Dear all,
I cannot keep up with the amount of random one liner comments in twitter, it seems, and the random words followed by exclamation points are building up to be an impenetrable wall of inside-jokes at this point. It's not that my schedule is any busier, per se, but after I get home and finishes all the chores I tend to spend the time either reading or drawing things in the 30-60min that I have left, so the blog just does not get updated, no matter how well meaning I was on the bus, on my way home from work.
20110924
Science twit
Dear all,
Blogger is still doing the weird thing where the cursor, after I tapped "enter" key twice, will not have moved, but the typing will show up at the right spot. It's still disconcerting.
In other news, the martial arts exam day is coming up. I am about three lessons away from it and everyone who's testing (there're around ten of us) is starting the rounds of "Are you ready?" Today I went through two hours of lesson before staying behind to run through the entire exam material with Cathe, to get the "feel". I am certainly feeling it now (as opposed to norm, where I feel it the day after). A nap would be nice, but sadly I still have a bunch of chores to do. Blogging is currently my break / procrastination method of choice.
Blogger is still doing the weird thing where the cursor, after I tapped "enter" key twice, will not have moved, but the typing will show up at the right spot. It's still disconcerting.
In other news, the martial arts exam day is coming up. I am about three lessons away from it and everyone who's testing (there're around ten of us) is starting the rounds of "Are you ready?" Today I went through two hours of lesson before staying behind to run through the entire exam material with Cathe, to get the "feel". I am certainly feeling it now (as opposed to norm, where I feel it the day after). A nap would be nice, but sadly I still have a bunch of chores to do. Blogging is currently my break / procrastination method of choice.
20110917
Still on the vigilance for ants
Dear all,
I realized that I haven't mentioned the ants problem in a while. It hasn't been solved...conclusively. I have left the landlady a note about it, received no reply, didn't have the time to bother her in person, and so a few weeks passed where there were errant ants, then there were fewer ants, followed by days when I swore the ants were gone, followed by a day of finding ants in the medicine cabinet (but only on one shelf, and why is that? They came out of a crack on the wall and disappeared into a crack on the wall so it is only one shelf that was infested), followed by now, another reprieve from ants that I may have just jinxed myself out of.
So there you have it: Ant Problem by Susan. Graded I for Incomplete.
I realized that I haven't mentioned the ants problem in a while. It hasn't been solved...conclusively. I have left the landlady a note about it, received no reply, didn't have the time to bother her in person, and so a few weeks passed where there were errant ants, then there were fewer ants, followed by days when I swore the ants were gone, followed by a day of finding ants in the medicine cabinet (but only on one shelf, and why is that? They came out of a crack on the wall and disappeared into a crack on the wall so it is only one shelf that was infested), followed by now, another reprieve from ants that I may have just jinxed myself out of.
So there you have it: Ant Problem by Susan. Graded I for Incomplete.
20110916
"You're beeping," says she
Dear all,
I was comparing Wordpress with Blogger this week and have, in conclusion, decided that though I like the fact that Wordpress is under the GPL and I am all for open-sourced things, the really cool things that caught my eye about Wordpress only applies to Wordpress.org and not Wordpress.com (for some reason I keep typing "Worldpress", which makes me think of some kind of newspaper), or in other words, only if you host your own blog. For the regular stuff the differences isn't that great, and frankly I've been with blogger for too many years (since what? 2003? Definitely by 2004 and christ that's a long time ago) to bother changing for the minutiae. (Though blogger? Being able to password protect an entry so only certain people can see it would be very very nice. Hint hint.) On the plus side, I did find out more stuff about blogger that I could do, that I didn't previously known I could. Like this
I was comparing Wordpress with Blogger this week and have, in conclusion, decided that though I like the fact that Wordpress is under the GPL and I am all for open-sourced things, the really cool things that caught my eye about Wordpress only applies to Wordpress.org and not Wordpress.com (for some reason I keep typing "Worldpress", which makes me think of some kind of newspaper), or in other words, only if you host your own blog. For the regular stuff the differences isn't that great, and frankly I've been with blogger for too many years (since what? 2003? Definitely by 2004 and christ that's a long time ago) to bother changing for the minutiae. (Though blogger? Being able to password protect an entry so only certain people can see it would be very very nice. Hint hint.) On the plus side, I did find out more stuff about blogger that I could do, that I didn't previously known I could. Like this
20110912
Dear all
Happy Mid-Autumn!
Today I have also discovered which plant the "rhubarb" is. Recipe suggestions, anyone?
Today I have also discovered which plant the "rhubarb" is. Recipe suggestions, anyone?
20110911
Well now that will be stuck in my head for the rest of the day
J. Coulton apparently wrote a song about Ikea and, thanks to last.fm, I just heard it. It is as catching as the DNA song but it's the most bizarre experience ever to have a chorus going "Ikkkeeeaaa Ikeeeaaa" in your brain.
Right.
Have either got bitten by something multiple times in my hand or am having an allergic reaction to something. Jury's still out on that one. I no longer have a backup sketchbook, which is a situation that hasn't happened in years (what? I can't be the only one who likes to have a empty book around as backup) and dire and requires immediate remedy. Luckily tomorrow is Monday and there's the school bookstore. The key point in this sudden proliferation mostly lies in my discovery that a) even though everyone "requires" you to have a plan for your future, no one expect you to follow through on your plans. It's a game where everyone's in on the rules that the future is fluid but for the sake of paperwork and funding you need to make it sound like you know exactly what you're doing with your life, down the length of time it will take to ...I don't know, breed three litters of mice. B) We're young, we're allowed to goof off and do other things in our spare time -- so long as we don't tell the PI (and any source that can get back to the PI). Apparently I have very musically talented classmates and there are all these band things that I didn't know about and so life suddenly seem to deflate a little from all the presumed pressure, which are actually mostly in my head. But.
Does Blogger have password protected entry type thing yet? Or I may have to switch to wordpress at some point. My LJ account is linked to too many things and it could get very confusing very fast but I don't want to get rid of it because of all the f-locked entries it gives me access to. And why does my entire apartment still smell like the French toast I made for breakfast? It's been airing for over five hours now.
Right.
Have either got bitten by something multiple times in my hand or am having an allergic reaction to something. Jury's still out on that one. I no longer have a backup sketchbook, which is a situation that hasn't happened in years (what? I can't be the only one who likes to have a empty book around as backup) and dire and requires immediate remedy. Luckily tomorrow is Monday and there's the school bookstore. The key point in this sudden proliferation mostly lies in my discovery that a) even though everyone "requires" you to have a plan for your future, no one expect you to follow through on your plans. It's a game where everyone's in on the rules that the future is fluid but for the sake of paperwork and funding you need to make it sound like you know exactly what you're doing with your life, down the length of time it will take to ...I don't know, breed three litters of mice. B) We're young, we're allowed to goof off and do other things in our spare time -- so long as we don't tell the PI (and any source that can get back to the PI). Apparently I have very musically talented classmates and there are all these band things that I didn't know about and so life suddenly seem to deflate a little from all the presumed pressure, which are actually mostly in my head. But.
Does Blogger have password protected entry type thing yet? Or I may have to switch to wordpress at some point. My LJ account is linked to too many things and it could get very confusing very fast but I don't want to get rid of it because of all the f-locked entries it gives me access to. And why does my entire apartment still smell like the French toast I made for breakfast? It's been airing for over five hours now.
20110910
Local insanity is insane
Dear all,
I am currently in lab, since the power outage from Thursday put me slightly behind schedule in terms of experiments, both in terms of actual experiment and in terms of equipment malfunction (sensitive equipment don't take well to sudden shut downs). The day had started off gloomy, moved toward sunny, and now the evening clouds have already crept in from the ocean. I am going to attempt to summarize the past week's events in the order that I remember them, which may seem random and definitely will not be chronological. You all have been warned.
Blogger's new posting window does the "save" thing automatically, much like Google docs, but somehow the lag is worse and so I end up pressing enter fruitlessly, trying to start a new paragraph, while the scripts are busy churning away, trying to store a snapshot of my typing, and then my cursor jumps to the start of the paragraph for no reason. It is annoying. Dear Blogger, please stop doing that.
The recovery from the blackout seems to be coming along fine. There are still traffic light malfunctions everywhere. It looks like any system that is tied to a timer is a little ditzy at the moment (and on Friday, all the outdoor lighting that's tied, I assume, to a digital -- as opposed to analogue -- timer that does not run on batteries was on the fritz -- as in all the night lighting were on during day time and that was interesting), but we have so far received no warning about the fragile system after Friday, and it looks like everything's still set to run on full power come Monday.
The side-view mirror from my car came this week. I got the first notice, in fact, on Thursday. I always get notice for these things since I am never home during normal working hours on weekdays, and they can never tell me exactly what time they were going to drop by (I can't exactly sit around all morning / afternoon waiting for one package), so am well familiar with the course of action required of me. Though I did refrain from calling Thursday evening since they keep all the records on computers and well, with the power out, even if they were diligent and didn't go home like the rest of us, they won't be able to pull out my record anyway. So: I called yesterday and have just picked up the mirror. It's currently sitting in the trunk of my car (the office for it is closer to lab than home). (Though on my way there I noticed a restaurant that declared "Japanese! American! Seafood! Chinese!" One of those is obviously not like the other. I was amused.)
...
It turns out the cursor only appears to be at the start of the paragraph, but when you type the font shows up at the right place. I am on Ivy right now, running Firefox 3.6.20 on Fedora 14. Dear Blogger, I do not understand.
...
Earlier this week I was ordering a copy of Persepolis (along with a set of jeweler's screwdrivers, heh) on Amazon when I realized that I have been talking about buying a nicer camera, which my parents did offer to do for me (then they talked to me and decided to get me a new laptop instead. Did I blog about that when they came over? I don't think I did. We had a joint almost-birthday thing -- belated for mine and early for mom but right on day for dad and they gave me a nice Dell laptop which I named Elev) for a really long time. And you know what? I have no idea why I haven't bought it yet. So: I ordered myself the Canon EOS camera that I've been crushing on for just over a year and a macro lens (with my obsession with plants this cannot come as a surprise to ...well, anyone) and that, everyone, would be very exciting indeed. Especially given that it's starting to look like that more people can make the Arizona trip over winter break and that Malvina would prefer a winter break trip and so I have Thanksgiving, which I refuse to spend ALL in lab (just most of it to make up for the time off that I'll now need at probably the end of December), so I'll probably go hiking somewhere nearby and play with my camera.
...
And now I'm home, having left lab to do grocery shopping, where I ran into a post-doc. This is not the 99-Ranch meeting of Chinese. My program has 4 predominant neurosci / genetics labs: I work in one, he and Wendy's best friend is in the other (our labs have a complicated sometimes collaborator, sometimes competitor atmosphere). He is French and the subject of much teasing when Wendy and I went over to borrow their guillotine tissue slicer and couldn't find it, in the sense that the girl we were with claimed that the French (man) stole it. (He didn't actually steal it. It was in a box with other boxes from another post-doc who left.) It was a health food store and I suppose that makes sense, given I see on him on the bus fairly regularly. I said "hi" and it was all very awkward, because I can never quite figure out how closely I must interact with someone before they remember me, and so must decide between accidentally ignoring someone who did remember me and creeping out someone who didn't. Luckily he remembered me, so that's one less Awkward Penguin in my zoo.
I've installed the new mirror (despite of the advertisement, the connectors aren't quite right, so I'm trying to figure out if I have the tools to slap on a new connector) on the car after that, and washed a lot of dishes and now I must go make dinner if I want to eat it by the time I get hungry. But before that I want to mention that Ivy's my carry-on "book" where I have it sync'ed to a lot of things and have a bunch of reading material there and Thursday night I did try to read HUNGER GAMES again (having downloaded a copy much earlier)...and quickly remember why I stopped: generally I don't like first person narratives, but I can tolerate it if I like the person OR the writing is really good OR the plot is really engaging. Katniss annoys me, the writing style is not what I would consider exceptional, and I failed to be wow'ed by the plot. So no, not for me.
There are some other things but a) I can't recall them off of the top of my head at the moment and b) FOOD! And I'm on Elev running Firefox 6.0.2 on Windows 7 and when I hit enter twice to start a new paragraph the cursor disappears, though the letters will show up at the right place afterwards. Dear blogger, I am confused.
I am currently in lab, since the power outage from Thursday put me slightly behind schedule in terms of experiments, both in terms of actual experiment and in terms of equipment malfunction (sensitive equipment don't take well to sudden shut downs). The day had started off gloomy, moved toward sunny, and now the evening clouds have already crept in from the ocean. I am going to attempt to summarize the past week's events in the order that I remember them, which may seem random and definitely will not be chronological. You all have been warned.
Blogger's new posting window does the "save" thing automatically, much like Google docs, but somehow the lag is worse and so I end up pressing enter fruitlessly, trying to start a new paragraph, while the scripts are busy churning away, trying to store a snapshot of my typing, and then my cursor jumps to the start of the paragraph for no reason. It is annoying. Dear Blogger, please stop doing that.
The recovery from the blackout seems to be coming along fine. There are still traffic light malfunctions everywhere. It looks like any system that is tied to a timer is a little ditzy at the moment (and on Friday, all the outdoor lighting that's tied, I assume, to a digital -- as opposed to analogue -- timer that does not run on batteries was on the fritz -- as in all the night lighting were on during day time and that was interesting), but we have so far received no warning about the fragile system after Friday, and it looks like everything's still set to run on full power come Monday.
The side-view mirror from my car came this week. I got the first notice, in fact, on Thursday. I always get notice for these things since I am never home during normal working hours on weekdays, and they can never tell me exactly what time they were going to drop by (I can't exactly sit around all morning / afternoon waiting for one package), so am well familiar with the course of action required of me. Though I did refrain from calling Thursday evening since they keep all the records on computers and well, with the power out, even if they were diligent and didn't go home like the rest of us, they won't be able to pull out my record anyway. So: I called yesterday and have just picked up the mirror. It's currently sitting in the trunk of my car (the office for it is closer to lab than home). (Though on my way there I noticed a restaurant that declared "Japanese! American! Seafood! Chinese!" One of those is obviously not like the other. I was amused.)
...
It turns out the cursor only appears to be at the start of the paragraph, but when you type the font shows up at the right place. I am on Ivy right now, running Firefox 3.6.20 on Fedora 14. Dear Blogger, I do not understand.
...
Earlier this week I was ordering a copy of Persepolis (along with a set of jeweler's screwdrivers, heh) on Amazon when I realized that I have been talking about buying a nicer camera, which my parents did offer to do for me (then they talked to me and decided to get me a new laptop instead. Did I blog about that when they came over? I don't think I did. We had a joint almost-birthday thing -- belated for mine and early for mom but right on day for dad and they gave me a nice Dell laptop which I named Elev) for a really long time. And you know what? I have no idea why I haven't bought it yet. So: I ordered myself the Canon EOS camera that I've been crushing on for just over a year and a macro lens (with my obsession with plants this cannot come as a surprise to ...well, anyone) and that, everyone, would be very exciting indeed. Especially given that it's starting to look like that more people can make the Arizona trip over winter break and that Malvina would prefer a winter break trip and so I have Thanksgiving, which I refuse to spend ALL in lab (just most of it to make up for the time off that I'll now need at probably the end of December), so I'll probably go hiking somewhere nearby and play with my camera.
...
And now I'm home, having left lab to do grocery shopping, where I ran into a post-doc. This is not the 99-Ranch meeting of Chinese. My program has 4 predominant neurosci / genetics labs: I work in one, he and Wendy's best friend is in the other (our labs have a complicated sometimes collaborator, sometimes competitor atmosphere). He is French and the subject of much teasing when Wendy and I went over to borrow their guillotine tissue slicer and couldn't find it, in the sense that the girl we were with claimed that the French (man) stole it. (He didn't actually steal it. It was in a box with other boxes from another post-doc who left.) It was a health food store and I suppose that makes sense, given I see on him on the bus fairly regularly. I said "hi" and it was all very awkward, because I can never quite figure out how closely I must interact with someone before they remember me, and so must decide between accidentally ignoring someone who did remember me and creeping out someone who didn't. Luckily he remembered me, so that's one less Awkward Penguin in my zoo.
I've installed the new mirror (despite of the advertisement, the connectors aren't quite right, so I'm trying to figure out if I have the tools to slap on a new connector) on the car after that, and washed a lot of dishes and now I must go make dinner if I want to eat it by the time I get hungry. But before that I want to mention that Ivy's my carry-on "book" where I have it sync'ed to a lot of things and have a bunch of reading material there and Thursday night I did try to read HUNGER GAMES again (having downloaded a copy much earlier)...and quickly remember why I stopped: generally I don't like first person narratives, but I can tolerate it if I like the person OR the writing is really good OR the plot is really engaging. Katniss annoys me, the writing style is not what I would consider exceptional, and I failed to be wow'ed by the plot. So no, not for me.
There are some other things but a) I can't recall them off of the top of my head at the moment and b) FOOD! And I'm on Elev running Firefox 6.0.2 on Windows 7 and when I hit enter twice to start a new paragraph the cursor disappears, though the letters will show up at the right place afterwards. Dear blogger, I am confused.
20110903
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?
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?
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