Schrodinger's Cat Strikes Back

Hosting PhysicsOverflow at Bielefeld University

Thanks to Christian Pietsch http://www.ub.uni-bielefeld.de/~cpietsch/ from the library of Bielefeld University, who is also the founder of the OpenScience Q&A community https://openscience.uni-bielefeld.de/ (restarted outside the SE network after an unsuccessful SE beta, using support from our side) we have obtained the offer to move PhysicsOverflow to a server of the library of Bielefeld University.

The moderators agreed to accept the offer; thus in the near future, PhysicsOverflow will be migrated to a server at Bielefeld University. To avoid any tiresome administrative procedures or even obstacles, this will at present not encompass an official endorsement of PhysicsOverflow by Bielefeld University. In the long run, obtaining the latter should probably be tried at some point in the future.

Moving to the university library of Bielefeld will have several advantages:

  1. It will do away with the technical issues and glitches caused by our current hosting provider One.com that polarkernel had to deal with without being given proper access to the server.
  2. It will provide direct and personal technical support as well as root access for polarkernel to the new server. This will ease debugging in case of future technical problems with the server.
  3. It will ensure additional support for keeping the PO-server running. As Christian Pietsch is the administrator of the new server, he will be able and willing to help if needed to ensure that the PO-server runs smoothly, for example in case (as last year) polarkernel is on holiday without a good internet connection.
  4. The move will constitute a big step forward to ensure a long time perspective for PhysicsOverflow and towards solving our long-standing issue that there is only a single person who can technically ensure the smooth running of the site.

Generally, users should not be negatively affected by the upcoming migration. Users should hardly notice anything special during the migration – certainly less than in the past during problems with the current provider. In the worst case there will be a break of at most 24 hours until the new domain address has propagated to all domain name servers in the world. However, our domain name “physicsoverflow.org” will not get changed by this migration.

In case of such a break, will inform here in this blog about the current status and what is actually going on.

This post is a slightly adapted version of the PO Meta Announcement

https://physicsoverflow.org/38745/hosting-physicsoverflow-at-bielefeld-university

Edit May 15, 2017 by polarkernel:

Christian Pietsch and me have finally prepared all aspects of the announced migration of PhysicsOverflow to the University of Bielefeld. It will take place at Wednesday, 17. May 2017, starting at about 07:30 UTC. Please save all your drafts before this time. During this migration, we have to shut down the server, move the content to the new server and also to move the domain name to another registrar. This process may take up to 24 hours for users, that are far away from Germany, given by the time required for the new IP to be propagated to all DNS servers of the world. We will keep you informed about the status of the migration below this edit.

After the migration, Christian Pietsch will continue to keep the server running in case of any issues and will replace me for this task when I am absent. Therefore I increased his level on PhysicsOverflow to SuperAdministrator. He will also be our advisor for questions around our webserver. It is a great progress for me to be released from this responsibility during my vacations and I like to thank Christian for his commitment. Naturally I will continue to take care for the code and its future development. However, on the long run, we will need a replacement also for this job.

Status of the migration:

May 17, 07:30 UTC: Planned start of the migration.
May 17, 07:40 UTC: Maintenance mode on, backup and migration of the database started.
May 17, 08:05 UTC: Database successfully moved. Starting domain migration.
May 17, 08:45 UTC: Got certificate, moved to Christian Pietsch who will install it.
May 17, 09:15 UTC: Email accounts generated, but not yet activated.
May 17, 09:35 UTC: Certificate is installed. Domain transfer activated.
May 17, 10:00 UTC: Still waiting for domain transfer confirmation.
May 17, 10:04 UTC: Got confirmation. Propagation of new IP to all DNS-servers started.
May 17, 10:30 UTC: The domain host provider did still not yet connect the domain.
May 17, 12:10 UTC: Much later than expected, the new IP starts to propagate now.
May 17, 12:30 UTC: First contact to the new server: It’s done!!

Personal directories in PhysicsOverflow

After a rather quiet period, here comes some good news about a nice new feature which will hopefully be useful to everybody 🙂

The following text is taken from Arnold Neumaier’s corresponding announcement on PhysicsOverflow:


Due to the nature of research, answers to research questions may come quite late. Old questions and answers on PhysicsOverflow may have a much longer lifetime than on other question & answer sites. However, with the standard Q2A software, it is difficult to trace questions visited – they tend to get drowned in the mass of posts, and are quickly dominated by what happens in currently active threads.

Due to the efforts of our system developer polarkernel, registered users of PhysicsOverflow with positive reputation are now offered a place to organize content of PO in a personalized, permanent, and arbitrarily detailed way.

This is achieved by associated to each registered user a personal directory, accessible only to the user owning it. The personal directory can be managed like a directory (folder) in any file system. The only difference to a file system is that the targets are not files but shortcuts – primarily links to PO posts (individual questions, answers, and comments) and links to external web addresses. These texts can  be arbitrarily nested to get fine-grained access to the content.

The purpose of the external links is to reference related papers (e.g., from the ArXiv) or personal notes on a PO-related subject, e.g., sketches of material for a future answer. However, the system also allows for shortcuts, one-line notes that appear directly in the personal directory.

PO posts are added to the personal directory by a click on a button under the post (”remember post”)  which then changes to ”post remembered”, and are managed either by clicking on ”post remembered” or by accessing the personal directory from the user’s profile page. The interface (together with its built-in help) should be self-explaining – if not, please ask on meta.

As already mentioned, the intended use is to organize content related to PO. For example, one can index in one folder posts read, adding key words why they were interesting. Another folder may contain the
posts that require further attention, together with a short reason why. Links to posts can act as a subfolder in which to store related arxiv URLs or bibtex files, or key words for potential later answers
or comments. The personal directory can also be used to group PO posts according to preferences not accounted for by the public tag system. One can use the one-line notes also to add priority information or time stamps. Creative users will find other useful ways to exploit the facility offered.

 

PhysicsOverflow at the 5th Offtopicarium

Since Wednesday lat evening, I am back happy and still a bit tired from the 5th Offtopicarium in Wegierska Gorka, Poland.  As the Offtopicarium is organized by science nerds for nerds ;-), it was a lot of fun to be together with the very nice small (about 30 people) group of young people. The program was rather interdisciplinary, ranging from biology, history, constructed languages, space projects of students, science communication and education, and many more things. I hope all talks will be accessible soon from the official homepage. In particular the talk about Opening Science  could be worthwhile to consider in some detail, as there is some overlap to what we want to achieve by the Reviews section. Getting to Wegierska Gorka from Bad Doberan (Germany) was a bit cumbersome and time-consuming.  From Katowice I still had to take another train for 2 hours. Considering different means of public transportation, proper time of the trip can not be reduced to less than 14h+  which is therefore the global minimum. route Therefore I was not able to arrive before Saturday afternoon. The meeting had begun on Thursday already and missed therefore about the first half of the talks. All talks have been very good and impressive generally, here you can see  for example Piotr Migdal giving a talk about how often the best and most innovative things are done by people with greatest passion and motivation in their free time, even though (or because) they do not get paid for it. As PhysicsOverflow for example …  😉 IMAG0284 My talk about PhysicsOverflow Happily, my talk about PhysicsOverflow was soon enough ready as you can see below. And surprisingly I realised that I did not even have to take notes about what I’m going to say (as for other talks related to my work) but I could just go on blathering  without effort … ! When bragging about PhysicsOverflow, I am obviously unstoppable 😛 Unfortunately, my laptop refused to connect to the WLAN in the meeting room, so I could not show a live demonstration :-/. You can find the slides of my talk here (the quality was better in PPT than it now is in PDF)  🙂 IMAG0290 In the introduction, I first explained why a new higher-level physics site was urgently needed, how PhysicsOverflow is organised in different parts such as Reviews, Q&A, Meta, etc as well as our most important principles and characteristics. On the next slides, I introduced the Q&A part as a physics analog of MathOverflow and explained the most basic things about how it works, scope, etc … To introduce the Reviews section I ranted a bit about how present journal peer-reviewing sucks ;-), then explained how paper reviewing is done on PhysicsOverflow, and showed two examples of a negatively and a positively reviewed paper. I also got a very good discussion to my talk (nicely supported by Piotr Migdal) , the following issues have been discussed (not in exactly the order listed here):

  • Why did we have to creat something new instead of using something that already exists, such as for example the SE platform?

To answer this, I had prepared in advance a slide (22) that summarises a bit why the goals of the SE company IMO clash with the intentions of a high-level academic community. Somebody mentioned that there are academic sites in the network too which is true but works only  for exceptional cases (I only know MO and CST) … Piotr helped by explaining that very high-level questions are not really high-lighted on SE for example. Also, conversely to the time when MathOverflow was created almost exactly 5 years ago (congratulations!) , SE does no longer give away its software today. There have also been

  • Some discussion about partitioning the site instead of supporting other communities in starting their own site (for example PhysicsUnderflow) to build an Overflow network

This is in principle doable as we have categories in addition to tags,  as for example explained on slide 20  about the differences between the PO and SE software.

  • Of course, I also called for a second developer

which resulted in the suggestion to upload the code on Github for other people to help us with the development and debugging, but as Polarkernel said we are not yet ready to do this … There have also been some

  • Questions about how many people we have, how many papers are submitted, etc :

About 250 newly registered, not all are active at the same time of course … The Reviews section (Reviews I) went online later than the Q&A section, so it is natural for it to have less content  (48 papers at present) than the Q&A section. Another questions was about

  • What could endanger the success of the site?

Here I said that at  the beginning, I and probably others were too enthusiastic about the Reviews section finally getting started, so we were too permissive about accepting submissions. But this is fixed now by our “reject to review policy”. There was also

  • Some discussions about the formula to calculate the final score of submissions:

Strong nonlinearity, the effect of additional points for one unit  accuracy and originality depends in  not plain obvious way on the votes the paper already has… As the accuracy determines the sign of the final score, crackpots who make unfounded “revolutionary” claims are punished which is a good feature. Does this formula really what we want to achieve in all cases? Final remarks The meeting was really fun, and there have been many cool nice people  :-). I am very happy about the positive response I got to my introduction of PhysicsOverflow and will also reconsider some of the other great talks I have seen. And I really liked it to meet Piotr Migdal in person 🙂 BTW he has now submitted his PhD thesis, congratulations ! Only the mud (literally!) sucked on our trip to the mountains because it was rainy the days before …  😀 P1110416 Joking … The trip was fun too 🙂

A long step towards the adult PhysicsOverflow

Today, the new category system, which allows an unrestricted number of category-levels, has been installed on PhysicsOverflow. This system was required to enable the categorization of submissions beyond the four levels provided by the actual Question2Answer (Q2A) framework. This new system is almost invisible for the user, but has the important function to make a (future) large number of submissions searchable by the user. About two and a half months have been required to develop this system, you had to wait for a long time. Therefore I like to give you some insights.

The original category system of the Q2A framework is a hierarchical database model. Every node (a category) is linked to its parent by the ID of the parent node. Such a model enables a fast writing of new nodes (you just create the node and link it to its parent), while queries through the tree are usually slow. Q2A solved this issue by a fixed number of 4 category levels. To be able to find parents in a short time, the path to the parent is hard-coded in every post. This means that every post contains four indices storing the way back through the tree. This is a clever and fast solution. However, it can not be extended to an unrestricted number of categories, it even gets slow if extended to 8 levels for instance. The category system is written in the core code of Q2A and spread over a large part of the system.

Another issue arising when we increase the number of category levels is the user interface. Actually, when the user asks a question, he has to select the category for this post. The user interface uses select tags like:

categories_old

It is clear that for instance for eight categories, the place on the page is too small to display all these tags side by side. Therefore also the user interface had to be changed. The new user interface take much less room and looks like this:

categroies_new

For the new category system, I have implemented another database model, called nested set model. It allows for an unrestricted number of category levels. While queries through the categories become very fast, the insertion of nodes is slow, because all indices of the whole tree have to be changed. However, changes on the categories will be used much less frequent than for instance to display the tree. Like this, it is well adapted to our needs.

As already mentioned, the original category system is placed in the core code of Q2A and is active in almost all pages provided by the framework (even in pages I never expected this). I had to replace 9 files completely, all select specifications for database accesses to the category system had to be renewed and, naturally, the code for the nested set model had to be written. To give you an impression on the size of the task, here some numbers: The original Question2Answer framework consists of about 36’000 lines of code. Until today, I have written 18’100 new lines of code for PhysicsOverflow in form of plugins, layers, overrides and changes in the core code, about half of the size of the system. The new system required 5’800 additional lines of code, which explains, why it took that long to realize it. I hope now that I was able to test all use-cases so that there remain eventually only minor bugs.

The next development step will be a surprise, stay tuned!

polarkernel

We have a talk at the 5th Offtopicarium :-) !

A few weeks ago, Piotr Migdal made me aware of the Offtopicarium (he is among the organizers), which is a mixture of scientific conference, workshop, and geek gathering ;-). Its purpose is to discuss topics and ideas, which are usually off-topic  to “regular” events and meetings, but nevertheless interesting and exciting.  The Offtopicarium welcomes (rather geeky 😉 …) people, who have a good idea and are passionate about it, such as scientists, entrepreneurs, people involved in startups, NGOs, and such.

So, after nice discussions and kind encouragement by Piotr Migdal, I finally submitted an abstract. It got just accepted, such that we will have  a (20 min + 20 min discussion)  talk  about PhysicsOverflow at the

5th Offtopicarium (26-28.09.2014, Węgierska Górka, Poland)

(Click the title for more information!)

Of course, I will shamelessly use this opportunity to introduce and advertise PhysicsOverflow:

The Q&A part as a revival of  Theoretical Physics SE and a physics analogue of MathOverflow, whereas the Reviews section should take the role of an overdue competitor of the (outdated and flawed in many ways) journal peer-reviewing process.

And who knows, maybe we will also find a second system developer there, to help and unburden Polarkernel …?

Anyway, summer holidays are mostly over (at least in Germany …) and members of PhysicsOverflow are heartily encouraged to make PhysicsOverflow look as awesome  as possible by nice contributions 😉 !

Even though I already have some ideas of course ;-), I would be happy to consider suggestions concerning the talk, they can be mentioned for example in the comments here.

Cheers !

PhysicsOverflow is Living and Animated

Wondering what happened on PhysicsOverflow while I have developed the preliminary phase of PhysicsOverflows reviews section, Reviews I, I have looked on the host providers statistic and have done some queries in the event log of our database. Here are some numbers illustrating the pleasant activity on our site:

Number of visits in May 2014 (provider’s statistic):

visits_may_2014

As you can see, the number is slightly growing. The number of visits has been above 300 all the time approaching now 400 by end of the month. Maybe somebody has an explanation for the peak after the second weekend?

In the event log table of the database, 14’482 events have been logged in May 2014. Some interesting numbers are

  • 4126 times, a user has logged in.
  • 200 questions have been written.
  • 353 answers have been posted.
  • 1002 comments have been added.
  • 4995 upvotes have been given.
  • 86 new users have registered on the site.

I think this is really not bad for the second month after publishing the site. Maybe we will already have quite a number of submissions in the reviews section by end of next month? Interested? Submit a paper to PhysicsOverflow!

We Have Liftoff!

Liftoff

PhysicsOverflow public beta is online now since 17 days. After a turbulent start with some database issues on our host and spam attacks, now the site is stable and working fine. After an ongoing and continuous improvement of details, the section with Q&A on physics takes now the main part of activity on the site. Since we have gone online at 4th April, more than 150 new users have registered on the site and many of them are already quite active. The number of visits per day exceeded the number of visits on Theoretic Physics on SE since the first day, as can be seen in the following graphics:

Visits_April_2014

This is great, since we aren’t even part of a huge network! Our questions per day is about 5.6 (excluding imported posts), which is a lot more than TP.SEs. However, as already stated, the site does not depend on these figures, there is no deadline, as it was on TP. Also the term beta does not mean that the site will go away, it means only that we have still much more ideas to obtain the full-fledged version of PhysicsOverflow.

Please Contribute

Now is the time where the site gets shaped. If you participate now with your votes, ideas, opinions, questions and answers, you contribute to build a site with contours as you like them. Don’t stay outside, have a look at PhysicsOverflow, register there if you like it, or contribute here on this blog.

Review Section

We are still a small team. However, we are working with full power to be able to leave the beta state and to complete the site, as intended. The main part for this will be the Review Section, as already announced in this blog. This is not only a reconfiguration of the site, it requires a considerable part of new development, because such a feature is not foreseen in the Question2Answer framework. In detail, the following main functionalities have to be developed:

  • Integration of new pages, called Submission and Review.
  • Two voting criterias, one for originality and one for accuracy.
  • New page design, enabling display of a score value from the votings.
  • Add feature to add multiple authors.
  • Redesign of voting mechanism, distributing votes to multiple authors.
  • Integration in the rep update and recount system.
  • Adding and managing the required database tables.
  • Increasing the category depth to realize hierarchical tagging system.
  • Integration of score as new sorting criterion.
  • Software for mass import from ArXiV.
  • Software for daily import from ArXiV.

We are on the way with all that and look forward to realize these steps within a reasonable time. Stay tuned!

 

Technical problems with the mySQL data base server :-(

Dear PhysicsOverflow community,

today we seem to face (for the first time within a time period of about  two months) some problems with the mySQL data base server on the host side. This lead to a short down time of PhysicsOverflow of about 10 min some hours ago, and to a new longer down time of an hour just now. This is very annoying, in particular as we have just started our public beta … :-/

So we apologize for this inconvenience, but all we could to is complaining to the administrators of our hosting provider, which is what Polarkernel did:

 

Hi
There seem to bee problems with the database on our host. Sorry, but I can’t change it. See here the transcript of my contact with our host provider (translated by Google):
Now talk to ‘Elodie’
Elodie: Hi – how can I help you?
You: I got today on my site “www.physicsoverflow.org” for the second time a “database connect error”. Can you figure out what’s going on?
Elodie: Yes, actually, there are some difficulties with the MySQL Server today.
Elodie: The technicians are already aware and working on it.
You: OK, I hope the issue can be resolved soon. I have opened my site tonight and it’s a shame, especially when such errors occur at the beginning.
Elodie: I see. I do not think it takes a long time. But at present we have not yet received any specific information from the technicians. Except to the confirmation that they know it and work on it.
You: OK, then I’ll wait. Thank you!
Elodie: No cause 🙂
polarkernel
Now PhysicsOverflow seems to work again for now
but new down times can not be excluded until the technicians of our host state that they have successfully resolved the issue …
We will report here as well as on the site itself as soon as everything is ok again.
But lets not hope that the worst is over now, I am so excited and happy about all the great nice wise people joining in so far 🙂
Cheers

Fine Tuning

I know, everybody is impatient to see our site running and I apologize the delay. During several tests I found some issues to be corrected before new questions are entered in our database. However, in my opinion we will be faster like this, because otherwise we would have risked to have an inconstistent database or even to lose questions on repairing it. Preparing the test technical beta phase turned out to be more complicated than we thought. Additionally, Dilaton has been severely handicaped by an extremely poor internet connection, which made the communication very difficult. But now, we are very close! I assume we can go online for the test-users during the coming week. Dilaton will advice them in an email, how to connect to the beta site and how to contribute.

These have been the main issues:

  • The way Question2Answer handles access restrictions on plugins is vulnerable. A plugin may be set to be invisible for unauthorized users, but this does not really prevent the access. Therefore I had to add code to realize a strong proof of authority.
  • In the A51 import, several users had multiple (up to 4) accounts with the same username. This is not allowed under Question2Answer. I was not capable to resolve if these users with the same name have been really the same person. As a temporary solution I have manually corrected the database and renamed these users to USER_1, USER_2, … and so on. Actually I am developing a simple plugin “Merge User Account”. This will be very delicate and I am not yet sure if this can be really handled properly. Users with multiple accounts should please contact me directly. However, this plugin will not yet been required for the beta tests and therefore this issue will not slowdown our project.

The contact to register as test-user is still open!

Going Online :-)

As you have already seen, we have a host now with a first short introduction for the new site. Don’t bother about details now (the link is now blue), I had only very few time available and in my ecstasy I wanted to show you something already running. For a computer scientist, an automatic web-editor, as it is available on our host, is sometimes quite confusing. I do not like these automatisms. However, in let’s say two weeks, I will have set up a first version of our new site and will not require such an editor to do that.As a first step I would like to set up a technical beta version with the following purposes:

  • Debugging: I have a more than 40 years of practical experience with IT-projects and I am sure that there will be some bugs in my code. It will be the task of some dedicated test users (you?) to help me finding these bugs.
  • Parametrization: Setting all the parameters of the site by the super-administrator.
  • Completion: Many details are not yet ready: Logo, introducing text, texts in emails, etc. During the technical beta, the site should be completed for takeoff.
  • Organization: During this phase, the first organization should be prepared (administrators, moderators, ?).

During his phase, new registrations will be prohibited, only test users will have access to the site. However, the site will be visible from outside (which could be some advertising?).  I could also place it at a secret place known only to the test users. I could also exclude robots (Google etc.) from the site during this run. Note: There will be a (small) probability that the content of the site at the end of this phase has to be deleted. This could only happen if tables in tha database would have to be altered, so the risk is small.

In order that we are able to organize the technical beta, please contact Dilaton if you are interested to participate. We will contact you with details for the registration, as soon as the site is up.

I will finance the hosting of our site for a while. However, we should also start to think about the responsibility for the site. Actually, I am the only one that is no more anonymous, because according to ICANN I had to provide my complete contact data. So, from a legal point of view, at the moment I am the only one who is responsible for the content of this site. I would not like to stay alone in this position. At least at the end of the beta phase, we should have some regulation (legal notes, about us, etc ?) about this subject. Has somebody alrady thought about that?

 

 

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