Arrays again

Considering the fact that I'm supposed to present a poster later this summer on the microarray data that my adviser has collected in collaboration with another lab, I figured it was time to brush the old data off again. I must admit that I've been so busy that I haven't taken a look at the data in about a year.

My research has taken off in a different direction, then I got busy taking written and oral qualifying exams, and currently I'm furiously trying to finish up research by the end of the summer to hopefully graduate in the Fall. In addition I had gotten a bit frustrated by my inability to find software that would allow me to look at the data, maybe suggest some biological pathways involved, without taking one or more courses in how to work the software. That dilemma hasn't changed yet, but the date of my poster presentation is creeping ever closer. If you know of any good idea for affordable microarray analysis software, don't be shy, tell me about it.

I'm currently looking into an online package called Expression Profiler. Wish me luck.

Happy shopping!

At first I thought it was one of those e-mail scams: "You won 2 million dollars," or some equivalent. However, the amount was a lot less, and it seemed so... legit.

I did some research, remembering that indeed, I had done a survey like that, and eventually responded. And voila! I actually did win $200 to spend at Amazon.com.

Ooooh, now what? I'm going to buy stuff that I would otherwise never get, but that I really want! Suggestions are welcome.

Final results for the shuffle meme!

Here are the final results of the shuffle meme, with links. If you're not into heavy metal, you might want to skip the first link. The song carries very special meaning to me, and the lyrics hit home, especially in these times of war, but it's not for everyone. Also, not always could I find actual video on YouTube, but the songs were there.

CAE wins with 4 right, 1 half right
Anonymous got 2 (I actually know this is a single individual)
Sciencewoman had 1
Canada had 1

1. Gun down cold on a raw deal, home turf my battlefield. Expendable youth-Slayer

2. You can dance, you can jive, having the time of your life. Dancing queen-ABBA

3. Stuck on you, got this feeling down deep in my soul that I just can't lose. Stuck on you--Lionel Richie

4. Te regalo una rosa la encontre en el camino. Bachata Rosa-Juan Luis Guerra

5. There is a rose in Spanish Harlem, a red rose up in Spanish Harlem. Spanish Harlem-Various artists, Tom Jones was the one guessed, I listened to Rebecca Pidgeon's version, which I will post on this blog in June.

6. Bomba! Un movimiento sensual. Azul, azul (Bomba!)-King Africa

7. Del caribe aflora, bella, encantadora. En Baranquilla me quedo-Joe Arroyo. I've never been able to sit still when this song is playing. Gotta move the feet, gotta move!

8. Por alto esta el cielo del mundo. Obsesion--Various artists, I listen to the version by Los Trio, the one linked to is by Pedro Flores.

9. Is this the real life, is this just fantasy. Rhapsody-Queen

10. No hay dia que pase que yo no me acuerde de ti. Contra la corriente-Marc Anthony. This is my all-time favorite song from Marc Anthony. I don't like his English-language songs, but I'm absolutely crazy about his songs in Spanish.

11. Toen ik van de week je brief kreeg na een lange tijd. Hou me vast-Ruth Jacott. I could not find a video of the whole original song, I did find a latinized medley version of the songs "Vrij me mij" and "Hou me vast," the latter starts at 1:16.

12. Tu vida se parece a una novela. Mujer de novela-Grupo Niche. My all-time favorite latin band, they have numerous fabulous songs for listening and dancing. And I think this is my favorite song by this band.

13. Let me tell you now all that's on my mind. The only one-Lionel Richie

14. Kijan zot fe m'pa ka kompran zot ka viv kon si pa ni pwoblem. Zouk la se sel medikaman nou ni-Kassav'. Great song in the French-Carribean style called Zouk.

15. Man it's a hot one, like seven inches from the midday sun. Smooth-Santana

16. Old pirates, yes, they rob I; sold I to the merchant ships. Redemption song-Bob Marley.

17. Joseph's face was black as the night . Under African skies-Paul Simon and Linda Ronstadt. The version linked to is with Miriam Makeba.

18. Procura seducirme muy despacio. Procura-Chichi Peralta. Fantastic song to dance to, by Chichi Peralta who used to be part of Juan Luis Guerra's band 4:40.

19. In the sunlight of your smile, in the summer of our life. Beautiful Maria of my soul-Los Lobos. Soundtrack from the movie Mambo Kings. This is the English version, there is also an equally beautiful Spanish version.

20. Takmis koluna elin adamini. Simarik-Tarkan.

21. Acordate Moralito de aquel dia que estuviste en Urumita y no quisiste hacer parranda. La gota fria-Carlos Vivis

22. If blood will flow when flesh and steel are one. Fragile-Sting

23. Without dreams of hope and pride a man will die. Children of Sanchez-Chuck Mangione. No good video of this song, but a decent sound version.

24. When the lights go down in the city. Lights-Journey

25. Would you know my name if I saw you in heaven. Tears in heaven-Eric Clapton

Shuffle meme

Links added!! Like CAE I think I'm going to have to give more clues, it looks like my musical choice is too uncommon. But I still think that even the songs in Spanish should be recognizable by most people with some interest in latin music. Clues in RED.

I was tagged by CAE for the shuffle meme. She's tagged me a few times before, and no matter how much I promised I would do, I always postponed it, until I never did it. This time I'd better do it right away, with some necessary caveats. If nothing else, this post should demonstrate how eclectic my music collection is, and this is just the tip of the iceberg!

Step 1: Put your MP3 player or whatever on random.
Step 2: Post the first line from the first 25 songs that play, no matter how embarrassing the song.
Step 3: Post and let everyone you know guess what song and artist the lines come from.
Step 4: Strike through when someone gets them right. (I'll do bold)
Step 5: Looking them up on Google or any other search engine is CHEATING.

Caveats:
1. Since I don't have my iPod with me, I'm using iTunes in shuffle mode.
2. At first I was going to skip all non-English songs, but that made it almost impossible, since so much of what I listen to is not in English. I did have to draw the line somewhere, but I left some in. Good luck on those, it will be a fairly select crowd that can guess those. For #14 and 20, I had to actually look up the lyrics. I don't sing them, I dance them.

So here we go:
1. Gun down cold on a raw deal, home turf my battlefield.
This heavy metal band was one of my brother's favorite. It's a very intense song about the waste of young people being sent off to war.

2. You can dance, you can jive, having the time of your life
3. Stuck on you, got this feeling down deep in my soul that I just can't lose

4. Te regalo una rosa la encontre en el camino.
One of my favorite latin artists. This song was a HUGE hit in the eighties. He is originally from the Dominican Republic.

5. There is a rose in Spanish Harlem, a red rose up in Spanish Harlem.

6. Bomba! Un movimiento sensual.
Definitely a song to dance very provocatively to. I'm looking forward to link to the YouTube version of this song once it's been guessed. Multiple artists, anyone will be excepted.

7. Del caribe aflora, bella, encantadora.
Ok, I admit, there is no way I would have been able to guess this one myself. It's about a city in Colombia. Again, very popular and danceable.

8. Por alto esta el cielo del mundo.
Multiple artists have performed this, any one of which is acceptable. It's somewhat of a classic ballad.

9. Is this the real life, is this just fantasy

10. No hay dia que pase que yo no me acuerde de ti.
This artist is a popular singer/songwriter, originally from New York, but his parents were Puerto Rican. He used to be married to a former miss Universe, and is currently married to a popular female singer, and they recently enlarged the number in their household.

11. Toen ik van de week je brief kreeg na een lange tijd.
This is a song in Dutch, and it is unlikely that anyone visiting this blog would guess it, except those from a handful of countries.

12. Tu vida se parece a una novela.
This song is my favorite song from my all-time favorite Colombian band. They are very popular, but mainly because of some of their older songs. I dont know of any very recent songs that are so popular.

13. Let me tell you now all that's on my mind.
There is another song on this list by the same artist, and that song has been guessed correctly already. He was very popular in the 80s, you don't hear much of him these days, but a close relative of him is often in the tabloids.

14. Kijan zot fe m'pa ka kompran zot ka viv kon si pa ni pwoblem.
I had to look these lyrics up, because I didn't know how to pronounce or spell them. The group that performed this song is from the Caribbean and has defined the genre (I think). This song was wildly popular in the 80s, and describes how the genre is the medicine everyone needs (or something like that).

15. Man it's a hot one, like seven inches from the midday sun

16. Old pirates, yes, they rob I; sold I to the merchant ships.
Come on!! How could no one get this one? Very popular artist from the Caribbean, sadly diseased. He definitely represents the genre, and made it popular worldwide. A lot of songs had messages criticizing world politics, anti-war, anti-discrimination.

17. Joseph's face was black as the night Sorry, I couldn't find a good video of the original with Linda Ronstadt, this version is live with Miriam Makeba.

18. Procura seducirme muy despacio.
The artist that sings this song split of from the band that performed #4. He may not be quite as well known as the original band, but most people listening to latin music are likely to have heard this one. Great beat, my fingers itch to link to the YouTube video.

19. In the sunlight of your smile, in the summer of our life.
There are both a Spanish and English version of this song, it is part of a soundtrack. The movie is about two men from Cuba who move to New York (?), one of which is madly in love with a woman who stayed behind.

20. Takmis koluna elin adamini.
I had to look up these lyrics too. I don't know the words, or how to pronounce them. It is a Turkish song, nice beat. The artist makes kissing sounds in the song.

21. Acordate Moralito de aquel dia que estuviste en Urumita y no quisiste hacer parranda.
Folksy song from Colombia, nice beat. The artist is from Northern Colombia and his songs reflect the genres that originated there. This song is one of his more popular ones.

22. If blood will flow when flesh and steel are one.
The artist is from England (come on CAE, you can do it!), and the band he was part of was very popular too. This solo song was released in the mid-late 80s.

23. Without dreams of hope and pride a man will die.
The artist had a very popular album in the late 70s. His genre is jazz. According to Wikipedia he has released more than 30 albums since 1960.

24. When the lights go down in the city
25. Would you know my name if I saw you in heaven


Tags: If you read this, you have a blog, and you haven't done this meme before, consider yourself tagged. But don't feel pressured, I won't hold it against you if you don't do this. I can't be too judgmental, considering I don't do memes too often myself.

Say NO to violence against women

Please sign your name on the list of UNIFEM, the United Nations Development Fund for Women. Say NO to violence against women. It's enough! No more hitting, beating, punching, kicking, shooting, rape, burning, yelling, you name it. No more violence. I just signed my name. Now go ahead and add yours.

That t-shirt is the wrong color!

When PZ posted this link, and I clicked on it, the title of this post is the first thought that came to my mind.

The guy in the cartoon looks way too much like Steve Burns in Blue's Clues (ask me how I know). The green-striped shirt is a dead giveaway. The only thing is, although Steve is kinda goofy, and he doesn't usually find the clues first, he strikes me as a very logical guy, a good scientist.

Picture credit

Steve patiently collects his data (the clues), doing all sorts of smart things while collecting the data (like counting to 10, matching shapes, recognizing colors). He takes careful notes in his handy-dandy notebook, writing down each clue (a good notebook is the scientist's bible). And then he sits down in his thinking chair and carefully analyzes the data: he thinks, thinks, thihihinks!!. He uses his mind, takes it one step at a time, and collaborates with subject matter experts (pre-schoolers) to figure out what the clues mean, and what Blue wants to do. And when he doesn't feel well, he concludes that eating Mr. Salt and Mrs. Pepper's vegetable soup will make him feel better, which seems much more intellectually sound to me, if not tastier, than prayer.

Steve's got this scientific thinking thing worked out much better than the guy in the cartoon. I propose to change the shirt color on the guy in the cartoon. It doesn't reflect well on Steve. And Steve is my son's hero. We demand Steve's name be cleared!

Managing references 2: The search

This is part 2 on managing references. Here is part 1.

So I needed to find some software to manage my references and citations that would overcome some of the recent changes in my computing preferences. The change to MAC and my adviser's and university's preferences resulted in a switch to Office for MAC, and this made reference manager obsolete.

I searched the internet, and eventually came on a Wikipedia site that compared several reference managers. I found this very useful, because it provided a lot of information on a single webpage, allowing me to narrow it down pretty quickly.

I first made a list of managers that would work on my MAC:
1. 2Collab
2. Aigaion
3. BibDesk
4. BibSonomy
5. Bibus
6. CitULike
7. Connotea
8. Endnote
9. JabRef
10. Papers
11. RefBase
12. RefDB
13. Zotero

Moving on to the next table on the page, I realized that I wanted to be able to share my database with my adviser and colleagues. This might not be necessary but I don't like to be restricted. The boss uses EndNote, so the software needs to export to EndNote. This cut the following options from the list: 2Collab, Aigaion, BibDesk and CiteULike. The import format options did not remove any additional programs. Nine programs left.

Citation styles. In my field several different styles for in-document-citations and lists of references are used. I'm not entirely sure which one I'd like to use, but again, more options are better than less. And if my style is unavailable, being able to define my own might help. BibSonomy, Connotea, and JabRef were scrapped. Because Bibus still allows user-defined styles, it's hanging in there. Down to 6.

1. Bibus
2. Endnote
3. Papers
4. RefBase
5. RefDB
6. Zotero

Not all of the table provide useful information for the elimination process. The next one that will help me bring down the number of choices is wordprocessor integration. That is a BIG plus.

The restriction that EndNote does not work on the 64-bit versions of Windows, is of no consequence to me, there is no information on Papers, and I'm too lazy to go find that out right now. If Papers becomes a serious option, I'll have to go back and look at that. But at this point we say goodbye to RefBase and RefDB. We have the following left:

1. Bibus
2. Endnote
3. Papers (keeping this Word-integration thing in mind)
4. Zotero

The next set of tables don't change anything to this list, so we go back to the first table where the prices are listed. Price is important, but I'm willing to pay some for great functionality. And as a student, I do often get deep discounts. That is why price only now comes into play.

1. Bibus-free
2. Endnote-Academic version roughly $100
3. Papers-$24-42
4. Zotero- free

I was really interested in taking a closer look at Zotero at this point. Free sounds great, but m ore than anything, the integration in FireFox, the browser I already use anyway, sounded intriguing. Clicking on the Bibus link, I read that Bibus' functionality of MAC is limited. It should probably have been eliminated quite a while ago based on this. Bibus is out. Papers was 29 Euro, not unreasonable, if it's good I'd be happy to pay that. Endnote, being the most expensive of the options, even as a student, was eliminated. So this left me with Zotero. I'm trying it out right now, and I reserve the right to hate it, and go back to the list to choose something else. But with free you can't go too far wrong. If it doesn't work out, I can simply remove it, nothing lost but some time, right?

To be continued....