Lab-Life on Jean-Etienne's blog

Notes en passant: how AI could unlearn in HEOR Modelling

Sun, 31 Aug 2025 21:13:12 +0000

In a recent paper, Tinglong Dai, Risa Wolf, and Haiyang Yang wrote about unlearning in Medical AI.

With more and more CPU and storage thrown at Large Language Models (LLMs) and Generative Artificial Intelligence (GenAI) in general, the capacity to “memorise” information grows larger and larger with each generation of LLM. This is further accelerated by the capacity to add specific details to generalist LLMs using Retrieval Augmented Generation (RAG) and agents (e.g., with the ability to query real-world systems at the interface with the physical world).

LLMs are learning more, but what about unlearning? Dai and colleagues didn’t evoke the analogy with human memory: our capacity to learn more relies, in part, on our capacity to forget, to reorganise, to summarise, and to prioritise the learnt information. Sleep and stress play a role in this reorganisation of information; this was the overarching topic of my Ph.D. thesis [link]. I will de-prioritise the visual cues along the path leading to a bakery if I no longer go to this bakery (“unlearning”). However, practising navigation to the bakery improved this skill, and this improvement will serve me later when I need to go to another place (something I could call “secondary learning”). It may seem we diverge from AI, but Dai and colleagues actually start their paper with the EU GDPR possibility for a patient to remove their data from a database, wondering how this is technically possible with LLMs (where data is not structured like in a traditional relational database and where the way data is retrieved is often unknown).

The “unlearning” process in LLMs can be considered from three encapsulated levels: algorithm, legal, and ethical levels.

What to look for at ISPOR25 - Artificial Intelligence

Sun, 11 May 2025 02:00:21 +0000

After Modelling and Regulations & Pricing, and just a few days before ISPOR25, here is my take on the potentially interesting sessions on Artificial Intelligence (AI, which generally means: the use of Generative AI, or GenAI, in HEOR).

First, Sven Klijn, William Rawlinson, and Tim Reason are again offering their introductory course on Applied Generative AI for HEOR. Last year, I followed it in Barcelona, and it was nice. In my opinion, “nice” means that although I didn’t learn much more than previous presentations by the authors and my own experience, it was a great course for beginners because it struck the right balance between theory (which too many sessions end up only covering) and practical examples. Don’t expect hands-on exercises (that would be too long, and the course synopsis doesn’t mention that either). But “nice” to me means that the presenters dared to show actual working code, with all the humility that it implies. This year, they mention they’ll cover Retrieval-Augmented Generation (RAG) and agents. Hopefully, their coverage of these aspects will be as good as last year’s on the other topics.

What to look for at ISPOR25 - Modelling

Sun, 20 Apr 2025 22:11:26 +0000

ISPOR25, the annual North American conference for the International Society for Pharmacoeconomics and Outcomes Research, is in three weeks. As usual, I’m planning for it by browsing its program. This time, I decided to share a few of my interests on my blog. ISPOR usually covers many topics, from “hardcore” statistical methods to top-level overviews of some issues, so I will focus on only a few topics. Feel free to connect with me if you want to discuss anything at or around the conference (or virtually). (And before we start, full disclaimer: I’m currently working for Parexel, but opinions shared here are only mine; otherwise, I would have written them on the company blog.)

COVID-19 cases in Maryland congregate living facilities

Sun, 15 Nov 2020 14:31:07 +0000

Five months ago, I was wondering why Maryland remove COVID-19 cases from its count in congregate living facilities (nursing homes, prisons, …). I still don’t have any answer but I found a technical solution :-)

The Python script (in src/ in the MD-coronavirus repo on Github) just fills in the latest data for days where data is missing. On a side note, it also fix some basic issues like a reporting date in year “0200” (instead of “2020”). You can play with the fixed data file here.

COVID-19 clusters in Belgium

Mon, 19 Oct 2020 22:15:08 +0000

Recently (I’m writing this on October 20), the (new) Belgian government decided to apply more stringent prophylaxis measures to contain COVID-19. One of the controversial measure is to close bars and restaurants for a month.

Unfortunately, in a way, at approximately the same time, AVIQ released its latest poll on COVID-19 clusters in Wallonia ( AVIQ is the Walloon agency for well-being, health, handicap and family). I wrote it was unfortunate because I read and heard several people who criticized the closing of bars and restaurants by citing this poll. But this poll cannot answer in favor or against this closure; it doesn’t look at that …

A third of Maryland counties tested more than 25% of residents

Tue, 11 Aug 2020 15:25:11 +0000

Sometimes, you think that you found something interesting but the Maryland Department of Health is already presenting it on its COVID-19 dashboard :-D

For instance, I calculated the percentage of residents of the different counties ever tested (regardless of the test result). I found out that a third of Maryland counties (8/24) tested at least once more than 25% of their residents. Indeed, as of yesterday (August 10), here are the counties in that category:

COVID-19 hospitalization by age in Maryland

Sun, 09 Aug 2020 17:37:08 +0000

Since mid-July 2020 in Maryland, we understood that the 20-59 yr age group was problematic, especially the 20-29 yr age group that is racing to overtake all age groups in terms of number of COVID-19 cases (relative to their population, see top chart below).

In terms of COVID-19 hospitalizations, we also saw a small rebound (see chart below; it seems that it subsides since beginning of August).

But what we didn’t know (for this small peak as well as since the beginning) was what is the age of these hospitalized populations. Did these hospitalizations impacted more the older adults? The younger ones? Or the children? The Maryland Department of Health COVID-19 dashboard doesn’t report that information (nor in the API).

What does release from home isolation mean in Maryland?

Wed, 05 Aug 2020 11:05:10 +0000

Since the beginning of this pandemic, one metric intrigued many of us in Maryland: the cumulative number of people released from isolation. Initially (before the data release via API, when there was only the MDH dashboard), it was even thought to be the number of hospital patients released from isolation. It’s not: the API page mentions:

Total Number Released from Isolation data layer is a collection of the statewide cumulative total of individuals who tested positive for COVID-19 that have been reported each day by each local health department via the ESSENCE system as having been released from home isolation. As “recovery” can mean different things as people experience COVID-19 disease to varying degrees of severity, MDH reports on individuals released from isolation. “Released from isolation” refers to those who have met criteria and are well enough to be released from home isolation. Some of these individuals may have been hospitalized at some point.

A first insight on COVID-19 contact tracing in Maryland

Mon, 03 Aug 2020 21:47:09 +0000

I may have missed when the data was first released but I discovered the Maryland Department of Health (MDH) is publishing some data about COVID-19 contact tracing (in Maryland). This data is not on the main COVID-19 dashboard but on the contact tracing page (and in the datasets that can be downloaded). Here is a first insight of what happened so far …

Note: if you just look for where to get tested in Maryland, the official information is here.

What is the COVID-19 positivity rate in Maryland?

Mon, 27 Jul 2020 03:32:50 +0000

Every day, Governor Hogan and members of his team are communicating news on the COVID-19 situation in Maryland via Twitter (and other media): @GovLarryHogan, @riccimike, @katadhall, … (and of course: @MDHealthDept too!). A number of data enthusiasts are also parsing the MD Department of Health data: @TylerFogarty7, @MikeBReporter, @JauquetW, @PrayagGordy, … and of course: @jepoirrier) … And this is only on Twitter!

But also every day, there is one thing that constantly changes: how everyone is calculating the COVID-19 positivity rate. Today (July 26), for instance, the different daily positivity rates announced are: 3.77% ( Hogan), 4.47% ( Hogan again in the same tweet, Hall, Ricci, MD Health Department, Fogarty) and ~6% (for me, the exact number behind the ~ is 6.14%). This doesn’t show the 7-days (or n-days) averages and other measures. And this is only on Twitter.

Gender of COVID-19 cases and deaths in Maryland

Wed, 15 Jul 2020 02:37:12 +0000

After my previous posts about age of COVID-19 cases and deaths in Maryland, it was logical that I write about the gender of these cases and deaths. Rest assured: this time, it will be much shorter ;-)

Indeed, in a nutshell, in Maryland (like in the rest of the world), women are more impacted than men by the disease. But men are dying of the disease a little bit more than women.

Note: this post was updated on July 15, 2020, to fix an error in my code!

Age of COVID-19 deaths in Maryland

Fri, 10 Jul 2020 03:51:31 +0000

After my previous post on the age of COVID-19 cases in Maryland, it was logical that I write about the age of COVID-19 deaths in Maryland. So far, media and State Departments of Health all agreed that the older someone is, the more risk this person has to die from coronavirus.

So far, this is unfortunately also true in Maryland. In the graph below, we clearly see that people 50-59 years old have more than 250 deaths, people 60-69 have more than 500 deaths, people 70-79 have more than 750 deaths and people 80+ have nearly … 1,5000 deaths! The graph at the bottom also clearly shows that people in age categories 60 and above provide most of the new daily deaths due to COVID-19 (even if we came back down from a peak at about 40 deaths in 80+ at the end of April).

Age of COVID-19 cases in Maryland

Thu, 09 Jul 2020 13:02:00 +0000

We recently heard in the US media that, if COVID-19 affected more the older population, beginning of 2020, the younger population was now more affected, especially young adults (various reasons were mentioned: the various academic breaks, being more active or “forced” to work, the sentiment of invincibility …). I wanted to see if one could see a similar trend in Maryland.

If you look at the section of the Maryland population by age (graph below), as of today (July 9, 2020), you see that cumulatively, people 30-39 have the majority of cases, followed by people aged 40-49, 50-59 and 20-29 years old. There are relatively few cases above 70 years old and fewer cases below 20 years old.

Why would Maryland remove COVID-19 data from nursing homes?

Fri, 26 Jun 2020 03:16:33 +0000

Since the beginning of the COVID-19 pandemic, we suspected and saw that nursing homes and other facilities where people are grouped together (prisons, …) could be at higher risk of transmission. The focus on nursing homes was because deaths seem to disproportionately affect the older population that also resides there. And nursing homes are also home for frail people with comorbidities.

In its dashboard, the Maryland Department of Health quickly started to build a dedicated page with numbers from different “congregate facility settings”. As I did for other metrics from this dashboard, I made a chart of what seemed the cumulative total cases, differentiating staff (who are stuck working there) and residents (who stuck living in these facilities):

COVID-19 inequalities in Maryland

Sat, 13 Jun 2020 01:54:42 +0000

The recent Black Live Matters protests made me think a lot - as a white man, as a husband and dad, as a biologist by training, as a health economist by day, as someone interested in COVID-19 data where I live by night … as a human, in summary. I don’t have grandiose pieces of advice or any deep thoughts, not for here (but if you call me, we can talk ;-)). Here, let’s continue our exploration of COVID-19 data in Maryland.

Weekly seasonality in COVID-19 deaths reported in Maryland

Wed, 03 Jun 2020 21:58:48 +0000

On its dashboard, the Maryland Department of Health is reporting confirmed deaths due to COVID-19 in two ways: by date of report and by date of death (updated as amendments to the death record are received). The definition of confirmed death is:

A death is classified as confirmed if the person had a laboratory-confirmed positive COVID-19 test result.

What I was intrigued is that reporting seems to follow a pattern influenced by the day of the week (see figure below). The top chart (cumulative) is just an addition. A plateau would be welcome: it would indicate death rate is slowing down. Today, the COVID-19 death rate is 41 / 100,000 population. The bottom chart shows the number of deaths due to COVID-19 reported each day: the black line represents the number of deaths each day they were reported; the grey line represents the number of deaths each day they occurred.

A glimpse at COVID-19 cases in some Maryland ZIP codes

Sun, 31 May 2020 03:24:47 +0000

A publicly-available MD COVID-19 metrics that I didn’t investigate much is cases per ZIP code. I created a dashboard where you can highlight one zip code at a time. Tyler Fogarty built a cool Treemap Explorer. Silver Chips has a nice heatmap of all zip codes as part of their extensive dashboard (a bit like the MDH dashboard). How can we make sense of all this?

A classical way to see it is to look at the daily number of positive cases, similarly to what I did for counties or the state.

Will it be the end of Stage 1 in Maryland?

Sat, 30 May 2020 21:00:18 +0000

Since May 14, 2020, Maryland is carefully reopening from an easy lock-down caused by coronavirus spreading thru the community (and all over the world). In this post, I’ll go through all the variables we have on the MD Health Department dashboard. But first, the official data comes from the MD dashboard and if you want scientific information about COVID-19, please consult the CDC website. If you are interested, you can read my previous posts on COVID-19 in Maryland from this page.

No visible impact yet of different COVID-19 Stage 1 strategies in Maryland

Thu, 21 May 2020 06:25:25 +0000

In my previous post, I was wondering if Maryland was ready to reopen, ready to enter Stage 1 of COVID-19 recovery. I also mentioned, in the end, that if Gov. Hogan announced the reopening of Maryland, he also gave counties the power to “fully” open, to be partially open or even to remain closed. You can see more info about Maryland Strong: Roadmap to Recovery: there is a map of what Counties decided.

Is Maryland ready to reopen?

Sun, 17 May 2020 03:59:11 +0000

A visual analysis of Governor Larry Hogan’s decision to enter Stage 1 of reopening Maryland.

(This will be a post based on a thread of tweets I posted on May 14 with updated graphs for today - one days after the start of Stage 1 - and more)

Maryland is in state of emergency since March 5, 2020 due to COVID-19. Governor Larry Hogan announced on May 14 that Maryland will " gradually reopen with flexible community-based approach" ( the official declaration is here). The MD Strong plan said " a 14-day downward trajectory of benchmark metrics - or at least a plateauing of rates - is required before recovery steps can begin". This Phase 1 started yesterday, May 15, 2020. So, are we there already?

MD counties COVID-19-specific death rate

Sun, 17 May 2020 02:32:22 +0000

Since a few weeks, I report the raw number of COVID-19 deaths in Maryland counties. If this gives an idea of the cumulative number of deaths - which is interesting - it doesn’t reflect the fact that some counties have more inhabitants than others. That’s why I plotted below the number of COVID-19 deaths adjusted for the population (i.e. the COVID-19-specific death rate):

Today (May 16, 2020), in terms of absolute number of deaths, Montgomery, Prince Georges and Baltimore County are the top 3 counties (this is the same for cases but not in the same order). In terms of confirmed deaths per 100,000 population, the top 3 counties are Kent, Prince Georges and Montgomery.

MD counties COVID-19 cases adjusted for population

Tue, 12 May 2020 04:42:23 +0000

Since a few weeks, I report the raw number of COVID-19 cases in Maryland counties. If this gives an idea of the cumulative number of cases - which is interesting - it doesn’t reflect the fact that some counties have more inhabitants than others. That’s why I plotted below the number of COVID-19 cases adjusted for the population:

Evolution of COVID-19 confirmed cases in Maryland counties, adjusted and not adjusted for population, on May 11, 2020

Trend in Coronavirus cases in Maryland (3)

Mon, 27 Apr 2020 16:12:00 +0000

Following up on my two previous posts ( here and here), I am writing a third post on COVID-19 in Maryland because I believe we enter a new phase.

Before continuing, please note that the same disclaimer as in my previous post applies here (in short: read the CDC and MDH websites for official information).

In the first phase, the importance was to detect and make sure COVID-19 patients were treated (also: make sure not to overwhelm the healthcare system, flatten the curve, lower the baseline, & stay at home!). My two previous posts were following these efforts, thanks to daily data released by the Maryland Department of Health (MDH) on its dashboard. My second post will still be updated with the latest data from there, go read it!

Trend in COVID-19 cases by Zip code in Maryland

Mon, 27 Apr 2020 00:43:35 +0000

Since the Maryland Department of Health (MDH) started to display number of COVID-19 cases for each Zip code in its dashboard, I was wondering how to display this information in a nice way. The MDH display the information as a map - very nice but it lacks from where each Zip code came from: is the number of cases increasing or decreasing?

Following on my busy chart with the evolution of all Zip codes (and highlighting just one of them - that may not be the one you are interested in, see previous post), I created a simple dashboard where you can select the Zip code you are interested in and see how cases are evolving. You can play with it here: https://jepoirrier.shinyapps.io/md-coronavirus-zip-app/ (screenshot below). Enjoy!

Trend in Coronavirus cases in Maryland, USA (2)

Sun, 29 Mar 2020 03:12:18 +0000

This post was last updated on April 26, 2020.
A new post from April 27, 2020 is here.

Following up on my previous post, here are updated trends in Coronavirus cases in Maryland (USA), the state I live in. I am writing a second post because the Maryland Department of Health (MDH) updated its dashboard with way more data than before (more on this below). Before continuing, please note that the same disclaimer as in my previous post applies here (in short: read the CDC and MDH websites for official information).

Trend in Coronavirus cases in Maryland, USA

Mon, 16 Mar 2020 23:17:29 +0000

Disclaimer: Although I work in infectious diseases, I’m not a specialist in Coronavirus. For the most up-to-date information on Coronavirus in the US, please visit the CDC website. For the most up-to-date information on Coronavirus in Maryland, please visit the Maryland Department of Health. That being said, now you can proceed at your own risk ;-)

This post was updated by one post on March 28 and another one here on April 27. Read the latest one here.

283 tweets about flu today

Wed, 14 Nov 2018 05:01:54 +0000

I wanted to use the TwitteR package for R since a long time, I tried but didn’t do much of it. Today I found a few minutes, followed simple recipes (I admit), and looked at the number of tweets about flu today (November 13, 2018). Result: 283 tweets in English (I wanted to focus on the USA but, for some reason, I couldn’t … yet!). That’s not a lot. But remember we are only at the beginning of the influenza season 2018-2019 in the Northern hemisphere.

Time commuting in Belgium

Mon, 06 Aug 2018 18:41:19 +0000

DISO1 - Data I Sit On, episode 1. This post is the first of a series of a few exploring data I collected in the past and that I found interesting to look at again … (I already posted about data I collected, see the Quantified Self tag on this blog)

Life is short and full of different experiences. One of the experiences I don’t specifically enjoy but is integral part of life is commuting. Although I tried to minimize commuting (mainly by choosing home close to the office) and benefit(ed) from good work conditions (flexible working hours, home working, etc.), a big change occurred when I took a new opportunity, in 2015, to work in the Belgian capital, Brussels.

Euthanasia in the Netherlands and Belgium, 1990-2015

Fri, 18 Aug 2017 23:24:59 +0000

While parsing the general literature, I found this paper from van der Heide et al. (2017) giving some numbers about end-of-life decisions in the Netherlands these past 25 years. I was wondering if one could see similar evolution in Belgium. And I didn’t have to look very far: van der Heide cited another NEJM paper with Belgian numbers ( Chambaere et al., 2015 ; an attentive reader will notice “Belgian” data is “only” about Flanders, not the whole Belgium).

Activity tracker: waist vs. wrist

Thu, 17 Aug 2017 16:03:36 +0000

A few weekends ago, I was challenged by a friend to do more steps than him. Of course, I won ;-) But I noticed he was wearing his activity tracker on his wrist while I was wearing mine on my waist. As I noticed several times before, when I had an activity tracker on my wrist, these devices tend to capture some movements even if you don’t actually walk (while typing energetically on the computer or while driving for instance).

So I took the opportunity of a small trip to wear 2 activity trackers, one Fitbit One on my waist and one Fitbit Charge HR on my wrist.

About antibiotic resistance and the price of drugs

Fri, 20 May 2016 18:09:00 +0000

Many headlines stated today that UK wants to tax pharmaceutical companies again in order to contribute to a pooled fund against antimicrobial resistance (AMR). The proposed ‘pay or play’ mechanism is a bit more subtle than that. The report ( full text here) is also suggesting other financing mechanisms (including the improvement of existing ones) as well as describing potential non-financial measures to reduce these resistances in the first place. Actually, financial measures occupy only about 6% of the report. But headlines need to be catchy. Let’s see a broader picture on tackling antibiotic resistance …

Apple HealthKit already created some disruptions ...

Sat, 19 Sep 2015 23:45:33 +0000

… At least in the minds of people.

Marketing is a powerful persuasion tool and you sometimes need a few early applications to create the impression that something radically new came and is changing an area.

I like to listen to podcast while doing repetitive activities that don’t require my brain too much. One of the podcasts I listen to is the Clinical Air from the Pharma Talk serie. A few weeks ago, I listened to episode #14 about consumer electronics in clinical research. It was all about the Apple HealthKit. In a sense it was very interesting to hear about it as it contained more details than its Wikipedia page for the moment ; another top-level summary of its capabilities is found in this Rahlyn Gossen’s blog post (Rahlyn was one of the guests of this episode). Episode #14 was published on July 21, 2015.

2013 with Fitbits

Mon, 23 Dec 2013 23:22:46 +0000

2013 is near its end and it’s time to see what happened during the last 360 days or so. Many things happened (graduated from MBA, new house, holidays, ill a few days, …) but I wanted to know if one could quantify these changes and how these changes would impact my daily physical activity.

For that purpose I bought a Fitbit One in March 2013. I chose Fitbit over other devices available because of the price (99 USD at the time) and because it was available in Europe (via a Dutch vendor). At that time the Jawbone Up was unavailable (even in the USA) and the Nike Fuelband couldn’t track my sleep.

Creating presentations with non-WYSIWYG tools

Sun, 24 Nov 2013 00:44:32 +0000

I work in a company that shifted from being R&D-driven to being project-driven. It is official since this 2013 but we saw it coming: the main pieces of memory are Powerpoint slides since a few years.

Everything is in Powerpoint, from agendas, discussions, presentations to minutes. Even when modelers want to show some results, they put them on a slide deck first …

For presentations I used to use Beamer but installing the LaTeX toolchain on a restricted, company-owned Windows laptop was a long and cumbersome process. I made a first presentation in Reveal.js this week. And I love it!

Belgium doesn't score well in the Open Data Index (not speaking about health!)

Mon, 11 Nov 2013 23:00:35 +0000

The Open Knowledge Foundation (OKF) released the Open Data Index, along with details on how their methodology. The index contains 70 countries, with UK having the best score and Cyprus the worst score. In fact the first places are trusted by the UK, the USA and the Northern European countries (Denmark, Norway, Finland, Sweden).

And Belgium? Well, Belgium did not score very well: 265 / 1,000. The figure below shows its aggregated score (with green: yes, red: no, blue: unsure).

Is it so difficult to maintain a free RSS reader?

Mon, 05 Aug 2013 12:04:10 +0000

A few months ago Google decided to retire its Google Reader (it stopped working on July 1st, 2013). As it was simple, effective and good-looking, a lot of people complained about this demise. A few days ago The Old Reader, one of the most successful replacement for Google Reader, also announced it will close its gates, only to keep early registered users. And today Feedly, another successful alternative, announced it is introducing a pro version at 5.00 USD per month.

Map of GAVI eligible countries in R

Sun, 10 Feb 2013 22:48:45 +0000

I was trying to reproduce the map of the GAVI Alliance eligible countries (btw I was surprised India is eligible - but that’s the beauty of relying on numbers only and not assumptions) in R. This is the original map (there are 57 countries eligible):

I started to use the R package rworldmap because it seemed the most appropriate for this task. Everything went fine. Most of the time was spent converting the list of countries from plain English to plain “ISO3” code as required (ISO3 is in fact ISO 3166-1 alpha-3). I took my source from Wikipedia.

Today is world diabetes day (Merck ends MK-0431E)

Wed, 14 Nov 2012 09:34:38 +0000

As WHO and other organisations are celebrating World Diabetes Day (WDD) it is always sad to read that a new potential drug is stopped.

This time Merck & co. stopped the clinical trial MK-0431E studying the co-administration of Sitagliptin and Atorvastatin in inadequately controlled Type 2 Diabetes Mellitus. Merck cites “business reasons” without further explanations.

Sitagliptin is sold under the trade name Januvia. It is an oral antihyperglycemic and one of the (if not the) best selling product of Merck with US$975 million revenue in the third quarter of 2012. On the other hand Atorvastatin is a statin lowering blood cholesterol. It was a blockbuster for Pfizer (sold under the trade name of Lipitor) until its patent expired.

Happy Halloween! (Pharma Q3 results and job losses so far)

Thu, 01 Nov 2012 09:58:19 +0000

Happy Halloween! It’s the season for Q3 reports a bit everywhere so also in Pharma: Abbott (↑), Elan (↑), Eli Lilly (↓), Bristol-Myers Squibb (↓), Sanofi (↓), Novartis (↓), Shire (↑), AstraZeneca (↓), Merck & Co (↑), Novo Nordisk (↑), GlaxoSmithKline (↓), …

Idea shared #2 - the feedback toothbrush

Mon, 22 Oct 2012 21:26:28 +0000

After the T-shirt that measures your sleep better than an app, here is idea #2: the toothbrush that provides some feedback.

The idea is simple - so simple it was already applied elsewhere. The idea is to provide feedback about the quality of the way people brush their teeth. The Brushduino focuses on entertaining kids to keep them brushing at the right place for the right amount of time. Other projects (with many variants) focus specifically on time spent brushing.

Idea shared #1 - measure your sleep

Sat, 22 Sep 2012 21:48:32 +0000

I don’t consider having more or better ideas than others. But I gradually realized I have less and less time for some activities like programming, electronics etc. Maybe that’s how we realize we are getting older now adults. So I decided to share these ideas rather than fueling the illusory idea that I will implement them one day.

So idea 1 is about measuring sleep. I recorded animals’sleep during my Ph.D. - but it was thanks to an EEG device. I think that if you want to understand or improve something you have to first measure it in a way or another. So I started to try to measure my own sleep with an app ( Sleep Cycle). But despite its good reviews it doesn’t work, at least for me.

Forget pills, here comes e-pills!

Wed, 15 Aug 2012 21:40:32 +0000

The US FDA recently approved Proteus Digital Health Ingestion Event Marker ( IEM). Basically, it’s a pill with some electronics attached (very tiny electronics: around 0.5mm in diameter for a total weigth of 5mg, see picture below). Once activated the pill transmit a signal and, coupled with a detector, you know when the pill got into your body.

Edible sensor for electronically confirming adherence to oral medications.

About stacked bar graphs

Wed, 08 Feb 2012 22:07:38 +0000

This afternoon I received a bunch of data accompanied by stacked bar graphs for each dataset. For example, this one:

The chart shows the incidence of disease X in various age ranges. That incidence is split by 8 severity levels. The chart shows that the disease especially affects age ranges 4 and 5, at different severity levels. However I didn’t feel comfortable …

what are the different levels of severity in age ranges 1, 2 and 3?
how can we compare levels C, D and E in age ranges 4 and 5?
is there anywhere some severity A?
(it’s even worst when some age ranges don’t have any incidence at all: what is happening?)
etc.

I looked on the web but couldn’t find much information apart from the fact " The Economist says they’re so bad at conveying information, that they’re a great way to hide a bad number amongst good ones" (but are still using them in their graphic detail section) or " a stacked column chart with percentages should always extend to 100%" (this doesn’t really apply here). Then in a post on Junk Charts, someone mentioned Steven Few who would have said “not to use stacked bar charts because you cannot compare individual values very easily and as a rule [he] avoid[s] stacked bars with more than six or seven divisions”. And Steven Few also participated in his forum here.

Reference Manager 10 with Wine

Wed, 14 Sep 2011 21:20:43 +0000

Reference Manager is a commercial reference management software package. It is extensively used in biomedical research, along with Endnote (sold by the same company), mainly because the main OS in these labs is Windows from Microsoft. I used it at the university and still have some reference databases in its format (with file extension .rmd).

This evening, I had to go back into one of those proprietary, closed databases I still had (most of my references were later re-entered in a BibTeX file). I could have borrowed my wife’s computer running Windows or tried some Open Source software that can open .rmd files. But it would have been too easy. So I tried it with Wine, a program that allows Microsoft Windows applications to run under Linux. In Wine AppDB, it is written people had tried version 9 and 11. In the old time, I bought a student license for version 10.

A good issue of Nature, obviously!

Tue, 19 Oct 2010 23:12:26 +0000

The October 14th, 2010 issue of Nature is obviously a good one. It had to be a good one! I usually advocate Open Access but it is always nice to reading complimentary issues of Nature which is Closed Access but is also publishing very good articles about science at the same time.

In this issue, I was interested in various topics …

First, there is a serie of articles about the US midterm elections and what (US) scientists feel about two years of Obama administration. Obama promised total transparency in American science, a new era of integrity and more freedom for scientists. From what I read, this isn’t the case yet.

"Facts & data"

Thu, 12 Aug 2010 23:09:45 +0000

A colleague of mine is always hammering home the message of bringing facts and data to a discussion rather than rumors, hearsays and daily newspaper articles. Since a few days (because H1N1 is not a pandemic anymore?), newspapers are coming with another “Superbug” or " Germinator", wrongly named " NDM-1". So, before spreading fear, uncertainty and doubt, please read the scientific litterature or, at least, read quality newspapers ( articles from The Guardian are quite fair and balanced).

FluTE makefile for wxDev-C++ (Windows)

Fri, 25 Jun 2010 01:27:57 +0000

FluTE is an influenza epidemic simulation model written by Dennis L. Chao at CSQUID. It works out-of-the box on GNU/Linux (just type make and run it).

I wanted to see how it works. But since I’m temporarily stuck with a Windows laptop, I downloaded a free C++ compiler for Windows ( wxDev-C++), imported all the files in a project and compiled. For those who want to try, here is the project file and the specific makefile in a zip file (2 kb). Just decompress the FluTE archive (I used version 1.15), copy the two files from the zip file above and launch the IDE. In the project options (Alt+P), specify the custom makefile (in the “Makefile” tab) as the one from the zip file above. Compile (Ctrl+F9). Done.

Ph.D. thesis

Thu, 25 Mar 2010 22:43:03 +0000

As I promised before, you’ll find here the text and slides of my Ph.D. thesis (btw text and slides are in French). The oral presentation was on March 24th, 2010 and everything was fine :-) Slides can be watched below.

Effets du sommeil et de la privation de sommeil sur le protéome hippocampique de rat après apprentissage topographique http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=3557617&stripped_title=effets-du-sommeil-et-de-la-privation-de-sommeil-sur-le-protome-hippocampique-de-rat-aprs-apprentissage-topographique-3557617

2.54

Thu, 08 Oct 2009 22:18:51 +0000

It’s the impact factor of the Open Access journal Proteome Science where I published my last article, last year.

I didn’t see that before but came to know when I downloaded the 453 remaining e-mails from an old account (3 months without fetching them). The announcement of this new impact factor was in one of the three interesting e-mails.

Redesigned Pubmed

Wed, 30 Sep 2009 22:41:32 +0000

I often wrote about Pubmed here. Briefly, it’s a search engine for publications in the biomedical domain. They recently redesigned their user interface and, although there are a lot of new things to save time that came with the new design, there is still a problem with their interface: the new search box takes too much space …

Redesigned Pubmed homepage ( bigger image)

Redesigned Pubmed result page: search box is hiding the logo, the display settings and the first result ( bigger image)

About file formats accepted by BioMed Central

Sat, 20 Jun 2009 21:32:48 +0000

BioMed Central is one of the main Open Access publishers in the world of Science, Technology and Medicine. On a side note, that’s where I published my two articles (in Proteome Science and the Journal of Circadian Rhythms). One might think that, given their support to Open Access, they would also support Open Source software and Open Format documents.

For the software side, it’s not very clear. Although they ask authors to consider releasing software described in publications under a free (or at least open source) license, they also support and advertise for a bunch of proprietary software. While it’s not a bad thing per se (it enlarges the number of potential authors), it’s sad to see they don’t cite popular free software like OpenOffice.org (to write your article), Gimp (to edit your figures) or Zotero (for reference management). These are the three main software in each category but the free software world has many more of them!

Ignite presentation style

Thu, 14 May 2009 21:25:29 +0000

Being away from presentations to my dismay since a few months, I always enjoy reading the Presentation Zen blog, Garr Reynold’s blog on issues related to presentation design.

Recently, Garr came back on the Ignite presentation style with a presentation from Pamela Slim. Here is a video recording:

[blip.tv http://blip.tv/play/AfDpaI73Pw]

I maybe liked this presentation for its content but above all for its style … At Ignite, you can have a maximum of 20 slides that automatically advance every 15 seconds (so max. 5 minutes talk). I like this kind of challenge. Unfortunately, there is no planned Ignite event in Western Europe soon where I would be able to watch this live.

Frequently Asked Questions about the Morris Water Maze

Wed, 06 May 2009 22:24:10 +0000

Since I published some videos of Morris Water Maze (MWM) experiments, I received questions about the set-up of the maze and its concept in general. I tried my best to answer them. I collected them and here are the Frequently Asked Questions about the Morris Water Maze. If you have some more questions, don’t hesitate to ask!

Presentation rockstar!

Wed, 01 Apr 2009 21:56:25 +0000

20040 views for my Gemvid presentation at FOSDEM 2009
100451 views for my random field presentation
200418 views for my OpenOffice.org Impress presentation

It’s good to be considered as a presentation rockstar (even if it’s an April fools joke).

E-conference about scientific patents

Mon, 11 Aug 2008 04:49:58 +0000

While looking for pictures related to patents, I found these interesting ones taken by Daneel Ariantho on Flickr. They depict a virtual conference about scientific patents. It could be interesting to get more information about 1) the content of this conference and 2) the kind of conferences organized in these virtual worlds. It could also be interesting to see the social aspects of these conferences (are your contact better/different in a virtual conference?) and the “quality control” (of speakers, of posters, of advertizers, …).

A seventh scientific paper from the Poirrier-Falisse!

Thu, 22 May 2008 20:25:38 +0000

Finally, a seventh scientific paper is published by the Poirrier-Falisse. After a huge batch of articles from Nandini, here is my second paper:

Poirrier J.E., Guillonneau F., Renaut J., Sergeant K., Luxen A., Maquet P. and Leprince P.: " Proteomic changes in rat hippocampus and adrenals following short-term sleep deprivation" Proteome Science, 2008, 6(1):14

doi: 10.1186/1477-5956-6-14

Very briefly, in this study we show the influence of 4 hours of prolonged wakefulness in rats hippocampus and adrenals proteome. As usual, this paper is published in an Open Access journal. Here is my updated BibTeX file (and I also updated Nandini’s BibTeX file).

"Word processors" are not meant to be usable

Thu, 20 Mar 2008 23:03:01 +0000

(… at least for large documents)

Two week-ends ago, I spend a whole day trying to apply a consistent style to a thesis. I spent hours trying to be obeyed by a word processor because it would systematically change the style of some element, somewhere in the 100-or-so pages. Including figures was also a nightmare: we had to keep an eye on the (limited) memory of the computer (otherwise we got unexpected screen freeze, a lot of noise from the hard disk (paging), etc). Generating a bibliography was also another daunting task, even with the use of a dedicated reference manager …

New website for the CNCM

Wed, 05 Dec 2007 19:07:29 +0000

One of the two labs where I’m working, the Center for Cellular and Molecular Neurobiology, has updated its website. You can see it here and browse its growing content. And this time, I did nothing (a company built the website for us).

Using free fonts if you work at a University

Tue, 09 Oct 2007 22:21:28 +0000

In the Free Software Movement, we believe computer users should have the freedom to change and redistribute the software that they use. The “free” in free software refers to freedom: it means users have the freedom to run, modify and redistribute the software. Free software contributes to human knowledge, while non-free software does not. Universities should therefore encourage free software for the sake of advancing human knowledge, just as they should encourage scientists and other scholars to publish their work.

The Vietnam War added a motive to go on studying

Sun, 07 Oct 2007 21:11:07 +0000

… And what about both wars against Irak?

Title from F.C. Thompson’s correspondence to Nature in Nature 449, 139

Un-published in Nature (NRSC)

Thu, 23 Aug 2007 20:45:30 +0000

In the last post, I told you one of my photo on Flickr was published in an article from Nature Reports Stem Cells. After some discussions with three friends, I decided to write an e-mail to the journal editors basically stating that, although I enjoyed my photo being shown in their journal, they did not comply with one of the two conditions of the CC-by-sa license (the “Share-Alike” part, more details in the copy of my e-mail). I chose this licence for this photo because it is there to give freedom to other people on some material while this freedom stays with the media even if the latter is modified.

The hardware side of Picklist Editor 0.1

Thu, 26 Jul 2007 20:34:42 +0000

This morning, I released Picklist Editor 0.1 with a text introduction … Hmmm … on my photos on Flickr you can see the hardware side of the picking process … (click on pictures to see details).

On the photo on the left, you can see a gel on a low-fluorescent glass plate. This plate is in part in a tray that firmly holds it when the robot is doing its job. The holes everywhere result from the picking process but there are proteins everywhere and you can’t see them in visible light since they are labelled with fluorescent Cy dyes. You can see two white round stickers on each side of the gel: these are the picking references.

Something is over ...

Wed, 11 Jul 2007 23:42:24 +0000

Don’t write to my ULg e-mail address (jepoirrier@ulg.ac.be) because I don’t have it anymore. No more ULg address … Something is definitely over now …

If you really want to contact me, have a look here.

Snownews

Wed, 20 Jun 2007 05:52:02 +0000

Taking advantage of my laptop crash, I went back to some text-mode tools ( vim, mutt, …): they are fast, easy to use (once you read at least the introduction section in the manual) and reliable (text files are more easily recovered after corruption than binary blobs). I also tested and adopted Snownews.

Snownews is a text-mode RSS newsreader. Installing it is very easy: download the archive, and type the usual “./configure; make; make install”. Since I’m following some blogs written in French, I configured Snownews with Unicode support: “./configure –charset=UTF-8”.

Chinese article

Fri, 15 Jun 2007 19:25:08 +0000

Source : Le 15eme jour du mois, 165: 4 (hÃ© hÃ©)

Is VoIP reliable?

Fri, 25 May 2007 22:15:12 +0000

I am wondering if VoIP is reliable … Since a few weeks, the university is deploying VoIP phones in the whole campus. The good thing is that everything was apparently planned since a long time: cables were already there, just next to the regular IP cables. But since then, some problems are occurring … No connection to the “old” phone network, a whole morning without phone due to “a problem in the software controlling one of the infrastructure device”, … A few days ago, I even received an e-mail from the lab computer specialist telling all the scientists how to reset the lab firewall in case it blocks all the IP+Voice communications (for an unknown reason). I am not criticizing the deployment model of this particular case but I’m wondering how reliable is VoIP …

Pure happiness

Sat, 12 May 2007 19:14:37 +0000

“Que du bonheur” (French) can be translated into “Pure Happiness”. I found this ad for a hotel/casino on the way back from Luxembourg where I won the best poster award at the Benelux Sleep Congress 2007. So, I’m really happy! :-D

The winning poster is the one on the left, on the photo above. The poster on the right was about Gemvid and was ranked second :-)

A third scientific paper for the Poirrier-Falisse!

Sat, 12 May 2007 10:08:48 +0000

Nandini published her second scientific paper in Journal of Proteome Research and it was just published “ahead of print” (i.e. in electronic version before the “official”, paper version). It’s:

Ruelle V., Falisse-Poirrier N., Elmoualij B., Zorzi D., Pierard O., Heinen E., Pauw ED. and Zorzi W.: " An Immuno-PF2D-MS/MS Proteomic Approach for Bacterial Antigenic Characterization: To Bacillus and Beyond" J Proteome Res., e-pub ahead of print.

PubMed ID: 17488104

DOI: 10.1021/pr060661g

Congratulations! :-)

A small post from Luxembourg

Fri, 11 May 2007 22:47:31 +0000

A small post from the Benelux Sleep Congress 2007 (where they left two unprotected wifi networks near and in the congress hall :-) ). It’s mainly a medical congress but I had very interesting discussions with, a.o., Prof. Peter Meerlo and Dr. Michel Cramer Bornemann, mainly about Gemvid and the proteomic aspect of my Ph.D. Let’s see what can I do with all these contacts …

Otherwise, the Domaine Thermal of Mondorf-les-Bains is a beautiful place (ok, it’s not as natural as landscapes aroung the highway and national roads going to Luxembourg). Unfortunately, I left my camera at home (and it’s really a stupid decision taken in this morning rush).

Re-examinated patents are still valid?

Tue, 08 May 2007 12:16:24 +0000

In " Patenting the obvious?" ( pdf), you’ll read about people fighting against a patent on methods for making embryonic stem cells from primates. I won’t go into the details about the patent in itself (although I think that there shouldn’t be any patent based on or containing living “things” or part of it). I just want to share my surprise when I read this (emphasis is mine):

In its 2 April statement, the patent office said that it accepted these arguments, and intended to revoke the patents. WARF has until June to respond to the decision, and if it is unhappy with the outcome, it can then initiate an appeal. The patents will be treated as valid until the re-examination process is complete â€” that is, until WARF’s response and the possible appeal have concluded. That could take years.

Disappointed by BSN meeting

Mon, 07 May 2007 22:38:58 +0000

I’m very disappointed by this BSN meeting. This event is organised every 2 years so you might expect some quality standards. Well, don’t expect too much … (don’t expect anything, in fact).

Morning talks were ok, nothing more: it was not better nor worse than any other congress. But the poster session was not organised at all and there was no support from senior scientists … Moreover, authors of about 1/3 of posters didn’t even deign to come and hang a poster! Most of senior scientists left before the afternoon poster sessions (usually, questions from seniors are more useful than other students’ questions); maybe 2-3 seniors were left (for the whole Belgium!!!). And the final touch, lunch was not free (not even sandwiches!) although we paid 45€ for registration (free for members - membership is 12€ per year for students). Instead we were redirected to the UAntwerp canteen … Are they not smart enough to find a sponsor? I think it would have been better to attend the Neuroinformatics Meeting only.

Contamination!

Sun, 01 Apr 2007 22:59:35 +0000

Last week, our proteomic group did a 2D of a purified protein but, unfortunately, it seemed we had a contamination. So, this week-end, we performed blank tests in order to see if the contamination came from our experiment (or from the purification). We tested our fluorescent markers and different 1D strip holders. At a normal gain, the image looks fine: contamination doesn’t come from the 2D

But when I increase the gain, the image (and thus our gel) is really contaminated! :-( We really have to look where did the contamination happen! Look at this:

Noise level due to ventilation

Fri, 16 Mar 2007 12:02:59 +0000

Since a few days, I am back to my previous laboratory to collect some more samples. While looking after my rats, I measured the noise level with a dBmeter. The conditions are:

8.30 am
doors are left open (except in the housing unit) as it is usually the case
five samples per room: one in each corner of the room (without moving any furniture) and one in the middle
measures taken at ear height
device: YF-20 (YFE)

Would you like to visit one of my lab?

Wed, 14 Mar 2007 21:42:34 +0000

It will be possible on this Saturday March 17th, 2007! For the EDAB Brain Awareness Week, one of my lab is organizing some conferences and you’ll also have the opportunity to visit the lab and see demonstrations on experiments we do and how we do. One of my mentors, Dr. P. Leprince, will tell (and show) you how we can identify proteins and identify their roles. Other workshops include microscopy, electrophysiology, behaviour. Conference topics include stem cells, drug addiction, injuries in the brain. You can have more info on the lab website (look for our activities, in French).

Colourful western blots

Fri, 09 Mar 2007 19:24:02 +0000

Last week, I received broken vials with(out) my antibodies. This week, as the company promised, I received new ones (not broken, this time). Thanks to our technician, I was able to get colourful western blots (using the ECL Plex system) :-)

How do I handle my bibliographic data?

Fri, 09 Mar 2007 05:38:27 +0000

In science, you have to justify nearly all your assertions and this is done by citing another scientific paper, called a “reference”. With practise and advices of some people, I arrived to a satisfactory references management system I’ll explain below. My “problem” is that in the academic world where I work nearly everyone use EndNote or Reference Manager, two proprietary reference management software for MS-Windows. And I want to use the simple yet powerful BibTeX system.

Receiving broken vials ...

Fri, 02 Mar 2007 23:53:57 +0000

I was eager to receive some new antibodies for western blotting (I was waiting for them since December 2006!). They finally arrived on Wednesday but everything was broken inside! :-( A plastic shell was supposed to protect the precious vials (about 300US$ each) but even that was broken. I immediately phoned the company and they promised me new vials for next Wednesday. Suddenly, it’s possible to get them in one week … Well, let’s see what I’ll get on that day …

GUI version of pyP2B

Thu, 15 Feb 2007 23:08:29 +0000

My python script pyP2B was command-line only. Tonight, I played for the first time with Tk, re-wrote pyP2B as a class and thus added a GUI.

Its webpage is updated ; the archive containing both command-line and GUI versions is here: pyP2B.tar.gz (3kb).

PhD photo tour

Tue, 13 Feb 2007 02:16:06 +0000

When I began my Ph.D., I don’t know if Flickr existed but, at least, I didn’t know it existed. So I didn’t know about this PhD vs Girlfriend comparison nor these work/motivation/courbature vs time charts. I didn’t get a canned Ph.D. where all the techniques are already used since a long time in the lab but then it would have been too easy! Finally, after my defense, if I have the opportunity to go to the USA, I’ll get this smart car (or the plate, at least).

A day in front of DeCyder

Tue, 19 Dec 2006 19:49:39 +0000

The whole day, I was busy working with DeCyder, a software to analyse spots of proteins in 2D gels. I hope I won’t dream of small red/yellow/green dots tonight:

The software use a 3D representation of the spot. If we change this view too fast (either by moving it or by quickly browsing through spots), the graphic diplay freezes and we fall back to an ugly VGA mode (screenshot below). Since the morning, the computer crashed 7 times! I reduced the screen resolution to 1024x768pixels in 24bits colours and it seems to work correctly now. :-)

A nice 2D-DIGE difference

Fri, 08 Dec 2006 01:03:26 +0000

This week is very stressful because I am doing a 2200+ euros 2D-DIGE experiment (*) on samples from a rat organ we never studied before and from which I cannot obtain any more new samples.

We found a new pattern of proteins dispersion (compared to our previous experiments on other organs) and, more importantly, we found a clear difference in protein expression in at least 2 spots. In the image below, all the whitish spots mean proteins in these spots are found in equal amounts in the 3 conditions. But spots in red or green mean proteins expressed at different levels (even on/off) between conditions!

Some websites to find antibodies

Mon, 27 Nov 2006 13:03:50 +0000

Just to remember, here are some websites to find antibodies:

abcam, the largest one, apparently
Biocompare antibody search (links to many vendors websites)
Invitrogen search engine (never found any antibodies there but, in case it could useful, …)

Links to information and protocols about antibodies on IHC World and the antibody resource page.

Plugins for Digital Object Identifier lookup

Fri, 17 Nov 2006 22:29:52 +0000

I’ve just written some “search plugins” for Firefox (1.x and 2.x) that allow you to quickly look for a specific Digital Object Identifier ( DOI). These DOI are more and more used in biomedical sciences. One of their interesting features is that they allow direct linking to the scientific article.

The plugins are availble here. If you already have Firefox 2, the installation procedure is very easy: all you have to do is go to the plugins page, click on the small arrow near your Firefox search box and choose the “Add DOI lookup” option; it will then automatically be installed for you.

Double quotes!

Tue, 14 Nov 2006 11:45:55 +0000

GGGRRrrrrrrr … I was quietly using R to analyse my data when, suddently, I wasn’t able to open the file containing these data anymore. It’s just a plain text file! How can it be corrupted? Here is the error message:

t < - read.table('ratsdata.csv', header=TRUE, sep=",") Warning message: incomplete final line found by readTableHeader on 'ratsdata.csv'

For hours, I tried everything: I counted the number of separators on each line, I counted the number of decimal points on each line, I removed double quotes around factors, I examined in details the final line, etc. (well, Python scripts did the job for me because my file already has > 700 lines). Finally, the solution was so dumb: I mistakenly deleted one double quote before a header. My first line looked like (1) and should look like (2):

Dry beveling micropipettes using a computer hard drive

Tue, 31 Oct 2006 14:41:22 +0000

I really like this kind of application: a person used an old hard disk to bevel micropipettes for electrophysiology [1]. It’s fast, simple, easy and the author got an article published at an impact factor 1.784.

[1] Canfield, J.G. " Dry beveling micropipettes using a computer hard drive" Journal of Neuroscience Methods 158 (1):19-21.

Automated Pubmed reference to BibTeX

Sun, 22 Oct 2006 21:44:15 +0000

In biology, we often need to use PubMed, a biomedical articles search engine for citations from MEDLINE and other life science journals.

In the MS-Windows world, you have nice, proprietary tools (like Reference Manager or Endnote) that retrieves citations from PubMed, store them in a database and allow you to use them in proprietary word processing software (in fact, in MS-Word only since nor Wordperfect nor OpenOffice.org are supported). If you are using BibTeX (for LaTeX) as your citations repository, there isn’t a lot of tools. The best one, imho, is JabRef, a free reference manager written in Java (for me, the only “problem” is that it adds custom, non-BibTeX tags). Or you can edit the BibTeX file by yourself with any text editor.

Free communication at the BASS Autumn Meeting

Sun, 08 Oct 2006 15:41:56 +0000

I went to Gent, last Friday, to the BASS Autumn Meeting. With “New drugs for sleep” as a title and mainly physicians and psychatrists in the audience, I didn’t expected to have a lot of “basic science” presentations but the University of Liege was well represented by T. Dang-Vu, P. Peigneux, C. Schmidt and me in the free communications section (btw, we are all four from the Cyclotron Research Center). I outlined some recent findings on proteins differentially expressed after a short-term sleep deprivation. I had a nice question from Prof. Verbraecken ( UZA) and, next time, I’ll focus more on pathways and physiological implications of proteins found rather than on functions only.

RNA-oriented Nobel Prizes

Wed, 04 Oct 2006 17:19:02 +0000

On 6 Nobel prizes, 2 were awarded to people involved in research about RNA. The 2006 Nobel Prize in Medicine was awarded to Andrew Fire and Craig Mello “for their discovery of RNA interference - gene silencing by double-stranded RNA”. And the 2006 Nobel Prize in Chemistry was awarded to Roger Kornberg “for his studies of the molecular basis of eukaryotic transcription”.

RNA interference is a mechanism where a “double-stranded ribonucleic acid (dsRNA) interferes with the expression of a particular gene”. And transcription is basically the process through which a DNA sequence is copied to produce a complementary RNA.

EURON Ph.D. days in Maastricht

Sat, 23 Sep 2006 00:29:48 +0000

These last 1.5 days, I was in Maastricht (NL) for the 10th Euron PhD days. Euron is the “European graduate school of neuroscience”. I presented a poster and did an 15 minutes oral presentation of my last results. It was a good meeting in its 1st meaning: I met interesting people. I also enjoyed listening to other Ph.D. students’presentations since it always gives you i) a glimpse at what other people (in other universities) are interested in (by other means that paper/digital articles) and ii) the impression that you are not the only one to have problems with your protocol, your animals, your proteins, … The location was great ( Fort Sint Pieter), sun was there. The ULg team was very small (only 4 Ph.D. students and 2 senior scientists on a total of about 100 participants) but this gave an occasion to know other students better.

Digital access to the ULg libraries

Wed, 13 Sep 2006 11:36:35 +0000

Although the University of Liege ( ULg) network of libraries webpage is very old and ugly, the network is starting to use new, technologically advanced tools to allow digital access to its content (articles, books, thesis and other media). Three tools are available since a short time:

Source gives access to all media currently available in libraries (it replaces the Telnet-based Liber, for those who used it before). Source is based on Aleph from ExLibris, a proprietary software.
PoPuPS is a publication platform for scientific journals from the ULg and the FSAGx. PoPuPS is based on Lodel CMS, a free (GPL) web publishing software. Articles in this database seem to be Open Access although no precise licence is defined (and some articles look strange : see the second picture in this geological article).
BICTEL/e is an institutional repository of Ph.D. thesis. It seems to be developed internally by the UCL

With these tools, the ULg try to catch the Open Access movement. Source is already connected to other types of databases but it seems that PoPuPS and BICTEL are not (yet) connected to cross-references systems like DOI nor using standardised metadata like in Eprints.

Lightweight installation of computer

Wed, 06 Sep 2006 23:51:10 +0000

This evening, I prepared a computer for the lab. Don’t blame me but it has to be under MS-Windows and with MS-Office. Knowing it’s only an Intel Pentium II MMX (“x86 Family 5 Model 4 Stepping 3”) with 64Mb of RAM and 2.4Gb of hard disk, I needed to find general software that has the smallest footprint in terms of both memory and hard disk consumption. Here is a small list of software I found interesting (mainly for me to remember):

Another scientific paper from the Poirrier-Falisse!

Fri, 25 Aug 2006 11:24:32 +0000

Finally, a second scientific paper is published by the Poirrier-Falisse (a first paper for me):

Poirrier JE., Poirrier L., Leprince P., Maquet P. " Gemvid, an open source, modular, automated activity recording system for rats using digital video". Journal of Circadian Rhythms 2006, 4:10 ( full text, doi)

It is still in a provisional PDF version but already available on the web and Open Access (of course)! Here is my BibTex entry. I will upload source code tonight on the project website.

Done some spot picking

Wed, 23 Aug 2006 23:24:33 +0000

Today, I did some “spot picking”. In 2D electrophoresis, you disperse proteins in a gel according to their electric charge and mass. You obtain a kind of map of proteins and, if you stain these proteins, you have a map of spots ( example here). After some analysis, it could be good to identify some proteins of interest. The problem is that they are in the gel! So, today, I used a robot called “spot picker” that … picks spots representing proteins of interest out of the gel. You can see what a spot picker looks like in my proteomic set on Flickr.

A first scientific paper from the Falisse-Poirrier!

Fri, 14 Jul 2006 14:07:40 +0000

Nandini published her first paper in a scientific journal:

Falisse-Poirrier N., Ruelle V., Elmoualij B., Zorzi D., Pierard O., Heinen E., De Pauw E., Zorzi W. Advances in immunoproteomics for serological characterization of microbial antigens. J Microbiol Methods. 2006 Jul 3 ( DOI access).

Congratulations! :-)

It is still in electronic format (ahead of print) but already available on the web (but not Open Access, unfortunately ; I think Nandini will auto-archive it somewhere). Here is Nandini’s BibTex entry (will be updated for volume and pages asap).

Interesting interaction between videotracking and computer games

Tue, 04 Jul 2006 09:01:00 +0000

In his blog, Jonas Hielscher wrote about an animal controlled computer game), where a player can play Pacman against real crickets! It is so cool, I shamelessly copy and paste his screenshot here :

I find it cool to see nice application of tracking, like I did (tracking) with my rodents:

Tracking of a rat in the Morris water maze
rat = big, red spot on top
its trail from bottom is also in red

Is there a pattern for paying parking lots?

Wed, 21 Jun 2006 22:51:59 +0000

Last Friday, I was still in my wife’s lab at 19.45. It’s on the 4th floor of the Liege Hospital. From there, I could see the parking lots (for visitors).

Far away, the free parking lots were congested, as usual. But I was more interested in the paying parking lots, the ones that are the nearest from the hospital. Despite the fact that it was 19.45, there were still some cars. Some cars were there since the morning or the afternoon but some of them were just parked there a few minutes ago. I tried to draw where the cars were.

KEGG can help you ...

Thu, 15 Jun 2006 16:32:50 +0000

… at least if you are a biologist interested in genes, genomes and pathways. KEGG is the acronym for “Kyoto Encyclopedia of Genes and Genomes”. I’ve found it while looking for genes involved in the circadian rhythm and in the long-term potentiation and depression. Of course, for a biologist strongly interested in computerised treatment of biological data, it’s a bit disappointing that these pathways in the KEGG PATHWAY Database are manually drawn but, well, it remains a very usefull tool to continue and digg further in the comprehension of these mechanisms.

Behavioural scorings reader

Sat, 03 Jun 2006 01:30:03 +0000

In our lab, we are (also) working on rodents behaviour. Some time ago, I wrote a very simple software that logs pre-defined behaviours to a file when the observer detects one of these particular behaviours and clicks on the ad hoc button. I accumulated quite some logs but I wasn’t able to really visualize how the rat performed. So, this evening, I wrote another small software to read those log files and to plot a graph of the rat activity. Here is a screenshot of the software in action:

New temperature record in the animal housing unit!

Wed, 31 May 2006 10:47:59 +0000

This morning, the temperature in the animal housing unit was 10.5Â°C in all the rooms and 13.7Â°C in the room where the rats are sleeping. As explained in the ad hoc page of the university website, they turned the general heating system off since May, 15th, regardless of the weather conditions. Since then, I’ve clearly observed a drop in temperature. But today is the worst, not only for scientists who are trying to work in these conditions but also for the precious animals we take care of (the recommended temperature range by all ethical committees is 20-25Â°C).

Bioforum 2006, ISAL cultural evening, experiments ... A very busy week!

Sat, 20 May 2006 22:18:18 +0000

This week was quite busy … In the proteomic lab, I released the first version of IPGPhor2 Reader (see also the previous post). Of course, since we didn’t fail any recent experiment ;-) we don’t see the immediate usefullness of this software. The main purpose of this software is that it allows to see where and when an experiment failed, how the current was given during the IEF and when it was not correctly supplied.

What about recruitment companies?

Mon, 08 May 2006 21:40:15 +0000

I am slowly beginning to look for a job ; at least, for what I’ll do after my Ph.D. (there is still a lot of work in order to finish it!) (some people find that I am too slow at this quest for a job). I worked hard to develop the behavioural lab but I think that I wouldn’t be able to continue in this field (behavioural science doesn’t get a lot of funding). Anyway, I have some other people to see before I perhaps decide to reject this career option for/by myself.

I really like LaTeX Beamer

Thu, 20 Apr 2006 01:26:45 +0000

As I previously wrote, I’ve discovered the Beamer class for LaTeX some months ago and I really like it! It’s very easy and straightforward to use (provided you know a little bit of LaTeX, of course). I’ve also noticed it forces me to actually prepare my slides and illustrations before beginning to create the slide show. This is a good point since 1) it forces me to stress the structure (rather than doing it as one goes along the slides) and 2) it allows me an easier and better re-use of illustrations and slides previously shown (in Powerpoint or Impress, you had to think of what objects you have to copy ; here, you have only text to copy).

Chronic exposure

Wed, 12 Apr 2006 19:07:44 +0000

Since nearly two weeks, we are chronically exposed to 50-200 radioactive disintegrations per second in the lab.

Nices curves...

Wed, 05 Apr 2006 12:22:47 +0000

Every morning since the beginning of my Ph.D., I check the temperature and relative humidity when I am arriving in the lab. Now, after nearly 4 years, I have really nice curves (ok: nice charts, if you prefer) …

As you can see, temperature for the animals is always between 20Â°C and 25Â°C (this is good) and relative humidity in their room usually fits in the 20-80% range (ideal range is 30-70%). For a lab where we are only able to monitor the temperature and relative humidity, it’s good. I am sure that if we had the possibility to control it, it will be better (we only have a pot of water if the relative humidity is too low or an additional heater if the temperature is too low).

International Sleep Day

Tue, 21 Mar 2006 08:45:26 +0000

Today (March 21st) is the International Sleep Day. The Belgian Asociation for the Study of Sleep contributes to the Sleep Day by inviting sleepcenters to organise information sessions ( list here).

Unfortunately, neither the University of Liege human sleep lab nor my animal sleep lab are participating (we lacked time to organise something good and we are lacking people to welcome the public). :-( But, if you have time, today, pay these sleep centers a visit.

Very small Bash scripts to retrieve multiple PDF and create a book

Mon, 20 Mar 2006 16:21:40 +0000

The National Academies Press are putting some of their books on-line. I was particularly interested in the Guidelines for the Care and Use of Mammals in Neuroscience and Behavioral Research. The only “trick” is that they provide the book one page at a time (either in HTML or in PDF format). If you want entire chapters or the whole book in one file, you have to purchase it. I think it is a fair deal (how many publishers do that?).

Getting rid of old hardware at work

Mon, 13 Mar 2006 23:28:40 +0000

Today was the last day to get rid of all the old computers and electronic devices we could “store” in our lab. As you can see below, they are mainly broken screens …

Again, some toys for geeks

Thu, 02 Feb 2006 16:43:07 +0000

After the IR camera, I bought a dB meter and a light meter for the laboratory. They were the cheapest ones available (but they are still costly, around 150 euros, knowing money is coming from my own pocket).

The dB meter measures noise level. In my office, it measured 62 dB (approximately). According to the Wikipedia article on Decibel, it’s between “Office or restaurant inside” and “Busy traffic at 5 meters”. The problem is that I am exposed to this continuous environmental noise everyday, at least 8 hours a day. Now I can put a number on the reason why I appreciate silence and calm. Fortunately, I only have a few months left, here.

Beginning with an IR camera

Mon, 30 Jan 2006 14:56:00 +0000

Two weeks ago, I bought a small IR camera on eBay. I received it this morning and I managed to have some time to test it. The camera is quite small (approximatively 15cm long, 10cm in height without the mounting kit) and comes from a Chinese factory ( Shenzhen Lianyida Science Co. Ltd ; I have the LYD-806C CCD model). The box is in plastic. It is said to be “weather proof” but, anyway, this one will stay indoor.

XML DTDs in biology

Sun, 29 Jan 2006 01:57:19 +0000

I was looking if a XMLDTDs already exists for my field in biology (and, of course, I didn’t find any). It seems that bioxml.org is not available tonight (and wasn’t available before ; a WHOIS search told me that it is owned by someone from the bioperl project). I’ve found three collection of links to biologically-related DTDs: one by Paul Gordon, one by XML.com ( XML.com DTD repositories) and one by Andreas Matern. If you are interested, you can even try a seach in the XML.org registry. Most DTDs are focused on genes / genetics / genomics, proteins / proteomic, … but very few DTDs exist in other biological fields. And, of course, I am looking for a DTD in another field! All right, all right, I’ll try to write my own definition …

First presentation with LaTeX Beamer: RFT in fMRI

Wed, 11 Jan 2006 01:01:24 +0000

Today at 11:00, I’ll be doing my first real presentation with the LaTeX Beamer class. It will be about Random Field Theory in functional imaging (fMRI), a topic I’ve never done, ever, in my life (I am working on other techniques in the same lab). But, anyway, preparing this presentation was a good challenge (to understand a new technique from scratch and to do it with Beamer). I am quite impressed with Beamer ease of use.

A step further "simple" Open Access to scientific litterature

Sun, 08 Jan 2006 12:11:36 +0000

Combining a trend from the free software world and a reaction to increasing subscription costs, the last decade saw the emergence of the “Open Access” movement in the scientific litterature. Instead of transfering all your rights (and copyrights) to an editor that will sell your work to other scientists, you can choose to publish your work in Open Access journals. In this case, you retain your rights (and copyrights) on the article you wrote. Moreover, your work is freely available to other scientists (at least in electronic format) while still being of some quality since the reviewing process is still there. As an article writer, you only risk to be cited more often (since your article is freely available). As an article reader, you only risk to gain more knowledge (since more and more interesting articles are published with various Open Access publishers like BioMed Central, the Public Library of Science, etc.).

Animal housing unit inspection :-)

Fri, 16 Dec 2005 15:35:16 +0000

This afternoon, the secretary of the university ethics committee came to visit (inspect) our animal housing unit. We (and I) can be proud of our work since he said quite a few times that we have a “model” unit, a unit that is clean, etc. :-D As I said before, the animal wellbeing is one of the top priorities in the lab. And it is always good to be congratulated for our work (since I am working alone in my unit, it doesn’t happen often and it is even more important for me).

Music for scientists

Sun, 04 Dec 2005 21:24:31 +0000

When they are not doing any experiments (or even while doing experiments), scientists can be good singers. Here is the proof with two bands: Les Horribles Cernettes and Science Groove. Of course, you need some science background to understand everything …

Oxford resumes work on animal lab

Thu, 01 Dec 2005 13:15:34 +0000

Oxford University is building a new facility to replace and regroup all its laboratories working with animals. In July 2004, after a campaign of protest from animal rights group, works stopped. They are now resumed ( BBC story).

I am working with animals in my laboratory and, if I can understand some arguments from the animal rights activists, I can’t understand why they are going that far. A big part of the “modern comfort” that Europeans and North American are used to comes from and needs animal experimentation. For example, if we take any drug, it has to be tested on animal first before coming to the market. Of course, you can use in vitro cells but the complex behaviour of an animal (including the human) won’t be there. Animals are a collection of cells; but these cells are not the same in the arm or in the brain: they are specialised. How can you be sure that a general in vitro cell will react in the same way as an animal (including the human)? If we completely abolish animal testing, will you still go in court if a drug have side effects (that would have been spotted if tested first on animals) on you?

When open source software teaching meets biology

Fri, 29 Jul 2005 13:28:03 +0000

Open source software are more and more observed (if not used) in the biological sciences field. They provide all the advantages of Open Source software, plus they bring needs for consensus on file formats, data representation and manipulation methods. I’ve just read a short article from Greg Wilson ( in Nature) who is working with the Python Software Foundation “to develop a course that will teach scientists and engineers the 10% of software engineering they need to solve 90% of their problems”. Their goal is to “introduce them to some open-source tools and working practices that can reduce the amount of time they spend programming by up to 25%”. The course is already available here ( Software Carpentry) … for free, of course!

Don't feed the rats! (at least not too much)

Tue, 19 Jul 2005 00:07:45 +0000

I am currently reading " The behavior of the laboratory rat" and I found a very interesting point : don’t feed your lab rats too much or they will suffer and your experiments can suffer from that too! Of course, letting them have food ad libitum is the easiest way of doing. And we may think that they will only eat what they need. But rats are greedy! Unrestricted access to food is “unnatural” and compromises the health of the rats : it may cause obesity, diabetes, tumors, it shortens the life span and reduces the cognitive performance (formation of free radicals and/or glycation reactions of sugar with proteins). On the other hand scientists showed that dietary restriction is associated with increased production of proteins enhancing neuroplasticity and increased protection against metabolic insults like BDNF.