Part I : IpFire - Howto: Ubuntu Home Server (ZFS + virtual IpFire)

Series: Ubuntu Home Server (ZFS + virtual IpFire) 

-->Part I   : Ubuntu install and setting up IpFire (this post)<--

Part II  : Setting up ZFS 
Part III : Setting up hardware monitoring and webmin
Part IV: How much space do you lose with a RaidZ1/RaidZ2/RaidZ3? 

Part V : Poor man's deduplication

Ubuntu install and setting up IpFire 

Table of Contents:

Towards a next generation file system at home
Home server hardware specs
Ubuntu installation
Virtual firewall preparation
Virtual firewall set-up
Automatic starting of headless firewall VM

Towards a next generation file system at home

A few weeks ago I decided I wanted to move my home server to a next generation file system.  I realized I have rather a number of files I do not want to lose and I don't want to be 100 % dependent on Crashplan (who says this company is forever). Moreover it stands to reason that I never realize my files have gotten corrupt before I actually need them from backup. 

There are a number of options, but basically it comes down to the choice between either btrfs or ZFS. Given the still relatively unstable state of btrfs (currently raid 5/6 partitions cannot be scrubbed or integrity checked) the choice came down to ZFS. Luckily there is ZFS on Linux (ZoL) which provides a native Linux kernel port of the ZFS filesystem and is maintained by Lawrence Livermore National Laboratory (LLNL). 

To make a long story short, setting everything up was not difficult but there are some tricks that wou have made live easier if I'd known them, hence this post. My OS of choice was Ubuntu based on the large community, ZoL availability, webmin availability, virtualbox availability, and previous experience with Linux. 

Home server hardware specs:

So here's what I set up:

• Ubuntu 12.04.03 LTS
• ZFS on Linux (6 disk RAIDZ2 , double parity)
• Virtual firewall (IpFire) running through Virtualbox
• DHCP / DNS / samba file sharing
• LAN runs in the 192.168.10.xxx range.

Running on:

• Athlon II X3
• 16 GB ECC RAM
• 3 Ethernet adapters (2 for the firewall and 1 for the host OS)
• 6 WD 2 TB disks (mix of Green and Red)
• 500 GB bootdrive (2.5 " WD)

Ubuntu installation

Using a standard bootable USB stick I set up Ubuntu on a 30 GB partition (enabling me to have a small image which can be restored to another disk in the case of boot disk failure). 

The roles that I selected were :

• LAMP (might want to host internal webpages)
• DHCP
• DNS
• Samba
• Postfix (configured as website but can also be smarthost (e.g. google))

After installation you will end up at a login prompt. Subsequently I installed the Xubuntu desktop for convenience using aptitude.

sudo apt-get install xubuntu desktop

After installation of the desktop I installed some tools via the terminal to enable hardware monitoring and make administration easy. Terminal can be found in 'Accessories' in the start menu.

Smartmontools:

sudo apt-get install smartmontools

lm-sensors:

sudo apt-get install lm-sensors

Afterwards configure with :

sensors-detect

Install gnome task manager:

sudo apt-get install gnome-system-monitor

chromium:

sudo apt-get install chromium-browser

Virtual firewall preparation

The next step is setting up the virtual firewall and configure it. In my case I had three dedicated network adapters I can use but obviously you can also work with vlans and a virtual network (though I prefer hardwired myself). Before you move forward there are some things to make sure you write down on paper to make identification easier later on. Decide which ethernet adapter should fullfill which role and note the (last 5 digits) of the mac address of each adapter. 

The data can be found using the gnome network manager (via the network icon in the menu bar or via settings in the start menu) or via ifconfig in terminal. Using the network manager I also rename the adapters for quick identification, for me:

Adapter   Name    Mac address
eth0      Red     x:xx:xx (Virtual firewall WAN / Internet) 
eth1      Green   x:xx:xx (Virtual firewall LAN / Network)
eth2      Host    x:xx:xx (Server LAN) 

This will allows you to connect the proper virtual adapters to the proper hardware adapters in virtualbox.

Should one of your network adapters be displayed as 'unmanaged' happens sometimes. You can resolve this in the following way.

Open a terminal and edit the network adapters config:

sudo leafpad /etc/network/interfaces 

In the file scroll to the section "# the primary network interface" and comment out lines "auto eth0" and "iface eth0 inet dhcp" (or eth1 depending on the one that was 'unmanaged' (by placing a # as a first character on the line), should look like:

# The primary network interface

# auto eth0

# iface eth0 inet dhcp

Then make the changes as mentioned above via the network configuration tool. 

Virtual firewall set-up:

Next steps are the actuall installation of the firewall, first install dkms to allow virtualbox to reconfigure the kernel modules for virtualbox:
sudo apt-get install dkms

also don't forget the kernel headers:
sudo apt-get install linux-headers-`uname -r` linux-headers-generic build-essential

Subsequently download and install virtualbox from https://www.virtualbox.org/wiki/Linux_Downloads

Open a terminal an navigate to download folder (when starting in home 'cd /Downloads' ) and install virtualbox (the xxx depends on the downloaded version):

sudo dpkg -i virtualbox-4.3.xxxxxxxxxx-amd64.deb

Note that you should download and install this way rather than using aptitude as aptitude will install an older version (4.1.xx) which does not play nice with the automatic startup / save stae script below.

After installation download IpFire from : http://www.ipfire.org/download

Open virtualbox under 'System' in the start menu and create a new virtual machine. Call it 'ipfire' (also make sure to use lowercase, this is important later on to have the machine autostart on boot).

The type of machine is a generic linux machine, reserve at least 512 MB of RAM (likely more than enough), 1 core, and create a 3 GB virtual hard drive (should also be plenty). After you have finished open the ípfire'virtual machine settings and go to 'network', now grab you note and pen. 

Hook up the first adapter to your 'red' ethernet adapter in 'bridged' mode. Create a second network adapter and hook it up to your green interface using again 'bridged' mode. Now add again the last digits if the mac addresses of the virtual adapters to your list (note that the host adapter has no virtual counterpart).

Adapter   Name    Mac      Virtual Mac

eth0      Red     x:xx:xx  x:xx:xx      (Virtual firewall WAN / Internet) 

eth1      Green   x:xx:xx  x:xx:xx      (Virtual firewall LAN / Network)

eth2      Host    x:xx:xx               (Server LAN) 

Next go to disks and select the virtual cdrom, klik next to the cd icon select mount image and browse to the downloaded IpFire image 'Choose a Virtual CD/DVD image' .

Before installing the firewall go back to the network adapters configuration tool. Open up your red adapter, go to Ipv4 amd set to 'disabled' , go to Ipv6 and set to 'ignore'. Also repeat this for the green adapter. This is to prevent bypassing the firewall and forcing the traffic through red, the firewall, and green from the WAN to the LAN network. 

Set your host adapter to the following settings in Ipv4:

ip address : 192.168.10.4
netmask : 255.255.255.224 (allows 30 hosts)
gateway : 192.168.10.1
dns : 192.168.10.4 (when you have installed a dns server, otherwise use your ISPs or Google (8.8.8.8))

Now start your virtualmachine and the ipfire setup should also autostart. Grab your note again (write down the root password and web interface password). Go through the setup and configure the 'Red' interface in ipfire to be connected to your first primary adapter:

Adapter   Name    Mac      Virtual Mac

eth0      Red     x:xx:xx  x:xx:xx      (Virtual firewall WAN / Internet) 

depending on your ISP you have to set it to DHCP (likely when using a router / modem) or use another configuration. But please refer to ISP documentation. 

Also set up the 'Green' adapter:

Adapter   Name    Mac      Virtual Mac
eth1      Green   x:xx:xx  x:xx:xx      (Virtual firewall LAN / Network)

Set this one to the static IP : 192.168.10.1 (will be the gateway for the network). After setup completes the virtual machine will reboot. If all has gone well connectivity to the machine. If not try to navigate to 192.168.10.1 , this should open up your ipfire webinterface and allows you to see if the firewall is correctly set up. If this is not the case chances are that you switched the red and green adapters. 

Automatic starting of headless firewall VM:

The last stage is to have your virtualmachine autostart / shutdown on boot and shutdown using a simple script (otherwise you have to do this manually every time, not very convenient):

sudo leafpad /etc/init.d/StartVM.

Copy Past the following in the file and replace "MyUser" with your ubuntu useracount name (mind capitals). If you used ipfire as virtualmachine name, you can keep that as is.:

#! /bin/sh

# /etc/init.d/StartVM
#
#Edit these variables!
VMUSER=MyUser
VMNAME="ipfire"
case "$1" in
 start)
   echo "Starting VirtualBox VM..."
   sudo -H -b -u $VMUSER /usr/bin/VBoxVRDP -s "$VMNAME"
   ;;
 stop)
   echo "Saving state of Virtualbox VM..."
   sudo -H -u  $VMUSER /usr/bin/VBoxManage controlvm "$VMNAME" 
savestate
   ;;
 *)
   echo "Usage: /etc/init.d/StartVM {start|stop}"
   exit 1
   ;;
esac
exit 0

Close leafpad and give the script executable permission with

sudo chmod +x /etc/init.d/StartVM

Tell the script be the first to shutdown and the last to startup.

sudo update-rc.d StartVM defaults 99 01

Now you should have configure a basic Ubuntu server with desktop and virtual firewall. Reboot to make sure everything works and your virtualmachine autostarts.

The next part will focus on the set up of ZFS, webmin and hardware monitoring.

Bring back smoking in pubs and bars (why?-how?)

Let me start with saying I am not a smoker, yet I find myself frustrated about the recent turn of events. Over the last few years smoking in pubs has been banned. The rationale was that smoking, contrary to drinking, is a habit which directly adversely effects others around you (second hand smoke). As such legislation has been put into place to limit smoking to a defined area ('smoking room' or 'rokersruimte') so that those actively smoking would not harm others around them..

This is a perfect example of a politician's naive solution to a problem. 

Some problems:
1 -small bars do not have the space / fund to create a smoking room 
-> smokers are forced to smoke outside in front of the bar
-> complaints due to clouds os smoke in front of bars (e.g. in good weather if the sun shines)
-> larger bars have a state supported competitive advantage over smaller bars
2 -smokers like to smoke a cigarette and drink a beer next to it 
-> people move to the smoking room permanently
-> the smoking room becomes overcrowded and a fire hazard
3 -smoking bar owners are not allowed to smoke a cigarette in their own bar

Some let's list some pro arguments:
1 -banning smoking is good for public health
-> Actually it has been shown that alcohol is much worse than smoking for public health
(Nutt, King et al, The Lancet, Volume 376, Issue 9752, Pages 1558 - 1565, 6 November 2010, doi:10.1016/S0140-6736(10)61462-6)
-> Moreover, it has been shown shown that if all people stop smoking health care costs actually rise (as smokers tend to die young after a short sick bed; Barendregt, Bonneux, et al, N Engl J Med 1997; 337:1052-1057October 9, 1997DOI: 10.1056/NEJM199710093371506)

Note how the most harmfull drug is legal whereas a drug causing less harm (both absolute and relative) to others is banned...

So I guess we can say this is certainly untrue...

2 - Second hand smoke is harmful for kids
-> Again, this might be true, but we have scientific evidence that what these same kids are doing in this bar (i.e. drinking, might even be worse...)
-> There is a reason there is a minimal drinking age, if people are old enough to vote, drive a car and get married  they are old enough to decide what they do with their bodies (as they do in the former 3).... So this is a non-argument in my view..


3 - Second hand smoke is bad for pregnant women
-> True, but one can argue about the positive effects that drinking and staying up late have on pregnant women
-> Moreover these women are likely much more comfortable at home than in a sleazy bar
-> People can choose not to go to a smoker's bar...


And this is where the debate becomes interesting. There is nothing stopping people from setting up a non-smoking bar.This would give people a choice in the way they want to damage their health (which in the end is of interest to the state as it generates revenue).

My own (naive) solution to the problem:
Why not force bars to have smoking permit. When present people are allowed to smoke in a bar, when not present they are not. This is very similar to a liquor license and makes the option of having a non-smoking bar a little more interesting than it is..(cheaper liquor in non smoking bars)! Moreover, people can see from the outside weather or not it is a smoking bar if you force owners to put up a sign. It would also solve the problems of people smoking outside, the absence of room for a smoking area, would allow bar owners who choose this to smoke in their bars, etc. And it would provide governments with another source of income.

Most importantly it would give people a choice... Perhaps I (and by this I mean we, i.e. me and others as I live in the UK not NL atm) need to set up some sort of platform to push this legislation. After all the current problems are very similar to those that led to the introduction of liquor licenses in the first place in the 1800s...

Please contact me when you are interested! :)

Government budget of the Netherlands (1950-2013) - Part 1

Here I present an overview of the government budget of the Kingdom of the Netherlands between 1950 and the present. Samples have been taken approximately every 5 years and after 2002 every year. I show that purchasing power of the total budget peeked in the late 90’s and after 2000 dropped down to pre 90’s levels. Furthermore, we observe a shift in funds being diverted from the Defence, Public debt and Finance right after the second World War; to Education, Defence and Infrastructure in the 70’s; to Housing, Public debt and Education in the 90’s; and to Health care, Social security, and Education in more recent years. (Please excuse my lack of jargon and the correct terminology as economics is not my field).

Total budget growth

Since the Second World War the economy of the Kingdom of the Netherlands has grown tremendously. In particular the 1950’s and to a lesser extend the 1960’s were characterized by a high growth rate.[1] This growth declined in the 1970’s and 1980’s to be partially restored in the 1990’s. [1] Contrary to this economic growth, the total size of the budget has been growing slowly during the 1950’s and 1960’s but has been growing significantly faster during the 1970’s and the 1980’s, and lagging during the 1990’s (Figure 1). 

Figure 1: Growth of the government budget since the 1950 as obtained from the Statistics Agency of the Netherlands. The amount is converted to Euro’s from guilders but not inflation corrected. Note the quicker growth in the 70s and 80’s, which is repeated after 2007. The thin line is a moving average using 2 intervals.

Yet these figures were used as is and not corrected for inflation, so the next logical step would be to couple them to a form of purchasing power before we can draw any conclusion.

Purchasing power of the government budget

Unfortunately I was able to obtain inflation corrected figures, hence I was forced to improvise. In order to convert these figures to values representing some form of purchasing power, I used the following metrics: Price of crude oil (dollar, 1950 – present),[2] price of gold (dollar, 1950 – present),[3] price Maize (dollar, 1985 – present),[4] price of commodity metals (dollar, 1985 – present),[5] and naturally the dollar – guilder and dollar – euro exchange rates.[6-8] These were chosen to represent heating (oil), food (maize) and raw materials (gold and steel). Inclusion of more commodities would lead to more reliable results but was not doable for this post (yet people are welcome to use my figures and expand!).

The procedure described above allowed me to normalize the figures and create a more reliable image (Figure 2). For Figure 2A the budget size was expressed as ounces of gold this budget could buy as well as barrels of crude oil. Those two ranges were normalized between 0 and 1 over the time period 1950-2013 and the average of the two metrics was used to create figure 2A. Similarly for Figure 2B the budget was expressed in ounces of gold, barrels of oil, tons of maize and tons of metal (a composite index value), subsequently these values were normalized over the period 1985-2013. We now observe that while the absolute value of the budget grew quicker during the 1970’s and 1980’s, the commodity price caught up leading to a lower absolute purchasing power (likely caused by the steep rise in oil price and the decoupling of the dollar from gold). Moreover, we see that the total budget value (here expressed as purchasing power) actually declines rapidly after the peak of 2000. The absolute value in 2013 declines to pre 1990 values (interpolated as I have not received the 1990 government budget from the Statistics agency). 

Figure 2: Budget size expressed as an index value representing commodities the total budget value can buy. We now observe that, while the absolute value of the budget grew quicker during the 1970’s and 1980’s, the commodity price caught up leading to a lower absolute purchasing power. However, we also observe that in more recent years the commodity prices have grown so fast, the total purchasing power of the budget has actually declined to pre 1990’s  levels.

Development of the budget 1950 – 2013

Over the mentioned time period I wanted to see how the budget developed. What costs declined over time and what costs did rise. Can we rationalize the changes (coming from the zeitgeist)? To do this, I have calculated the percentage all individual expense categories makeup of the total budget. While this is not perfect, it should give an idea of prioritization and choices made in the past. However, a large number of different budgetary items have been introduced and removed over the years. Hence I more or less standardized this by using the categories as they are described in Table 1. It should be noted that ‘Inkomsten en Uitgaven Collectieve Sector’, which contained most social security costs upto 2009, was unavailable to me. These numbers were not provided by the statistics agency and I invite people who DO have these numbers to append to this work (the excel is available as a download).  

Table 1: Used standardized budgetary items.

Budgetary Item

General affairs and house of the Queen

Social Security

Public Health

Education/Culture

Public Debt Interest

Municipalities and Provinces

Foreign Affairs

Infrastructure

Defence

Finance

Justice

Home Affairs

Economic Affairs

Agriculture

Housing

Balkenende Item (Youth and integration) *

Mixed Balkenende Items *

Other *

Subtotal

Deficit *

Debt reduction *

Total

Items marked with an asterisk are only used when applicable.

Budgetary items reduced on average (1950 – 2013)

Let’s first examine the public debt interest costs (Figure 3). Very high right after World War 2 this figure declined quickly in the immediate post war era. However during the early 1980s recession, declined again and really peaked in the early 2000s.

Figure 3: Total public debt as a fraction of the total government budget. Declining after the Second World War, rose in the 80s recession and the early 2000s. While the total public debt rose over the last years, the actual interest resulting from the loans decreased.

While it is often considered a good thing to keep the burden of public debt interest as low as possible, there are other budgetary items that have been reduced over the years as shown in Figure 4.

Figure 4: Budgetary items that have been reduced over the period between 1950 and the present. While it is understandable that defense expenses have been reduced greatly after wartime levels, it can be stated that reducing them to about 2-3 % of the total might be another extreme. Similarly, it can be argued that infrastructure, something that the Netherlands are renowned for, should receive ample funding. With regards to agriculture, it could be argued that these expenses are transferred to EU budget. The ministry of housing has been absorbed by the ministry of Economic Affairs.

Budgetary items not showing a trend (1950 - 2013)

Next to items that show a decrease in spending there are some items that not show a clear trend. These items can increase or decrease with the zeitgeist and examples are shown in Figure 5. While most make up a small fraction of the total, the dominating line represents the money available for education and culture. Peaking in the 1970s (and likely responsible for the current educated professionals in society) is has been on the decrease over the last years. This could be considered a short sighted approach as the investments made in the 1970’s are still paying off today. 

Figure 5: Budgetary items showing no clear trend, increasing or decreasing with individual governments. However it can be seen that education / culture has always made up a significant fraction of the total budget whereas justice has made up a significantly smaller fraction.

Budgetary items rising on average (1950 – 2013)

This brings us to the final section, budgetary items making up a much large fraction of the budget over time. Not surprising this includes social security and public health. However it is noteworthy that the reforms of 2006 have not done much to decline the health spending growth. Both items are responsible for half of the total budget every year since 2010!

Furthermore, the provinces and municipalities are the 4^th largest item on the budget, rising steadily over the years (Figure 6). According to Wikipedia the Netherlands went from 24th worldwide (when healthcare is expressed as % of the total) in 2008 to 2nd in 2010 ! (right after the US) See also the figures at Worldbank.[9]

Figure 6: Budgetary items growing as a fraction of the total over the period 1050 – 2013. While health costs and social security costs are expected to rise due to the ageing population, it could be considered that a 60 % cut of the total budget might be somewhat extreme.

Conclusion

Here I tried to organize and some figures about the Dutch government budget. While my overview is crude at best it serves to illustrate a shift in government spending. We observe clearly some high impact events like the fallout of the Second World War, the 1970’s energy crisis and initiation of the welfare state; the 80’s recession; the 90’s bubble and the recent crisis. Some general observations could be considered reason for change. The most important being the appearance that education, infrastructure and defense are being systematically sacrificed in favor of social security and health care. On the short term this might seem reasonable, but this could have some nasty long term consequences.

Needed follow up

What I have shown here is in need of a follow up. 

• The numbers should be recalculated using the proper inflation corrected figures. 
• Furthermore the 'Collectieve sector' should be included as far back as applicable. 
• Moreover the missing samples (1990, 1980) should be included. 

Interesting other possible calculations could be:

• Calculations of the size of the government budget as a fraction of GDP (inflation corrected).
• Amount of people (e.g. police officers) that could be hired as a result of the changing budget.
• Total size of the government budget expressed in times the average salary (or average people that can be hired.

A preliminary plot is here, when we divide the total budget by the height of the average wage as obtained from GemiddeldInkomen.nl.[10] We get an approximation of the number of people that can be hired through the total budget. Interestingly this rises slowly (but steadily) from 2.000.000 in 1970 (earlier figures were not at my disposal) to 5.000.000 in 2008, to 8.000.000 (at 33.000 euro's average wage) in 2010!! That is a significant fraction of the population. This could indicate that (1) average wage is relatively low (has risen very slowly contrary to government buget), (2) government budget has grown out of proportion with people income (which could be indicating that taxes rise out of proportion, Figure 7).

Figure 7: Government budget divided by the average wage as an indicator of how many personnel the government could higer and hence the relative government size. Note the steep growth post 2010 / post crisis following a relatively stable period. 

Naturally this analysis should be redone using the proper number of people employed, it could also be (option 3) that those people employed just started to make significantly more money than average wage....

Please find the excel form I used here feel free to build or debunk my figures!

References

1.         van Ark B, de Jong HJ: Accounting for Economic Growth in the Netherlands since 1913: University of Groningen. Groningen Growth and Development Centre; 1996.

2.         Crude Oil Price [http://inflationdata.com/Inflation/Inflation_Rate/Historical_Oil_Prices_Table.asp]

3.         Gold Price [http://onlygold.com/tutorialpages/prices200yrsfs.htm ]

4.         Maize Price [http://www.indexmundi.com]

5.         Commodity Metal Index [http://www.indexmundi.com]

6.         Historic Dutch Guilde Exchange Rate [http://en.unciatrends.com/us-dollar-dutch-guilder-usd-nlg-exchange-rate-1971-2001/]

7.         Wisselkoersen [http://www.statistics.dnb.nl/index.cgi?lang=nl&todo=Koersen ]

8.         Converter in the past [http://fxtop.com/en/currency-converter-past.php]

9.         Health expenditure, total (% of GDP) [www.worldbank.org]

10.       Average wage 1970-2012 [http://www.gemiddeld-inkomen.nl/inkomens-vanaf-1970.php]

The ACTA treaty to be ratified by EU?

D66 member of the European Parliament Marietje Schaake placed a call on Reddit recently. (http://www.reddit.com/r/politics/comments/ow1v5/acta_note_from_marietje_schaake_member_of_the/)
The European Commission is to sign the ACTA treaty on January 26th, BUT the EU parliament has a decisive voice.

She urges European citizens to contact their representative in the EU parliament to stop the ratification of ACTA. I have contacted several members using the letter below (in Dutch), please feel free to reuse it!


Geachte Europarlementariër,

U zult ongetwijfeld op de hoogte zijn van de controverse die er de afgelopen weken rond de Amerikaanse wetsvoorstellen SOPA en PIPA speelde. Hierbij wil ik u mailen om de parallel met het ACTA verdrag te schetsen. U heeft eind 2011 tegen de motie gestemd die meer openheid af moest dwingen in dit verdrag. 

Laat mij eerst schetsen waarom openheid van belang is. De discussie draait niet langer om het wel of niet downloaden van mp3tjes en ook niet langer om nagemaakte A merken zoals Gucci of Apple. De discussie is veel fundamenteler van aard. Op dit moment zijn er voldoende legale wegen beschikbaar om illegale websites en het illegaal namaken van producten te stoppen. (Zie ook de recente successen van BREIN in Nederland en de FBIinternationaal)

Wat is / was nu het probleem met SOPA?

1. Het schenkt de aanklager tevens immuniteit (dat betekent dat elke klacht gegrond of niet resulteert in het offline halen van een site, denk ook aan het narren van een concurrent zoals we reeds nu in de tomeloze patent zaken zien)

2. De bewijslast ligt omgekeerd, niet degene die de klacht indient moet aantonen dat de beklaagde fout is. Na offline halen moet de beklaagde aantonen dat hij niet fout was.

3. Elke vorm van connectie (hyperlink etc) is per definitie inbreukmakend. Wat erin resulteert dat als ik een link naar wikipedia op mijn persoonlijke site heb, ik ook in overtreding ben wanneer wikipedia ergens een link naar illegale content heeft staan. Of als ik een link naar google heb, omdat die zoekmachine langs illegale content kwam.

Deze wetgeving zal downloaden niet stoppen, nee deze wetgeving zal juist legaal gebruik van het internet hinderen. Sterker nog, deze wetgeving geeft private organisaties teveel macht en plaatst hen in een rol van wetshandhaver. Iets dat nu reeds te zien is in de carte blanche die BREIN (een stichting) kreeg om het vonnis aan te passen. Deze satirische website is helaas erg waarheidsgetrouw: BREIN, NS moet zwarte markt in Beverwijk blokkeren.

Wat is / was nu het probleem met ACTA?

Het probleem met ACTA zit hem erin dat deze wetgeving op een niet transparante manier in voorbereiding is en dat die dingen die uitgelekt zijn niet veel goeds voorspellen. Het ACTA verdrag legt ook verregaande verplichtingen op aan de internetproviders en beperkt de vrijheden van burgers. 

Misschien is het goed om niet het symptoom downloaden aan te willen pakken, maar de achterliggende oorzaak. Dit brengt ons bij de volgende vraag:

Waarom downloaden mensen illegaal? 

Ook hier zijn een aantal redenen voor te bedenken:

1. Op elk moment wil een ieder welke serie / film / muziekstuk dan ook kunnen kijken of luisteren. Dit is technisch mogelijk. Deze dienst wordt op dit moment geleverd door de piraten en niet door de industrie, DAT is de grote drijfveer achter downloaden.

2. Een illegaal gedownloade film vrij van beperkingen. 1 maal downloaden betekent dat je de film kan kijken op de PC, de thuisbioscoop, de laptop en de iPad. Een film die via een legaal platform wordt gedownload doet het vaak op 1 apparaat. En, in sommige gevallen, niet eens op de pc waar je het kocht ivm compabiliteitsproblemen van de rechtenbescherming (niet de film zelf). (of games, vb SecuROM)

3 Het aanbod van legale alternatieven is vaak beperkt en slecht up to date. De illegale versie van een lopende serie is vaak 3 uur na uitzenden op het net beschikbaar. Legale content zou hier een voordeel kunnen hebben door gelijktijdig te verschijnen, maar doet dit niet.

Let op dat deze redenen niets te maken hebben met kosten, sterker nog uit onderzoek blijkt dat men liever een legaal product download vanwege de risico's op virussen die aan illegale content kleven en dat downloaden de verkoop stimuleert! (vergeet ook niet dat het afgelopen jaar wederom een record gebroken heeft in bioscoop bezoeken)

Zolang de piraat een beter product levert dan de industrie zal piraterij niet verdwijnen. 

Een heel logisch liberaal principe waarbij de beste aanbieder de grootste rol in de markt speelt!

Ik wil u middels dit schrijven oproepen om uw rol als volksvertegenwoordiger serieus te nemen en meer openheid af te dwingen voor een voorstel wat verregaande gevolgen zal hebben voor de vrijheid van de burger. Een wet die eerder geboren is uit de noodzaak een defect en verouderd business model te handhaven en dermate een desastreus effect op innovatie zal hebben. 

In afwachting van uw reactie,

Gerard JP van Westen

PhD Student Computational Medicinal Chemistry

Website: http://www.gjpvanwesten.nl

Twitter: @Gertdus

Reactie op 'Liegen doen we allemaal, en wel voortdurend' verschenen in Trouw

Origineel artikel zie hier.

Beste Asha,

Ik moet zeggen dat ik hoogst verbaasd was over de toon die jij in deze brief aanslaat. Een toon die ik ook bij andere mensen uit jouw vakgebied tegen kwam, zelfs op nationale televisie. Als ik jouw tekst lees als wetenschapper, dan ben ik geneigd te denken dat een deel van de mensen werkzaam in jouw vakgebied dit vakgebied niet als wetenschap ziet. Jij demonstreert hier een groot gebrek aan wetenschappelijke ethiek, ja zelfs een minachting voor hen die dat wel bezitten!

Je begint je betoog met een stelling waar je het leugentje om bestwil in een voorbijgaande sociale interactie gelijk stelt aan een wetenschappelijke publicatie puur gebaseerd op het feit dat beiden door mensen uitgevoerd worden. Met andere woorden, je stelt dat je op professioneel gebied niet meer mag verwachten van mensen dan het niveau van amateurs, tijdens het roddeluurtje met de koffie pauze. Om jouw analogie te vervolgen: Stel iemand verft zijn kamer en gebruikt de verkeerde, slecht dekkende, verf. Dit kan je dus eigenlijk ook van schilders verwachten en is helemaal zo gek niet, want het betreft in beide gevallen mensen.  

Mijn aandacht was hierdoor inderdaad gevestigd en ik was benieuwd wat je aan ging voeren om dit te onderbouwen. 

Je stelt vervolgens dat 70 % (!!!!) van de psychologen liegt over hun data. Zonder bronvermelding maak je het leeuwendeel van je vakgebied uit voor leugenaars! Ik wil je graag naar deze [1] pagina van de KNAW verwijzen betreffende wetenschappelijke integriteit. Besef je dat een wetenschapper een expertise op een bepaald gebied heeft, hierom heeft hij de plicht ethisch te handelen. Als expert ben je in de positie dat je makkelijk mensen kan misleiden, vooral om de doodeenvoudige reden dat je een autoriteitspositie hebt. Dat je bewezen ethisch verwerpelijk gedrag vergoelijkt door het merendeel van jouw vakgebied zwart te maken verdient natuurlijk niet de schoonheidsprijs. 

De wetenschap bestudeert en verklaart de wereld in verscheidene vakgebieden. Zij kent drie belangrijke pijlers:

1. De wetenschappelijke methode
2. Publicatie van resultaten
3. Reproduceerbaarheid van resultaten

De kern van de wetenschappelijke methode is dat je antwoorden zoekt op onderzoeksvragen. Het is belangrijk eerst een vraag te formuleren en dan systematisch onderzoek hiernaar te doen omdat dit voorkomt dat je valse verbanden gaat zien in data.

Ten tweede is het van belang je data te publiceren, dit om je 'peers' van jouw inzichten op de hoogte te stellen zodat het vakgebied als geheel progressie boekt. Nieuwe resultaten zullen nieuwe vragen opwerpen, welke weer onderzocht worden. 

Ten derde is reproduceerbaarheid van jouw bevindingen erg belangrijk. Je kan gerust stellen dat als iets niet reproduceerbaar is, het geen vaststaand feit is. Immers, als je iets niet kan reproduceren onder identieke omstandigheden, is er iets fundamenteel anders en levert jouw hypothese geen verklaring van jouw resultaten. Met andere woorden, als iets niet reproduceerbaar is, heb je iets over het hoofd gezien. 

Dit houdt dus in dat een publicatie vereist dat je ruwe data mee stuurt. Hoe anders kunnen jouw 'peers' jouw resultaten reproduceren, hoe anders kunnen zij deze interpreteren en gebruiken voor hun eigen hypothesen? 

"In een vakgebied waar de weg naar succes geplaveid dient te worden met publicaties in topbladen als Nature en Science, en die bladen alleen papers accepteren met ronkende resultaten, is het niet verwonderlijk dat je als onderzoeker de werkelijkheid zo nu en dan een handje wilt helpen."

Hoe kan iemand gefabriceerde resultaten publiceren en zonder wroeging de carrière van andere wetenschappers erop zien rusten? Fabriceer jij data dan worden nieuwe promovendi, 'peers' hier de dupe van, iets dat zich manifesteert in de affaire Stapel. Hoe gaat iemand ooit nog een naam opbouwen waneer hij/zij slechts met Stapel gepubliceerd heeft? Hoe gaat zo iemand ooit nog zijn vak kunnen uitoefenen? 

De kern van de wetenschap is de werkelijkheid bestuderen en verklaren "..de werkelijkheid zo nu en dan een handje helpen.." is geen wetenschap. Wanneer iemand dit toch doet is hij/zij per definitie niet bezig met de beoefening van wetenschap. 

"De wetenschap is het meest gebaat bij een cultuur waarin onderzoekers niet worden afgestraft voor hun mislukkingen maar juist worden aangemoedigd om er openhartig over te zijn. Dat bereiken we niet door degenen die fouten maken aan de schandpaal te nagelen."

Er is een groot verschil tussen mislukkingen (oftewel verworpen hypothesen) en moedwillig liegen / bedriegen. Inderdaad zijn negatieve resultaten ook resultaten, maar deze persoon heeft zijn negatieve resultaten niet gepubliceerd maar verzwegen. Deze persoon heeft resultaten gefingeerd en hiermee de wetenschap niet verder geholpen maar eerder een hoop schade berokkent! Als jij denkt dat hij aan de schandpaal genageld wordt voor het feit dat hij geen resultaten boekte sla je de plank mis.

Tot slot wil ik je graag wijzen op 'Good Clinical Practice' [2] (GCP). GCP is de standaard waaraan klinisch onderzoek dient te voldoen, deze standaard omvat alle regels die jij aanhaalt en meer. Misschien is het goed om de regels van GCP in de (sociale) psychologie ook toe te passen. Vergeet niet dat dit reeds verplicht is in een deel van de psychologie, dat gebied wat belast is met het onderzoek naar interventies/behandelmethoden. Dit verplicht een minimum standaard voor onderzoeken en ontdoet een geplaagd vakgebied van twijfel. 

[1] Thema Pagina Wetenschappelijke Integriteit, Website KNAW (www.knaw.nl), bezocht 10-11-2011

[2] International Conference on Harmonisation Topic E 6 (R1), Guideline for Good Clinical Practice, Website European Medicines Agency (www.emea.europa.eu ), bezocht 10-11-2011

Component to calculate Matthews Correlation, Sensitivity, Specificity, PPV and NPV with PP

(I am seeing about 5-10 views a day on the Pipeline Pilot pages, please be so kind to acknowledge / cite my blog when you use these tools and guides)

Why would we want such a thing?
Like with the regression validation parameters, I found that PP lacked a component to calculate correlation coefficients between two properties in the data stream in classification. 

Therefore I have written a component to do just that. One of the features I find useful is the option to include a bar chart that displays the values of the calculated properties on a scale between 0 and 1. This allows a quick visual inspection of your model reliability. When applied to the 'KNN classification of Estrogen Antagonists' from the example protocols, it looks like this:

In addition it outputs the parameters in a shaded table: 

The component calculates these parameters between two properties. Therefore, when using in external validation of a model, the modeled values have to be pre-calculated. 

The component requires that you give the names of the properties carying the measured value, the modeled value and the classes that were modeled. Currently it can only be used in a two class classification. In addition you can choose to also output the original unmodified records through the fail port, while the correlation plot and table are output through the pass port. I have not written a 'how to use' in the help, but will do so next week. In the meantime, the component can be found 

here.