Checklist for Writing Manuscripts

Around August and the end of an academic year in UP (that's around Feb and March) I suffer headaches and high blood pressure from reading my students' manuscript - be it SPP papers or thesis manuscripts. Yes, reviewing student papers is an occupational hazard.

Paano ka naman hindi mapupundi e kung yung mga simpleng rules ng pagsulat ng paper, hindi sinusunod! (GRRR!@$)352$#*%@$20)

So to minimize stress, because right now is one of those episodes, I'll make here a list of my top 10 6 pet peeves in manuscripts and I'll tell my students to check the list before they send in their papers. (And mind you, I'm VERY busy right now, but I have to get this off my chest by writing about it. That's how seriously stressed I am.)

1. Figures too small. 
A picture speaks a thousand words but if it is too small to see the details or embedded labels, well forget it, I'd rather you describe the story in three paragraphs. Look, an A4 page with a one-inch margin on both sides has a width for text or figures which is 6 inches plus. 6 INCHES! So why is your figure only 2 inches wide? Maximize figures so their width fill the whole page, My Gulay! That's what figures are for, to be seen!

2. Poor grammar
Nothing gets my goat faster than poor English. Please, if you have problems, have your text checked by labmates or groupmates who have a better command of the language.

3. Poor  or no citation
Listen, this can get you kicked out. Seriously. You can be accused of plagiarism. You either cite the source or don't include that text or figure. If you will use a figure from another paper the appropriate way is to write the author and ask permission. Don't ever forget to cite the source of the figure. Even if you have cited the source in the text, you must also cite the reference in the caption. Visit this site for a primer on plagiarism. There are more sites, just google.

4. No storyline,  poor construction
Writing a paper, even a scientific one, is a form of story telling. So before you write, think about your best friend. Think how you would tell a story to your best  friend. Now think about how you will tell the story of your thesis or research paper to your best friend.  You'd explain it in a way that he or she gets the premise right? Good stories have an arc. Go make one.

5. A long intro- 7/8 about the work of others, 1/8 about your work
A good introduction answers four questions:

1. What are you doing?
2. Why are you doing it?
3. What has been done before?
4. What is new with your approach?

Yes I can see that you did your review of literature but if you think I am impressed, well no,  unless you can put your own work in the context of the work of others.

6. Turning in a revised paper without a detailed list of changes made
When the manuscript has passed through the initial review and you've made the changes, be kind to your suffering reviewer and give a  detailed list of the changes you made. In this way he or she doesn't have to go through the agony of reading your whole paper again but can go straight to check the revised parts. This will speed up the review process too.  Detail means you enumerate the points raised by the reviewer, then you indicate the page number, paragraph, and sentence where you inserted the recommended change.

I'll probably add to this list when I get cranky again. I'm ok now. Nakalabas na ng sama ng loob.

Teardown,Takedown, Having Fun Disassembling Laptops

My mom's laptop (an Acer Aspire 4736Z) recently stopped booting, it would show the motherboard logo, show a scrolling bar with the Windows logo, then turn itself off. I asked for the chance to tinker with it and I got the green and go.

But how to open up a laptop? Google and YouTube to the rescue. I found two excellent takedown/teardown videos and proceeded with  testing my first two hypotheses:

Hypothesis 1: Laptop won't start because a chip or component is broken.

Tools needed to do the delicate task are:
1. A Philips screwdriver with a magnetized tip. Perfect for picking up the screws entrenched in those deep holes.
2. Tape to keep the screws in order. You would want to remember which screw goes where. You may take notes, pictures, even a video of yourself while you're at it.
3. Magnifying glass, to  closely inspect if a chip or component is broken.


Hypothesis 2: Laptop won't start because something is overheating. 

So I got down to removing the cooling system and, HOLY GUACAMOLE BATMAN!, blocking the fan vent is the thickest, blackest dust cotton I've ever encountered since cleaning my stand fan after 14 months and 27 days ( I exaggerate of course, specifying length of time just sounds theatrical). Cleaning the vents, I  learned a few more things from our friendly neighborhood Google.

1. Use acetone or isopropyl alcohol to remove old thermal grease and thermal tape.
2. Thermal grease is preferred over thermal tape.
3. Applying thermal grease is an art.

Well, after doing all i can to make everybody cool, nada, nilch, nunka. Still no booting.

So back to the Google boards again and searched here and there for answers. Aha, more hypotheses to test:

Hypothesis 3. CMOS battery might be drained - Replace
Hypothesis 4. One component has a short - remove and reboot to see which one affects booting process.
a. If its memory, make sure you have a spare memory card to use or you can put your memory card into another computer.
b. If its the harddisk, try to put the harddisk into  an enclosure and try to see if you can read the contents.

Converting Structures to Matrices in Matlab

I use imfeature a lot (now regionprops). Since the output of imfeature(regionprops) is a structure I sometimes need to access the values of a feature for all blobs preferably in matrix form. I am not so sure if it can be done in one line but what I've discovered is a two step process.

Suppose a call to regionprops is made as follows:

stats = regionprops(L,'Area','MajorAxisLength','MinorAxisLength');

The first step is to convert the structure into a cell:
c = struct2cell(stats);

Then the cell is converted into a matrix:
m = cell2mat(c);

m now would have the same number of rows as features and columns would be as many as the number of blobs processed.

How to Skip Every nth Row in Excel

I recently acquired data which had a temporal resolution that was much too fine than necessary. Imagine plotting a graph with 121,957 data points! Horrendous! It slows down everything in Excel.
Data came from eight RH and Temp sensors that have been logging a little under every second over a span of two days.

I don't need to know that temp every second, maybe every minute or every 5 minutes should be ok. So I searched the net for solutions and found this:

http://www.lytebyte.com/2009/06/02/how-to-select-every-nth-row-in-excel/

First time to use the mod and data filter function and they work like a charm!

In 3 easy steps here is the trick:

1. On a blank column beside the data type =mod(A(1), 60). Copy and drag all the way down to the last data you'd like to include. Replace 60 by any row number you'd like to skip. This will generate a column  which cycles from 0 to 60.
2. Use Data/Filter on the modulo column and select the number you'd like to remain. Say you choose 25. Every row labeled 25 in the modulo column will remain and the rest will be hidden.
3. Et voila! Select remaining data rows and plot away!

Hidden Folder No More

When a disk gets corrupted by a virus, some antivirus software change the attributes of the files and folders to "Hidden". I'm not sure why this is done. Anyway, it gets to be a headache sometimes. Imagine my horror when I was about to deliver a lecture saved in my portable harddisk only to find that I could not see not only the file but the whole folder itself!

To "unhide" a folder in Windows, type the following in the command prompt:

(Assuming H: is the directory where the hidden folder is)
H:\attrib -H -S "Hidden Folder Name" /S /D

Online Backup

I discovered DROPBOX. And I'm happy I did. I almost threw away an IT news magazine that Eisen has torn to pieces. Good thing I took a look at the write-ups. If I hadn't I would not have read about free and convenient ways of backing up and syncing files.

I have two laptops, the old one is a desktop replacement at home and the other is my netbook which I carry around a lot. If I wrote a document on one of them I usually back up by writing an email to myself with the document attached. Cumbersome. And if I get lazy, I'll forget to do it and curse myself when I need the document elsewhere.

When I read about Dropbox I was amazed to find that it is cross-platform. MAC, Windows, Linux- can do. Free space is 2GB. If you need larger space you'll have to pay $9.99 per month for 50GB or $19.99 per month for 150GB.

You need to install Dropbox in each of the computers you want to have sync and backup access to. In Windows, a My Dropbox folder appears inside the My Documents folder.

Just drag your files to the My Dropbox folder and it will sync the copies in all your computers once they are online. Pretty neat.

Remember to save the modified file in the My Dropbox folder, though. Better yet, open it from there and save it there. If you have a copy of the file in a local folder it won't sync or backup unless you drag it again in My Dropbox.

Now I don't have to tear my hair and gnash my teeth when I've written a file in my desktop replacement. Simply by dragging it to My Dropbox I can have access to it anywhere.

Beeps when turning on your computer

The PC won't turn on properly, instead you hear patterns of beeps. They are actually built-in diagnostic alerts. They can tell you what's wrong. I got this from http://www.pcstats.com/articleview.cfm?articleID=1223 while googling what those beeps mean.

• No beep - no power, loose peripherals, bad motherboard or cpu
  
• One beep - ok
  
• One long, one short - motherboard problem
• 1 long, 2 short - video problem
• 1 long, 3 short - video problem
• 3 long - keyboard error
• Repeated long - memory error
• Continuous high, low - CPU overheating
  

I was trying to fix some old PC's in the lab since the students were complaining only 2 were working. Heard repeated long beeps in three computers - memory problem. Opened the hatch and placed the RAMS in a different slot and made sure they were snug and completely in.

Et voila! They worked!!!