8 posts tagged “wordpress”

This is a post from my wordpress blog. As I have switched over to vox, I have imported all posts from that blog. You will find all such posts marked with the tag "wordpress".

As Nature reported on the 26th of October this year in the article of the same title as this entry, Polish scientists have released a letter of protest against their deputy education minister Mirosaw Orzechowski, who has stated that “the theory of evolution is a lie”. Orzechowski is a creationist and a member of the ultra-right-wing LPR party. Fellow party member Maciej Giertych is, according to Nature, “lobbying for obligatory inclusion of creationism in Polish biology curricula”. Fortunately, neither the general scientific population nor Poland’s minister of science agrees with this minister’s views, and the scientists who wrote the letter hope that their quick action will prevent lasting damage to the educational system.

It is not about what they believe — it is about them attempting to force that belief onto the science curriculum. Hopefully, the scientists and their open letter will win the day.

This is a post from my wordpress blog. As I have switched over to vox, I have imported all posts from that blog. You will find all such posts marked with the tag "wordpress".

Although I sound like The Count from Sesame Street, various news sources (BBC and others) have picked up on the PNAS article entitled “Self-recognition in an Asian Elephant.” I thought it was worth a mention here, as it describes the experiment used to determine that at least one elephant has passed the mirror self-recognition (MSR) test. This test is where two X’s are painted onto a part of the face that the animal cannot see without being able to see their reflection. One X is painted white, and the other is colorless and meant as a control so that the smell or feel of the paint can be ruled out as reason for the animal noticing the X.

As the authors report, “MSR is thought to correlate with higher forms of empathy and altruistic behavior” and therefore elephants were a logical choice. They only used 3 elephants, and of those elephants only 1 passed the test, but this is still an interesting result. After all, they say that fewer than half of tested chimps actually past the test. However, all 3 elephants did spend time in front of the mirror in a way consistent with them using the mirror to explore their own features, and did not act in a manner that suggested they thought they were looking at another elephant. Their final point is that this may show an example of “convergent cognitive evolution” in social and cooperative interactions, and whether or not this holds true, the paper does highlight our growing awareness that consciousness — which many people, right or wrong, define as being self-aware — may not be restricted to us humans and our very close relatives.

This is a post from my wordpress blog. As I have switched over to vox, I have imported all posts from that blog. You will find all such posts marked with the tag "wordpress".

Hi folks,

A real techie post today. I’ve just spent most of an afternoon trying to track down a complete list of steps for changing your default data source in JBoss 4.0.4.GA from Hypersonic to MySQL. I’ve had to visit at least a couple dozen forum posts, but have only found the 5 linked in the steps below to be useful in answering my question.

However, none of those 5 had the entire answer, which leads me to the reason for this post. I hope it can help other people out!

1. (From OnJava.com): With your MySQL driver jarfile downloaded and added to your classpath, copy it to the [jboss-location]/server/default/lib directory.
2. Changes to the /server/default/deploy directory:
   1. Remove [jboss-location]/server/default/deploy/hsqldb-ds.xml (or move to a location outside of your jboss directory)
   2. (From OnJava.com and EPFL): copy [jboss-location]/docs/examples/jca/mysql-ds.xml to this location. Modify the <local-tx-datasource> element inside the mysql-ds.xml configuration file to match the following (Note there are some parts below which you will have to change!):
<local-tx-datasource>
<jndi-name>DefaultDS</jndi-name>
<connection-url>jdbc:mysql://your-hostname:your-port/your-database-name</connection-url>
<driver-class>com.mysql.jdbc.Driver</driver-class>
<user-name>your-user</user-name>
<password>your-pass</password>
<security-domain>MySqlDbRealm</security-domain>
<exception-sorter-class-name>org.jboss.resource.adapter.jdbc.vendor.MySQLExceptionSorter</exception-sorter-class-name>
<!– should only be used on drivers after 3.22.1 with “ping” support
<valid-connection-checker-class-name>org.jboss.resource.adapter.jdbc.vendor.MySQLValidConnectionChecker</valid-connection-che\cker-class-name>
–>
<!– sql to call when connection is created
<new-connection-sql>some arbitrary sql</new-connection-sql>
–>
<!– sql to call on an existing pooled connection when it is obtained from pool - MySQLValidConnectionChecker is preferred for n\ewer drivers
<check-valid-connection-sql>some arbitrary sql</check-valid-connection-sql>
–> <!– corresponding type-mapping in the standardjbosscmp-jdbc.xml (optional) –>
<metadata>
<type-mapping>mySQL</type-mapping>
</metadata>
</local-tx-datasource>
3. Next we have to change and replace some files in [jboss-location]/server/default/conf:
   1. (From OnJava.com, Experts’ Exchange and EPFL): In standardjaws.xml change the following two elements, and leave the rest in place:
<datasource>java:/DefaultDS</datasource>
<type-mapping>mySQL</type-mapping>

   2. (From OnJava.com, Experts’ Exchange and EPFL): In standardjbosscmp-jdbc.xml change the following, not necessarily contiguous, elements only, leaving the rest in place:
<datasource>java:/DefaultDS</datasource>
<datasource-mapping>mySQL</datasource-mapping>
<fk-constraint>true</fk-constraint>
   3. (From OnJava.com and EPFL): Introduce the following set of tags (ADDING, not replacing anything!) into login-config.xml:
<application-policy name = “MySqlDbRealm”>
<authentication>
<login-module code = “org.jboss.resource.security.ConfiguredIdentityLoginModule” flag = “required”>
<module-option name = “principal”>your-user</module-option>
<module-option name = “userName”>your-user</module-option>
<module-option name =”password”>your-pass</module-option>
<module-option name = “managedConnectionFactoryName”>jboss.jca:service=LocalTxCM,name=DefaultDS</module-option>
</login-module>
</authentication>
</application-policy>

4. Next we have to change and replace some files in [jboss-location]/server/default/deploy/jms:
   1. (From OnJava.com and EPFL): Replace file hsql-jdbc2-service.xml by file [jboss-location]/docs/examples/jms/mysql-jdbc2-service.xml, and change the one mention of MySqlDS to DefaultDS
   2. (From Experts’ Exchange): Rename hsqldb-jdbc-state-service.xml to mysql-jdbc-state-service.xml. NO modifications within this file are required!

That’s all, folks! Let me know if I’ve gotten something wrong.

A full list of all the threads that helped me:

• Experts’ Exchange
• OnJava.com
• EPFL
• JBoss wiki
• DBForums

This is a post from my wordpress blog. As I have switched over to vox, I have imported all posts from that blog. You will find all such posts marked with the tag "wordpress".

New Scientist released an article last week summarizing the work of Finlayson et al in Nature. Their work shows that “the Neanderthals survived in isolated refuges well after the arrival of modern humans in Europe.” Gorham’s Cave, Gibraltar, was systematically - and deeply - excavated by the authors between 1999 and 2005 over an area of 29 square meters. There was a low population density for both Neanderthals and humans during the time that they both lived in the area, and “the late survival of Neanderthals and the arrival of modern humans was a mosaic process in which pioneer groups of moderns and remnant groups of Neanderthals together occupied a highly heterogeneous region for several thousand years”. Up until this paper, the survival of Neanderthals past 35,000 years ago had not been proven. However, this new data proves that Neanderthals used Gorham’s cave until 28,000 years ago. as modern humans began moving into Europe around 32,000 years ago, this makes an overlap of at least 4,000 years.

It doesn’t sound like much, in the larger context of the evolution of the species, but 4,000 is still - obviously - a long time. One can imagine, even with low population densities, many encounters between groups of “moderns” and remnant groups of Neanderthals. This can lead to trying to imagine what the answer would be to one of the “ultimate” questions: what would it be like to meet another sentient species? Whether via sci-fi or prehistory, it makes for some fantastic daydreams.

This is a post from my wordpress blog. As I have switched over to vox, I have imported all posts from that blog. You will find all such posts marked with the tag "wordpress".

The second day of IB2006 was the longest of the three days, and the only “full” day. From my point of view only, the talks were more relevant and interesting to my work. The second evening was also the conference dinner, which was very sociable and the conversations continued straight through the dinner and into late in the night back at the conference hotel. But back to the day itself: there was a fantastic keynote by Pedro Mendes, and a number of other interesting talks. The highlights are presented below.

Top-down modeling of biochemical networks, a grand challenge of systems biology (Pedro Mendes)

Systems biology, in his view, is the study of a system through synthesis or analysis, using quantitative and/or high-throughput data. Origins of systems biology as early as 1940s, but with a large amount of work done in the 1969s-70s. It didn’t really take off during this time due to lack of computing power and lack of experimental “ability” for getting the large amounts of data required.

Pedro is interested in the top-down modeling approach because there is a large amount of data, with a lot of numbers, and people naturally want to make models from them. Many people think this isn’t the way to build models, but he believes otherwise. In bottom-up modeling you start with a small number of known reactions and variables, while in top-down modeling you start at a coarse-grained level, with loads of data and you try to work “backwards” (compared to traditionaly modeling procedures) to find the steps that will produce the HTP data you started with. In other words, it derives elementary parts from studying the whole.

BASIS (Colin Gillespie)

Colin gave an interesting talk on the availability and usefullness of a web-based stochastic simulator. You can create, access and run sbml models via web services (and a web-page front-end to the web services). Their aim is to make their own models available to other researchers and also to provide a framework for others to build their own models. In general, their models can be envisaged as networks of individual biochemical mechanisms. Each mechanism is represented by a system of chemical equations, quantified by substrate and product concentrations and the associated reaction rates. The connected series of reactions are then simulated in time. Simulation may be stochastic or deterministic depending on species concentration. They have funding for another 6 years and are planning many additions to the tool.

Multi-model inference of network properties from incomplete data (Michael Stumpf)
Estimates for rates of false positives range from 20 to 60%, and in connection with this he recalls a quote he read at one time stating that gene expression is as close to scientific fraud as is accepted by the scientific establishment. At least at the moment, it appears to be a trade off between data quality and data quantity. In other words, you must take noise into account in any analytical work you do.

For most species, you only have interaction data for a subset of the proteome. Missing such data means that you can get quite different networks (currently known versus “actual” network). This affects summary statistics, among many others. They discovered that generally, inference for networks comprising less than 80% of the full graph should be treated with caution, however above that value the inference model developed is very useful. Given a subnet it is possible to predict some properties of the true network if we know the sampling process. (independent of the process by which the network has grown). For different data sets, there seems to be a huge difference between different experimental labs, and how each has mapped parts of the interactome. However, overall this is a good way of estimating total interactome size by performing this test on multiple subnets from different PPI experiments. There are limitations, though: it ignores multiple splice variants and domain architecture, so any organism affected by these will not necessarily have as good a result. By interrogating all these different models, and averaging over that, useful estimates of total interactome size is possible. Useful estimates can even be retrieved when using partial data as long as the number of nodes is at least 1000.

Other interesting talks included Stuart Moodie’s discussion of the current state of affairs in standardizing systems biology graphical notation and visualization (sbgn, kitano and others), Jab Baumbach’s work on performing knowledge ‘transfers’ for transcriptional regulatory networks from a model species to 3 other similar species important to human pathogen studies, Jan Kuentzer’s biological information system using both C++ and Java called BN++, an eye-opening overview of the current status of biocomputing at Singapore’s Biopolis by Gunaretnam Rajagopal), a lovely swooping demo of a targeted projection pursuit tool for gene expression visualization by Joe Faith, and a wonderfully presented (which in my mind equates to “easily understood” because of her skill as a speaker) statistical talk on modeling microarray data and interpreting and communicating biological results by Yvonne Pittelkow. (Yes, a couple of those were from day one, but they still deserved a mention!)