Organizing scientific research files

Until now, most of my scientific papers were written in a background context, like my MSc thesis or a course. So, all the conference and paper related files were stored in a subdirectory of the broader subject.

Now, I want to advance to a more research-centered approach to my work, so I need to organize my files in a more structured way for this purpose.

After some thinking and experimenting, the outline of the directory structure I’m using is the following:

/Research

-/ Conferences
-- disapproved.doc (list of disapproved conferences, for their questionable scientific merits)
--/
--- agenda.doc (list of incoming conferences for the year, including all relevant dates, including, sorted by submission deadline)
---/ (ex. IEEE ICWS)
---- url.txt (web address of conference web page)
---- desc.txt (conference name and topic keywords)
---- … (other conference related files: forms, rules of submission, templates etc.)

-/ Journals
… (similar to conferences)

-/ Researchers
--/ me (my research)
---/ presentations
----/
---- …
---/ publications
----/
---- … (my papers)
--/ other
---/ ,
---- …

I hope this way I can more easily store my files, helping me to work in a more practical approach, similar to what happened in the final stages of my MSc. If I target specific publications, I can use the conference’s deadlines as Occam’s razors for my work – keep it simple, keep it focused, reach results!

Let’s see if it works ;-)

Starting LaTeX

I wrote my MSc thesis in Microsoft Word, and took great advantage of Word’s easy to use features, especially the Outline view, that allowed me to hierarchically structure my document and to view it at a glance, during the writing process. However, the handling of references – a core aspect of scientific writing – was cumbersome, to say the least.

So, I decided to try the most used tool for writing scientific papers: LaTeX. Actually, LaTeX is one extension to the basic language TeX. Whereas TeX specifies basic text and math expressions formatting, LaTeX adds capabilities to structure documents, with indexes. Also, there is BibTeX to handle references. There any many library packages for TeX. In fact, its extensibility is one of its key features. You can find lots of information about these widely used tools on the Internet. However, beware; they are not in the same difficulty level as Word, because they require the use of the command prompt.

There is a myriad TeX variants, for different platforms. The most complete I found out for Windows is MiKTeX. The main command line tools are latex and pdflatex. The latter one produces output directly in PDF format.

I still haven’t actually written any full document, just a couple of tests, but I plan to do so in my future papers.

Best regards!

Setting up a minimally furnished house

If you don't find a furnished house, or it's too expensive, you'll have to go shopping.

For this, be sure to check Walmart, Target, Wegmans, or other big stores. They have most of the things you need, at a convenient price. For complementary things, check the $1 stores, because they have lots of cheap stuff with minimum or average quality.

Having a car is also a pratical requirement.

So, here is a shopping list:

Bathroom:
- bath towel
- hand towel
- rug

Kitchen:
- knifes, forks and spoons
- cooking utensils
- cuttlery set (cooking knifes)
- dish set
- drinking glasses

Bedroom:
- airbed
- bedding set (sheets, bed cover)
- pillows
- clothing hangers
- support table

Living & dining room:
- table and chairs
- table towel

For the initial cleaning, don't forget:
- kitchen cleaner
- bathroom cleaner
- odor remover (especially if former tenant had pets)
- aromas

For laundry:
- collect quarters ($0.25 coins)
- washing detergent
- softner
- laundry basket

This is the minimum, and goes for around $500. You'll probably end up buying more stuff. However, keep in mind that you'll be leaving and that you won't be able to take most of the stuff back home.

Remember: live and learn!

Going to America (for three months)

Hi,

After the MSc, my next adventure has been moving to the United States of America for three months and working in an American University.

From my experience so far, here are some tips:

#1 bring credit & atm cards. The trip budget will be around $10000, including travel expenses.

#2 bring cash (at least $2000) - useful for living expenses in first days, and to pay the first month rent and security deposit, if required by the landlord

#3 check your appliances power adapters - the wall sockets are different, and so is the voltage (110 Volts instead of 220 Volts in Continental Europe) - most of laptops transformers support both voltages, so you'll just need the socket adapters. You can find them at the US airports

#4 book at least 5 days in hotel, to search for an apartment to rent

#5 also rent a car. Even if you like walking (like I do), you'll soon find out that the car is indispensable to doing most things in the US, and that includes looking for a house

#6 get a mobile phone. There are great options, like Tracfone or Mojo Mobile, that are cheap, and easy to set up over the phone. Having your own phone number will also be very useful.

#7 get a city map. A good one will have all the street names in it and street name index. It's very useful to look around for houses for rent - you'll probably find interesting places that don't appear on internet listings...

#8 when talking to landlords, be sure to state that you'll be staying for short term, and if you want furnished or unfurnished apartment. These conditions will probably increase your rent value, but you are better knowing it in advance

#9 before deciding on a particular house, ask at the university around about security in the area. Prefer to spend more to be in a safer neighborhood

If you follow these tips, and are a little lucky (or have good guardian angels ;-), you'll settle in the american town of your choosing in about a week.

Next, you'll have to go shopping...

We have master!

:-) Finally!

We have thesis!

:-)

Using JabRef to keep track of references

Hi,

I've just finished the references section on my thesis. It was tiresome!

As I mentioned in a previous post, I had my references sorted in directories, in alphabetical order. However, to build the references section in the thesis, I had to check which references were actually used. Not easy to do when you're using Microsoft Word. I developed a couple of macros for Ultra-Edit http://www.ultraedit.com to extract the references list - values within squared brackets - from the text. Then I sorted and removed duplicates from the result.

To produce the listing I used JabRef http://jabref.sourceforge.net/ an excellent free tool that uses the BibTex format, from LaTeX. Even though I was using Microsoft Word it still proved very useful. I did the references section using the custom export option, for results just like I wanted them.

I absolutely recommend using JabRef, it is excellent! Especially if you're starting your thesis now or still have a long way to go. Believe me, it will spare you a full working week (and a boring one, I can add).

Evaluation and Conclusions

I've finished writing the Evaluation and Conclusion chapters of my thesis. I wrote them in parallel because they were very interrelated. I started outlining the chapters from the ideia register document, collected over the course of the work. It made it much easier not to forget anything at this late stage.

For the Evaluation, I identified the most relevant results. In my thesis, almost all results were qualitative and not quantitative. Still, it was very useful to include summary tables to capture the overall results in a quick, visual way.

For the Conclusion, I wrote three subsections: Contributions, Future Work and Final Comment.

In Contributions, I identified the contributions from each chapter of the thesis in bullet points, adding some comments. I summarized using short sentences like "A is better than B at something because of this and that". I ended with a main contributions list with just three items, that I considered the "juice" of the work, i.e., what people would most likely find useful.

In Future Work I wrote down the new work ideas and opportunities. It was a fun subsection to write, because you realize how your work opened up new improvement paths to explore.

To finalize, in the Final Comment subsection, I gave my personal opinion about the subject. It was the time and place to "make the strike on goal" (in soccer terms) or to "take the ball to the basket" (if you prefer basketball).

The hardest work of thesis is finished. Now I'll wait for additional comments from my advisor and I'll finish the references section.

More about the 'refs' on my next post. Bye!

Writing wrap-up

This last month i've finalized the thesis prototype and started writing the dissertation. It's a challenge condensing years of work in a 100 page document. You have to do a sort of 'movie directing', writing not everything you learned, but the most relevant things you learned, in a build-up, meaningful, sequence.

So far i've written 4 complete chapters, including Introduction, Context, Service Platform, and Security. The remaining chapters are Case Study, Evaluation and Conclusion. They are the most challenging, let's hope I can write them well (and fast - my deadline is now overstretched...).

Wish me luck and work.

Yours truly,

Full time Engineer ;-)

Still busy, after all these months...

Just a brief MSc status update post.

I've been working 'full throttle' on my MSc prototype, envolving a Notary, a Buyer and a Seller (sounds a little like a Narnia style title, doesn't it?). There is still much work to be done, but things are beginning to (finally) converge.

Like me and my colleagues massou and jpsn in LEIC used to say: "I see the light at the end of the tunnel... Let's hope it's not a train..." ;-)

Since my last post, I've been trying and testing different Web Services Security implementations. It's a long story, but I've switched from Dot Net to Axis2, then from Axis2 to Sun's JWSDP 2 with XWSS package. You'l be able to read the full review when my thesis is published.

All the best!