Finish putting the right banner on science posts that did not have tags

_posts/2006-01-09-moving-not-yet.markdown

@@ -9,6 +9,8 @@ wordpress_id: 21
 categories:
 - S.T.E.A.L.
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Today I thought I was going to move from my current location (LITA building, [University of Milano](http://www.unimi.it) ) to the new one, the CISI. However I didn't think up that some stuff (including the arrival of 3 new people at our laboratory, Sarah, Guya and Alessandra) would have held me back. I won't relocate till next Monday. In the mean time I spent the day testing out some procedures and creating a draft proposal for the new laboratory's network structure, and getting the equipment to put that in place.

_posts/2006-01-11-always-needed.markdown

@@ -9,6 +9,8 @@ wordpress_id: 22
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 I haven't been able to write because I always end up extremely tired from work. Since I'm moving to the CISI next week, it looks like everyone needs me. I managed to study a bit, then I had to help a couple people with a protocol, then work on the firewall/router migration (we're restructuring our Intranet once I move a few computers there) then help with a software, etc.

_posts/2006-01-16-moved.markdown

@@ -9,6 +9,8 @@ wordpress_id: 24
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Finally today there was the (largely) anticipated move from the LITA to the CISI. I actually showed up at the CISI first, to do some research work, then after the lunch break I and a colleague went to the LITA to pack things up. We almost looked like robbers (and for sure got some funny looks from people as we moved to put things in the car): we had four computers, four monitors and keyboards, lots of cables, my notebooks, and more. It took an hour to pack things, and another 30 minutes to unpack them at the new location. That is, they're in place but they're not actually _working_ - I'll have to do that tomorrow (and I hope everything works). 

_posts/2006-01-20-office-take-2.markdown

@@ -9,6 +9,8 @@ wordpress_id: 27
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Now that the office is more or less in working order (if we exclude the lack of chairs) I thought I'd post something about it. I finally finished setting everything up (including the 250 Gb network drive) today, so I can finally resume my _real_ work next week (that is, bioinformatic analysis). I plan on buying a cheap chair this weekend so I can get at least a place to sit: there are two chairs only for 6 stations.

_posts/2006-01-26-badly-written-software-or-policy.markdown

@@ -9,6 +9,8 @@ wordpress_id: 31
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Today while working I got stuck in what probably is an intentional flaw of the software we're using. When we scan [Affymetrix](http://www.affymetrix.com)'s GeneChips there are a number of files produced by the GeneChip Operating Software (GCOS in short) including raw acquisition images and various analyses. Now, a certain number of people need to use those data to work (including myself), but I don't want people to fiddle on the scanner workstation unless they know what they're doing. So I bought a network hard drive a week ago and I decided to sync the data from the workstation to the network drive. Affymetrix has a proprietary solution to access data in a centralized fashion, but it costs € 65,000, plus the MS SQL2000 Enterprise Edition license and not including the actual server machine! They also have a stand alone tool (Data Transfer Tool) but it doesn't support unattended operations (obviously). I thought by copying over files and using one mode of operation of this software to transfer data to the other machines (some data are stored in a database, that's why you can't just copy the flles over).

_posts/2006-01-30-clarissas-birthday.markdown

@@ -9,6 +9,8 @@ wordpress_id: 33
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 That was the only noteworthy event of today's work. I arrived late (took 1 hour and 30 just to get there) and then during lunch break we moved again to the LITA to celebrate. We got a sort of necklace for her which she liked quite a lot, and we got time to have a toast and eat some cake. It took way more than I expected - I was back at the CISI at around 15. I managed to get more stuff done, and so I'm more or less on time with my work schedule.

_posts/2006-02-05-all-in-one-entry.markdown

@@ -10,6 +10,8 @@ categories:
 - Anime
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 First of all, the strangest oddity ever. On Friday once at the laboratory I was contacted by an Affymetrix representative regarding [this entry ]({{ site.url }}/2006/01/26/badly-written-software-or-policy/). She wanted to know why I wrote it and that it seemed that I "didn't contact Affymetrix to see if the problem could be solved". She wasn't offended or anything (she will even get me in touch with someone from the software department), but nevertheless this is my blog and I'm entitled to my personal opinions. Hence, any IP from affymetrix com (and its European branch affymetrix.co.uk) is now banned from accessing this page.

_posts/2006-02-06-woes-of-a-scientist.markdown

@@ -8,6 +8,8 @@ title: Woes of a scientist
 wordpress_id: 36
 categories:
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Not everything can be fun in the life of a scientist. For example, my work in the bioinformatics field of our laboratory makes me see a lot of annoying problems related to files, to be precise file formats. A lot of sofware in the biological sciences uses plain text files to export data to other programs (sometimes binary data, but that's another matter). The problem comes when you have to use the output into another program. As a matter of fact, all kinds of programs use differently formatted text files, making a conversion or integration a pain. That is, unless you use some shell scripting (on Linux, obviously) to handle them. Today my editing window looked like this:

_posts/2006-02-28-bertinoro-di-romagna.markdown

@@ -9,6 +9,8 @@ wordpress_id: 46
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 After sorting out the bureaucracy, finally I was able to enroll for the [6th Course in Bioinformatics for Molecular Biologists](http://www.eurogene.org/body.php?t=1&l=l&p=pages/train/courses/crsprogr.php&r=72) that will take place in Bertinoro di Romagna in three weeks. I'm glad I was able to, the course program looks really interesting and perhaps I'll be finally able to learn bioinformatics in the right way, since so far I'm entirely self-taught, and sadly, it shows.

_posts/2006-03-11-trento-march-7th-8th.markdown

@@ -8,6 +8,8 @@ title: Trento, March 7th-8th
 wordpress_id: 49
 categories:
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Finally I have some time to give an insight of what happened Tuesday and Friday, when I left for Trento to attend to the ITC-irst's meeting called "Biobanks for functional genomics". The trip was mostly uneventful, though we had to wait a lot once we arrived at the ITC-irst because we were way earlier than expected. I spent time talking to some people there, they work in an interesting field: applying computational methods to microarray expression data. I was the only one with a biological background there, the rest had degrees in mathemathics or physics.

_posts/2006-03-16-random-entry.markdown

@@ -12,6 +12,8 @@ categories:
 - Science
 header:
     image_fullwidth: "banner_other.jpg"
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 I haven't blogged in a while, mostly because I'm either doing something else, or when I want to, I find out I'm really tired (this and the past week have been very tiring for me). In any case, I'll make a big, random entry.

_posts/2006-03-19-bertinoro-arrival-day-1.markdown

@@ -9,6 +9,8 @@ wordpress_id: 51
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Finally I got hold of a stable Internet connection so I can post about my experience in Bertinoro di Romagna so far.<!-- more -->

_posts/2006-03-21-bertinoro-day-3.markdown

@@ -9,6 +9,8 @@ wordpress_id: 53
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 I just came home and I'm terribly tired, so I'll be rather brief. This morning we had four lectures, including two interesting ones on protein structure prediction, though one speaker was too fast and I almost couldn't take notes.

_posts/2006-03-22-bertinoro-day-4.markdown

@@ -9,6 +9,8 @@ wordpress_id: 54
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Talks, talks, talks. That's all about this day. Some were also extremely difficult to understand, and I'm not sure I took good notes. Talks went on from 8.30 to 18.00 (excluding lunch break) and then a workshop until 19.30. I'm really beat. I retired to my room while the others wanted to play karaoke, but I was too tired.

_posts/2006-03-30-mixed-entry-yet-again.markdown

@@ -10,6 +10,8 @@ categories:
 - Final Fantasy XI
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 I haven't been writing on this blog as much as I wanted, partly because of tiredness, partly because of my always-present tiredness.

_posts/2006-04-06-windows-and-missions.markdown

@@ -10,6 +10,8 @@ categories:
 - Final Fantasy XI
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Finally, we have windows in the office. Before that it was just a room with walls, and it looked a little claustrophobic. It took a good deal of time (4 months) to get these works done, but I think the result is worth it. At least the whole room looks a little more human, now.

_posts/2006-04-10-outage.markdown

@@ -9,6 +9,8 @@ wordpress_id: 60
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Today one of our desktops won't turn on at all. I didn't even see the POST lights turning on (this is a Dell computer), so I assume that the PSU is dead. I'd have already called for support but since the box has been bought in the USA (part of a bundle of our GeneChip systems) I had to request a warranty transfer (notice that I don't even **know** if there's still a warranty!). I'll probably call support tomorrow.

_posts/2006-05-05-continuous-analysis.markdown

@@ -8,6 +8,8 @@ title: Continuous analysis
 wordpress_id: 65
 categories:
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 This week has been quite busy at work. As I finally got the two lists of differentially expressed genes that I needed, I started my analysis work. Perhaps analysis is not quite appropriate, as what I to is mostly to annotate the genes (i.e. I try to find out everything about them, or certain features I need) and to see if the lists are "enriched" by a particular feature. From this I try to see if what I see has a biological relevance, or not. In practical terms this means I use a lot of web-based tools and some basic statstics to evaluate my work. A typical session on my computer is shown by this image.

_posts/2006-05-08-security-breach.markdown

@@ -10,6 +10,8 @@ categories:
 - General
 - Linux
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Today I found out that a computer running Windows had been "self-writing" words when an Internet Explorer window was open. This obviously led to the conclusion that there was some kind of malware running. I immediately unplugged the network cable but the typing continued - this is a good sign meaning that it was just some random program doing it. It only affected IE, no other programs. I wonder how it got there, I can only suspect the current user, as I never do any network-based activity there, only analysis (and I run a much safer Linux box - no Windows for me).

_posts/2006-05-17-stress.markdown

@@ -9,6 +9,8 @@ wordpress_id: 67
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 This has been a rather stressful period work-wise. Things are looking extremely confusing on the (upcoming) paper we need to write and even a small doubt can cause huge time losses (I spent the whole morning checking to see if my analysis was correct or not while in fact it was correct in the first place). I've been shown a new software for microarray analysis, well, at least some brochures. I'm going to inquire about pricing (the most important part) and platform availability (I'd love if it could run on Linux). I'll also ask for a demonstration if possible.

_posts/2006-05-25-biological-software-and-hig.markdown

@@ -9,6 +9,8 @@ wordpress_id: 70
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Today I obtained a trial license of a data analysis program. I plan on using it for the next two weeks to see if it could improve the analysis workflow in our laboratory. I noticed this software uses the Tk widget set to achieve cross-platform capability (in fact, it can run on Linux, which is a big plus for me). However, in my opinion, Tk widgets look rather ugly. I wonder why the company didn't consider using Trolltech's [Qt](http://www.trolltech.com/products/qt) widgets. Mind, I don't have any ties with TT but I appreciate their toolkit (licensed either under the GNU GPL or a commercial license) in the [KDE](http://www.kde.org) desktop environment.

_posts/2006-06-08-classes-and-meetings.markdown

@@ -9,6 +9,8 @@ wordpress_id: 74
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 This week has been absolutely exhausting. I've been having PhD classes (statistics, effective writing, and more statistics) almost every day (save tomorrow) and also heaps of work piled up. I've got new data to work on, and also I've been assigned to do something else along with my current bioinformatics work.

_posts/2006-06-17-busy-busy-busy.markdown

@@ -10,6 +10,8 @@ categories:
 - General
 - S.T.E.A.L.
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 I haven't been writing a lot here mostly because of the rather hectic work schedule I'm having. We're nearing the completion phase of a paper that includes quite a bit of my work (and also a lot of other people's contributions), and I'm also swamped with PhD classes (two weeks to go). Also, one of my bosses has assigned me another project which I've yet to tackle, and I got to help my colleague with a poster as well.

_posts/2006-06-20-upgrade.markdown

@@ -11,6 +11,8 @@ categories:
 - General
 - Linux
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 I got upgrade hardin (my laptop)'s memory at least, bringing it to 1Gb, at last. However I had two 256 Mb modules installed, that means I had to buy two 512 Mb ones. Oh well, I'll just try to sell those ones. Everything seems snappier now, and even Firefox seems not to clog the CPU when loading pages (I need to experiment more, since I have no clue why that should have changed).

_posts/2006-07-08-the-power-of-the-shell.markdown

@@ -10,6 +10,8 @@ categories:
 - General
 - Linux
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Yesterday I was trying to adjust some files in order to make a program use Affymetrix SNP arrays data (instead of arrayCGH data like the program was designed for). I had a big (116,000 rows) tab-delimited text file and I needed to use only part of the columns there.

_posts/2006-07-28-perspectives.markdown

@@ -8,6 +8,8 @@ title: Perspectives
 wordpress_id: 95
 categories:
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Our paper's completion has probably been delayed till September or so pending some (in my opinion puzzling) organizational issues within a group that works with us. My research work is also pending due to the fact that I'm waiting for someone to prepare a "data matrix" for me, and the person doesn't seem to know that leaving other people hanging is somewhat impolite.

_posts/2006-07-29-computational-biology-wheres-the-biology.markdown

@@ -8,6 +8,8 @@ title: Computational Biology...  biology?
 wordpress_id: 96
 categories:
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 In the past few months I've been wondering about the state of bioinformatics and computational biology in general. When I attended the school in Bertinoro (as [I wrote about previously]({{ site.url }}/2006/03/19/bertinoro-arrival-day-1/)). The development in this field can be regarded as quite astounding, just a look at journals like [BMC Bioinformatics,](http://www.biomedcentral.com/bmcbioinformatics/) [Bioinformatics](http://bioinformatics.oxfordjournals.org) or others can give an insight of that.

_posts/2006-08-29-im-back.markdown

@@ -10,6 +10,8 @@ categories:
 - General
 - S.T.E.A.L.
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 I'm finally back from holidays and since there's almost no one in the office here I thought I'd write a little mixed entry, while quant is busy compiling a patched 2.6.17 kernel (but quant as an odd overheating problem that I will describe in another entry, so I have to compile it by steps).

_posts/2006-09-13-annotations-and-linux.markdown

@@ -9,6 +9,8 @@ wordpress_id: 106
 categories:
 - Linux
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 A lot of my bioinformatics work involves performing _functional annotation_ on genes. This means that given lits of genes I need to resolve their known function, or if they're part or some metabolic pathways and so on. Even with the current trend in our laboratory, that is investigating DNA copy number changes using SNP microarrays (it's a rather new form of analysis, but [some relevant papers](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16897747&query_hl=3&itool=pubmed_docsum) are out already), in the end we have to go back to the genes affected by such changes (in order to find interesting/marker genes - we study solid tumors).<!-- more -->

_posts/2006-10-11-my-first-real-world-python-program.markdown

@@ -9,6 +9,8 @@ wordpress_id: 120
 categories:
 - Linux
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Although I'm still studying the language, finally I managed to create a program that actually does _something I need_. The need arose from a gene list I was given, made up by [Entrez Gene](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) IDs. I need to annotate it, but in a form that wasn't able to be produced by the usual functional annotation tools I have. Actually it could have been done, but what I needed was to make something that I could _automate_.

_posts/2006-10-23-text-files-with-python.markdown

@@ -10,6 +10,8 @@ categories:
 - General
 - Linux
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Finally I cleaned up my code enough to post it here. It's probably still ugly, but not as ugly as when I wrote it down the first time. It's all about manipulating text files, to be precise tab-delimited files. All the snippets are published under the [GNU GPL](http://www.gnu.org/licenses/gpl.html) v2 (not that I think that anyone would use them, but just in case...).

_posts/2006-11-02-software-and-biological-research.markdown

@@ -8,6 +8,8 @@ title: Software and biology
 wordpress_id: 125
 categories:
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 I've noticed that the journal [_Science code for Biology and Medicine_](http://www.scfbm.org) has finally launched. While some said that would be a journal if someone is desperate for a publication, I think it fills in a gap that's very felt in bioinformatics: the availability of source code.<!-- more -->Perhaps I'm being too naive, but I think that at least academic groups should always release their source code, if they develop a new program or an algorithm, or just give a proof of concept so that others can reproduce their work. This will also help in finding and squashing bugs. Bugs that are sadly much present in a large part of the biological software outlined in publications.

_posts/2006-11-07-phd-students.markdown

@@ -9,6 +9,8 @@ wordpress_id: 127
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 After discussing my second PhD year today, and after noticing that not even a single professor from the commitee was there (save my boss and a person that joined later on), I realized that the situation for students like me isn't really the best.

_posts/2006-11-10-the-joy-of-meta-analysis.markdown

@@ -8,6 +8,8 @@ title: The joy of meta-analysis
 wordpress_id: 128
 categories:
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Recently, I've been in need to retrieve some records regarding renal cell carcinoma referenced in papers by [Zhao _et al._](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16318415&query_hl=1&itool=pubmed_docsum) and[ Higgins _et al._  ](http://ajp.amjpathol.org/cgi/content/full/162/3/925)The records of the former were hosted on [NCBI's Gene Expression Omnibus](http://www.ncbi.nlm.nih.gov/geo), while the latter records were uploaded to EBI's [ArrayExpress](http://www.ebi.ac.uk/arrayexpress) database. Getting data from others and using it for your own analysis is called _meta-analysis_, and it's often used to validate methods and algorithms with different data sets.

_posts/2006-11-15-more-studying.markdown

@@ -9,6 +9,8 @@ wordpress_id: 129
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 EURASIP Journal on Bioinformatics and Systems Biology is having a [special issue](http://www.hindawi.com/journals/bsb/si/tmb.html) on text mining for biology. My boss wants to publish something there, and asked if I and a colleague could work on that. I'll probably focus on evaluation methods, since I'm not an expert in text mining or language processing.

_posts/2006-11-17-random-photos.markdown

@@ -9,6 +9,8 @@ wordpress_id: 131
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Since recently (thanks to my brother) I got a new cellular phone with better capabilities, photo-wise, I decided to take a few photos of my workplace. I changed office a while ago, now I'm located on the first floor of the building, sharing the office with 5 other people: Raoul, Michele, Giorgio, Roberta and Alessandro. This photo shows my current computer setup:

_posts/2006-11-25-a-simple-annotator.markdown

@@ -10,6 +10,8 @@ categories:
 - General
 - Linux
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 In the past two days I've written a simple annotator program, that given an input list of RefSeq genes, automatically determines the relevant Entrez Gene IDs and annotates them using the flat files provided by the [NCBI](http://www.ncbi.nlm.nih.gov). A direct conversion was not possible due to limitations in Biopython's parsers, but I managed to use the GenBank parser to identify and extract the references to the Gene IDs (and putting them in a list).

_posts/2006-12-01-probably-useless-but.markdown

@@ -9,6 +9,8 @@ wordpress_id: 135
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 [A post I wrote](http://www.nodalpoint.org/2006/12/01/software_fit_for_publication) ended up on the front page of [nodalpoint.org](http://www.nodalpoint.org). I liked that, even though it may not seem a lot to many: at least it shows that some of my concerns are shared with other people in the scientific community.

_posts/2006-12-13-working-with-genome-browser-data.markdown

@@ -9,6 +9,8 @@ wordpress_id: 138
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 In the past two days I've been tackling an annotation problem. I'm trying to provide annotations for genes found in regions that are significantly altered, DNA copy-number wise (thanks to the [STAC](http://www.genome.org/cgi/content/abstract/16/9/1149) method). The idea would be to annotate those regions (that span one megabase) using [UCSC Table Browser](http://genome.ucsc.edu/cgi-bin/hgTables).

_posts/2007-02-03-a-day-with-an-apple-xserve.markdown

@@ -10,6 +10,8 @@ categories:
 - General
 - Linux
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Yesterday I and another person went to the server room to do the basic configuration of the Apple Xserve we have bought, along with its Xserve RAID unit. Despite the general "idea" that anything Apple does is user-friendly, our experience was plagued by problems.  <!-- more -->First of all, I don't understand why even with two fiber channel cables, the RAID must be configured via Ethernet. I can understand when you have multiple RAID units and you want to manage them remotely, but I still don't see why the fiber channel is not used for this purpose. After fiddling a bit with the network addresses (the two cards default to DHCP, and we don't have DHCP on this network) we were able to access the  machine.

_posts/2007-02-11-two-days-in-firenze.markdown

@@ -8,6 +8,8 @@ title: Two days in Firenze
 wordpress_id: 157
 categories:
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 I've just came back from a two days' trip in Firenze. On the first day we had a long (4.30 hours) meeting on some interesting research topics, such as cellular aging and about oxidative damage in yeast.

_posts/2007-02-25-a-lot-of-work.markdown

@@ -9,6 +9,8 @@ wordpress_id: 170
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Work is getting hectic as we're finally gathering a lot of data for a new publication. This means reading a lot of literature, choosing the figures and planning results and discussion properly. On top of that, I'm starting to study [pathway analysis](http://en.wikipedia.org/wiki/Metabolic_network_modelling) for my thesis, and of course, seeing how I can use that to study our own data.

_posts/2007-03-01-deadlines-and-domains.markdown

@@ -8,6 +8,8 @@ title: Deadlines and domains
 wordpress_id: 173
 categories:
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 I just learnt today that the paper I'm writing with my colleague has to be in an acceptable state (almost submission ready) by the 20th. Considering I'm still behind with the analysis, it will be certainly challenging to complete the task, considering I also have other duties to attend to. _In primis_ I need to study more and more papers (I add more and more to my TODO list).

_posts/2007-03-12-old-code.markdown

@@ -9,6 +9,8 @@ wordpress_id: 185
 categories:
 - General
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 Today I went over my old Python code, back when I first started programming. I'd say that I found what I had written to be largely amusing to say the least. Loads of ugly hacks all over the place, duplicated functions, etc... in short, a real mess.

_posts/2007-03-13-a-bed-file-builder.markdown

@@ -9,6 +9,8 @@ wordpress_id: 196
 categories:
 - Linux
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 As I anticipated, I can finally release this small script. Its purpose is to build [BED files](http://http//genome.ucsc.edu/goldenPath/help/customTrack.html#BED) out of tab-delimited text files. I made this because I had several files to make and moving columns left and right (not to mention writing a heading line for the [Genome Browser](http://genome.ucsc.edu)) was becoming annoying. Its use is fairly straightforward, as the help itself says:

_posts/2007-03-29-genbugg.markdown

@@ -8,6 +8,8 @@ title: GenBUGG
 wordpress_id: 205
 categories:
 - Science
+header:
+    image_fullwidth: banner_other.jpg
 ---
 
 This entry already shows what I think of a popular open source pathway analysis and visualization program, [GenMAPP](http://genmapp.org). It's quite used to map gene expression data coming from microarrays to metabolic pathways, and in addition to that you can also evaluate enrichment for both pathways and [Gene Ontology](http://www.geneontology.org) terms. Last but not least you can create and contribute new metabolic maps.

_posts/2007-04-14-bioinformatics-sequence-analysis.markdown

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 - Science
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 This post sums up my frustration in trying to use Python for my daily work. Like Perl and Ruby, it has [its own Bio version](http://biopython.org) to deal with biological data. However, the current implementation leaves a lot to be desired. A lot of stuff that doesn't deal with sequence analysis, even for simple tasks such as fetching annotations from [Entrez Gene](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene), is missing (but present in Bioperl, for example). Also, documentation for some modules is lacking or non-existant (why keeping a parser for Affymetrix CEL files when there are no information on how to use it, let alone know which formats does it support?). Basically, maintenance is good for everything related to sequence analysis... the rest is somewhat in slumber.

_posts/2007-04-21-python-usefulness.markdown

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 - Linux
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 I've again seen how useful and powerful Python can be. The other day I had to prepare an Excel spreadsheet (sadly) which among other things needed to contain links to the [GeneCards ](http://www.genecards.org)database for each gene listed. There were more than 2900 genes listed, so adding links by hand would have been suicidal.

_posts/2007-04-25-databases.markdown

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 As I've been working to get some results done for my Ph.D. thesis, I've stumbled across the problem of having different data obtained through different software. Even if it's just a matter of text files, the fields are all different and even if dealing with the same data, trying to infer relationships is a pain.<!-- more -->

_posts/2007-05-18-thesis-work-and-wikis.markdown

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 - Science
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 I've been able to complete most of the analysis for my Ph.D. thesis work, at last. I need a few runs more but I am arranging to work at a location of one of our research partners, as I don't have a powerful enough computer to handle the calculations (apparently, 1Gb of RAM isn't enough). At least the results I have look promising. Now all it's left (and that's not an easy task, heh). is to write them down in the "thesis summary" (deadline: June 30th) and then in the thesis itself. I'm already studying a bit on the topic and papers are quickly piling up on my desk.

_posts/2007-05-28-more-meta-analysis-difficulty.markdown

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 **UPDATE:**  Today I found out that J Brooks (the corresponding author of Zhao's paper) has agreed to send the  data I needed. Thanks a lot!

_posts/2007-06-20-data-handling.markdown

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 As the people who read my science related posts already know,[ I'm in the middle of doing meta-analysis]({{ site.url }}/2007/05/28/more-meta-analysis-difficulty/). That brought up a problem, so to speak, and it's related to annotations.

_posts/2007-06-25-publish-or-perish.markdown

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 The idea to blog about [this common phenomenon](http://en.wikipedia.org/wiki/Publish_or_perish) came after I read a post over at Bioinformatics Zen [on the matter of open science](http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/). There, Mike describes the situation quite clearly: mostly, you need a middle ground between complete secrecy and absolute openness.

_posts/2007-07-12-full-speed-ahead.markdown

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 After giving in the summary of my thesis today, I also started writing the actual thing. Of course this is not something I will finish in a few days. It's a long journey that will go on until I deliver it.

_posts/2007-09-01-science-and-microsoft-word.markdown

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 At the time of writing, a lot of people (even in bioinformatics) uses Microsoft Word to write their papers. I personally think it's not a good idea, and not just for the file formats (like Microsoft lobbying semi-legally to get OOXML approved by ISO), but because for scientific papers the WYSIWYG paradigm is not appropriate.

_posts/2007-09-11-new-office.markdown

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 After little more than a year, I've been moved to a new office, because new people needed to be put in the room I was in. The new place is slightly bigger (four desks instead of six) and for now quieter. I spent most of the morning fixing things and setting up network connections.  This is how it looks now:

_posts/2007-09-19-the-tower-of-babel-of-bioinformatics.markdown

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 The title of this post tries to give some insight on a problem that I've stumbled upon a lot of problems when doing microarray data analysis: the plethora of different file formats. In "conventional" (as I call it) bioinformatics this is less problematic, as [FASTA](http://en.wikipedia.org/wiki/Fasta_format) or [PDB](http://en.wikipedia.org/wiki/Protein_Data_Bank_(file_format)) are quite standardized by now.