more active (or so it seems) developer group and they really impressed me by setting up this system where every user gets 10 votes and you can vote (or suggest) on which key issues the developers should look at next. You can vote more than once on any issue, but once you run out of votes you have to wait until one of the issues you voted on gets solved so you'd get those votes back. The issues / suggestions with the most votes of course, gets worked on first. The level of dedication it takes to set up something like this is just...wow. You can export things out from Zotero and Mendeley, by the way, and they are compatible with each other and with Endnote.

So those are the main 5. Other stuff I've compared includes:

Firefox vs. Opera vs. Chrome vs. Safari vs Internet Explorer -- I still prefer firefox. Nothing else has that many selections of free add-ons so that I can pretty much custom tailor the functions of my browser. Then my preferences goes: Chrome, Safari, Opera, IE. I really don't like IE. Firefox also runs on all platforms and comes with any Linux install.

Clementine vs iTunes vs Media Player vs Mufin player -- I don't own an ipod, so iTunes for me would just be a music organizing tool, nothing more -- I can't sync it with my mp3 player. I prefer Clementine because it deals with multiple file formats the best (all the others have things they won't open), though Mufin has a better user interface. I'm not sure if Mufin does this, but Clementine also can be linked to last.fm so anything I play on my computer gets added to my library there, which I thought was pretty cool. My favorite feature though? "Music info". If I leave that tab open as each song is played Clementine will automatically pull up the lyrics for that song from the internet. No idea what else does this, but it saves me from dealing with the annoying popups (and possible viruses) from the lyrics websites. Linux and Windows compatible.

Crash Plan vs Dropbox -- I prefer Dropbox mostly because it suits my needs best at the moment. Crash Plan is better if you want to back up your entire hard drive constantly buuuut for me that's not really necessary. I have an external drive that I store all my files on and don't do long-term storage on my computer anyways. (Oops -- Annie I forgot about the Dropbox invite / quota thing until a few days after I signed up. Sorry!) I never got Crash Plan to work quite as I intended on either system. Or at least I'm not happy with its function. Dropbox I have installed on both Ivy and Kerral, so Ubuntu and Windows, certainly.

Other things I like:

Audacity -- still the best when it comes to freeware for sound editing. Linux and Windows compatible.

Google Docs -- THEY FINALLY PUT IN THE THING TO ALLOW PAGE NUMBERS ON THE WORD DOCUMENTS! I used all caps so you can get an idea of how much that originally frustrated me. I still prefer Libre Office for work, but for other stuff, Google Docs makes it easy to share stuff and also, without needing to download anything, I can work on my files anywhere that has internet, on any computer, which is awesome. To coordinate the interview weekends, the orientations, lunch seminars and such in our program, we frequently have things in Google Doc and just share them / update them that way.

Lablife - download free online place for inventory, orders, protocols, files, notes, lab announcements, all rolled into one, for free. It's amazing! If we can convince everyone in our lab to join we will never had the issue of spending 15 minutes digging through boxes in the -80C trying find samples from two years ago. The inventory / shopping list allows you to pull information directly from the internet, so the lab tech (ours thankfully uses this) can get the exact catalog number to order exactly what you wanted and, when she orders it, the status of the order changes to let you know it's ordered. There's a record of all orders placed as well so re-ordering things is super easy. There's a personal page and a lab page, so you can export protocols to only yourself or to share with the entire lab. All the inventory and data can also be exported as .xls spreadsheet so you have a copy on your computer as well. The only issue is a) they don't have sample type for "DNA", only "plasmid"...so what do I do with DNA that's not plasmid? and b) they have too many options for information for inventories so it takes forever to fill it out. I mostly operate by having spreadsheets on my computer that I periodically upload onto the site, titled "Inventories".

Media Player - confusing because of the name, but this is actually a Windows Media Player look-alike except it's open source and has a gazillion of codecs you can get for free and so can play pretty much anything under the sun. The quality for some of these things may not be as good as if you installed the native program for it, but since I don't watch things much, I usually prefer to get this rather than having half a dozen programs scattered around. Linux and Windows compatible.

Whew that was a huge post. Well, that's what I get for being nerdy and wanting to share.

[edit immediately after] Blogger apparently no longer renders a skipped line in HTML as a line break. And every time I hit "enter" under the "compose" tab the window skips to the end of the entry so I have to scroll back up to find my cursor. Why, Blogger, WHY?