Paper published on Biomolecules
Although the current focus of our job is on the Homo sapiens genome, in the recent past we also ran some gene expansion experiments on the Vitis vinifera organism. We are still evaluating those results, in collaboration with the Edmund Mach Foundation and the Universitat de València (Spain), also involving some students.
We are pleased to inform you that our article "Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families" has been published in Biomolecules as part of the Special Issue Gene Regulatory Networks Controlling Secondary Metabolism in Plants: Computational Approaches and Mechanistic Insights and is available online: https://www.mdpi.com/2218-273X/11/12/1744
Thank you all for your invaluable contribution! 23 Nov 2021, 18:42:01 UTC · Comment
The University's storage system (that we heavily use) is having big performance issues thus everything is painfully slow. I stopped the work generator, which actually was not working because of this. No new tasks will be generated until the assimilator will be able to move the finished results to the proper place. There is nothing else to do but wait until the problem will be solved, no ETA, unfortunately. 14 Oct 2021, 11:35:54 UTC · Comment
World Gene Expansion Challenge 2021
The volunteers belonging to the BOINC.Italy group have organized the usual (end of winter) challenge on this project: Start: 8th March 2021 12:00 UTC, End : 15th March 2021 12:00 UTC.
Please follow this thread for further info https://gene.disi.unitn.it/test/forum_thread.php?id=307 2 Mar 2021, 10:24:30 UTC · Comment
Paper published on IEEE Transactions on Emerging Topics in Computing
The following article, "A Computing System for Discovering Causal Relationships among Human Genes to Improve Drug Repositioning," is available under the "Early Access" area on IEEE Xplore. This article has been accepted for publication in a future issue of this journal, but has not been edited and content may change prior to final publication. This paper appears in: IEEE Transactions on Emerging Topics in Computing, Digital Object Identifier: 10.1109/TETC.2020.3031024. You may find it here: https://ieeexplore.ieee.org/document/9224179
Thank you all for your invaluable support! 16 Oct 2020, 9:18:59 UTC · Comment
AMD COVID-19 HPC Fund Adds New Research Institutions
Our gene@home project (hosted by the University of Trento, Italy) has been chosen by AMD as a recipient for their COVID-19 HPC fund, see the official announcement https://www.amd.com/en/corporate/hpc-fund
We are really grateful to receive this donation, it will give us access to high performance computing nodes, boosting our research. More info and comments here: https://gene.disi.unitn.it/test/forum_thread.php?id=291 16 Sep 2020, 22:53:39 UTC · Comment
Server unreachable (2020-09-09, from 05:30 to 08:00 CEST)
Wednesday 09/09, from 05:30 to 08:00 CEST, the IT services of UniTrento will not be available because of a planned IT maintenance. The TN-Grid server (hosted by UniTrento) will probably be not reachable during this period. 8 Sep 2020, 8:44:17 UTC · Comment
World Gene Expansion Challenge 2020
The volunteers belonging to the BOINC.Italy group have organized a challenge on this project, from March 16 at 12:00 UTC up to March 23 at 12:00 UTC.
Have a look at the challenge banner here: https://www.boincitaly.org/media/kunena/attachments/6725/TN-GridCh.jpg and the boincstats announcement/chat page: https://www.boincstats.com/stats/challenge/team/chat/1072 21 Feb 2020, 18:06:57 UTC · Comment
No news is good news (sometimes)
Just wanted to say that everything is going on smoothly. The server is stable, the scientists are happy with the results and are doing their analysis. Thanks all! 13 Feb 2020, 10:11:09 UTC · Comment
Server stop for maintenance (2018-12-27, 9:30 CEST)
The next 27th December the server will be down for some planned maintenance tasks, starting at around 9:30 CEST (GMT+1). The most important will be upgrading the o.s. to the latest stable release. Hopefully, the server will be back online the afternoon of the same day. 21 Dec 2018, 14:49:58 UTC · Comment
We will shut down the server the next Monday (November 26) at 12:00 CEST (GMT+1) for some planned maintenance work. The stop should last less than on hour. 23 Nov 2018, 12:39:32 UTC · Comment
Publication about Vitis vinifera
A new scientific paper on Vitis vinifera has been published. Details here: https://gene.disi.unitn.it/test//forum_thread.php?id=225 24 Oct 2018, 10:47:47 UTC · Comment
The experiments on Vitis vinifera are almost finished, thank you all. We will soon switch to a new organism. We made some tests some time ago but we found that the outputs of the Windows and Linux applications didn't match each other. The new forthcoming Windows applications should behave correctly.
The next Monday we will distribute them and (slowly) start creating new work. 11 May 2018, 16:50:17 UTC · Comment
Server down this weekend
Our storage system (managed by the University) has some serious problem. They are working to fix it but they cannot estimate for how long it will be down. We decided to stop the server at least until the next Monday.
Thank you for your understanding. 20 Apr 2018, 18:02:34 UTC · Comment
New application (v 1.10)
A new application version will be distributed soon, starting with the Linux platforms. The new application contains some major speed enhancements and bug fixes. Look at the following thread for further info http://gene.disi.unitn.it/test/forum_thread.php?id=135. 5 Dec 2017, 14:07:15 UTC · Comment
Another experiment on E. coli
We are ready to start another experiment on Escherichia coli, using the same expression dataset of the previous one but changing one of the algorithm's parameters.
Execution times should slightly faster than the last one on Vitis vinifera. 18 Oct 2017, 9:53:02 UTC · Comment
Vitis vinifera: new dataset
We are starting to distribute another experiment (single gene expansion) with a new Vitis vinifera dataset. This dataset contains the same number of genes but a much larger expression data; running times are therefore expected to be much longer (around twice). 29 Jun 2017, 9:08:20 UTC · Comment
We rebuilt some parts of the whole system and are almost ready to go full speed. Please look at the following thread https://gene.disi.unitn.it/test/forum_thread.php?id=165#952 14 Mar 2017, 11:24:23 UTC · Comment
No new work
I decided to stop the work generator until we solve our storage problems and have the new application (small output files). Most of our systems are now busy just moving things from here to there, this also implies a lot of (boring) micromanagement.
Hope you all understand. 2 Mar 2017, 11:12:40 UTC · Comment
New application (v 0.11)
In the next few hours the new v1.1 optimized applications made by Daniel will be promoted as the official ones (version 0.11). This version is faster than the previous one. If you are using the anonymous platform and want to safely 'come back' remember to: wait until the workunits queue is empty, stop boinc, delete app_info.xml, start boinc. 6 Feb 2017, 11:31:51 UTC · Comment
New application (v 0.10)
We are deploying the new version of the application (v 0.10), for all the platforms, including sse2, avx and fma. The new application is way faster than the previous one, thanks to the user Daniel who made it. See this thread (http://gene.disi.unitn.it/test/forum_thread.php?id=135) for further info. 13 Jan 2017, 10:16:40 UTC · Comment
I've recently doubled the size of the workunits. Credits should scale up accordingly. 5 Jan 2017, 12:27:17 UTC · Comment
In the next days I will install a SSL certificate, thus allowing secure communications via the https protocol. You may notice it when your boinc client will start complaining about it, saying something like "This project is using an old URL. When convenient...". You may simply ignore this message or detach from the project and re-attach using the new https url (it will be the usual one, just with https:// at the beginning).
Please do this when your queue is empty. 21 Dec 2016, 11:40:22 UTC · Comment
First international challenge on TN-Grid
The BOINC.Italy Team has opened the first international challenge on this project.
Title: "Despite my age I don't live in the past, but in the future" 4th Rita Levi-Montalcini memorial and 30 years from Nobel Prize.
Start 10 Dec 16.00 UTC - End 16 Dec 16.00 UTC
Check http://boincstats.com/en/stats/challenge/team/chat/831 for more info. 2 Dec 2016, 17:08:39 UTC · Comment
Credit badges are now available, please check the following thread http://gene.disi.unitn.it/test/forum_thread.php?id=130#608 29 Nov 2016, 17:09:00 UTC · Comment
Upgrading the server
Today, in about 1 hour from now we will shutdown the server for an upgrade (ram, cpu and storage). It shouldn't take a long time, maybe one hour or less.  Everything went well. 10 Nov 2016, 13:48:39 UTC · Comment
Public invitation code
The (new) invitation code is now public, written on the home page. 11 Oct 2016, 9:39:56 UTC · Comment
gene@home: Vitis Vinifera experiments
We just started a new 'experiment' on a Vitis Vinifera (grapevine) dataset. Your client will automatically download a ~100Mb files which contains the necessary dataset (shared among all the Vv workunits). We will distribute just a few batches, at the beginning, just to see if everything works as expected.
For further (scientific) information please look at the following thread: http://gene.disi.unitn.it/test/forum_thread.php?id=117 24 Dec 2015, 14:09:26 UTC · Comment
gene@home: Scientific Results (June 2015)
We are very happy to share the scientific results achieved so far, thanks to the help of all you volunteers. Please look at this thread. 10 Jun 2015, 11:06:55 UTC · Comment
We are almost done with our current batch (E. Coli local gene network expansion for 10 networks). We will first analyze the results (this will take some time), then we will be able to choose the best, smaller set of algorithm parameters and use it for the other 100 networks we plan to expand, thus optimizing the computation. In the meantime we will start another experiment on Arabidopsis Thaliana but, before starting it, we need to wait until all the work on E. coli has been generated. This will be done manually, hopefully the next Monday.
For this reason there could be a shortage of workunits in this weekend. 7 Mar 2015, 12:10:41 UTC · Comment
gene@home: Server down next Friday, February 27th
due to maintenance work in the datacenter, we need to temporarily switch off the server. The machine will not be accessible next Friday, February 27th, starting from 9am (CEST). We don't now how long will it take to bring the server up, hopefully just a few hours. Thank you all for your understanding. 25 Feb 2015, 17:38:05 UTC · Comment
gene@home: Holidays are approaching
The winter holiday break will shortly begin, it will be from the 24th December to the 6th of January. During this time the server will (hopefully) be up and there will be plenty of jobs. However, in case of any problems it will be very difficult for us to fix them (a lot of people will be on vacation and also my office will be closed). Season's greetings (and a big thank) to everyone! 22 Dec 2014, 17:05:09 UTC · Comment
gene@home: Server down the 14th December
There will be some server downtime the next 14th December (Sunday). The data-center hosting the server will be moved (physically) to another building. We don't know exact timing nor for how long the server will be down. 9 Dec 2014, 17:43:02 UTC · Comment
gene@home: Re-issue of old 'experiments'
Due to a partial storage hardware failure we need to redo some old experiments. We already used the results we got for the paper we are writing, therefore we need to keep the raw data for future reference. This old work will produce workunits which name starts with N_At_fos (with N less than 100). 20 Nov 2014, 11:56:21 UTC · Comment
gene@home: Escherichia coli experiments (Update)
We distributed a small batch of E. Coli workunits (their names contain the 'Ec' string). Unfortunately our algorithm for the estimation of the running time is not working for them. So, until we'll fix this, the 'remaining (estimated) time' you see on the boinc manager will be underestimated by a factor of 2 to 10. However, despite of this, the workunits will run fine. 12 Nov 2014, 19:25:04 UTC · Comment
gene@home: Escherichia coli experiments
We are starting a new series of experiments on a new organism, Escherichia coli, with the goal of mapping the complete gene network of this prokaryote. We just started to distribute a small set of workunits for testing the system. We already find some problems: the boinc client 'estimated time remaining' seems completely wrong (too short, almost zero) although the progress bar is normally stepping up, we will see...
[UPDATE] We aborted/canceled them all... They ended all with the 'Maximum elapsed time exceeded' error... we have to fix this before going further. 7 Nov 2014, 16:29:00 UTC · Comment
gene@home: October update
This project is partially linked to the Laboratory of Biological Data Mining class of the Master's course in Computer Science at our University. Now the class has started. The students need a little bit more knowledge of the whole system before starting new 'experiments', thus creating new work. We all think that another couple of weeks will be needed. 8 Oct 2014, 10:20:39 UTC · Comment
gene@home: August news
We are not yet ready to start new 'experiments', i.e. delivering new workunits. We were focusing on writing a paper about the algorithm we use (it's almost ready). Now it's exam time for students and vacation time for a lot of people so I declare the project as 'suspended' until the mid of September. 11 Aug 2014, 17:51:29 UTC · Comment
gene@home: Planning new 'experiments'
We are waiting for all the recently distributed workunits to come back (just one missing by now) before taking some time to analyze the results and planning new work distribution. We are still in the validation/testing phase of the algorithm we developed, we have obviously to check it thoroughly before going into the production phase. In the meantime we are writing a scientific paper describing it and this also takes some time. However, expect some more news at the beginning of the next week. Thanks all again for your help. 25 Jun 2014, 18:10:47 UTC · Comment
gene@home: Leave one out phase
we started a new phase for leave-one-out processing. Our goal is to evaluate the recall of our algorithm w.r.t. different parameters. We removed from the starting local gene network one gene at time in order to see if we are able to find it.
Have a nice crunching, and thanks to all! :) 5 Jun 2014, 16:32:59 UTC · Comment
gene@home: Break! Post-processing phase
Hi all gene@home supporters!
We just empty our experiments queue, do not worry new works will be available soon! ;-)
For the moment we are collecting and processing all the results (just few are not yet come back). We are also checking the feedback provided for the application, in order to see if there are things that should be fixed or improved.
We hope in a few days to put here http://gene.disi.unitn.it/test/forum_forum.php?id=2 some results from this last experiments.
Thank you all for crunching! :) 27 May 2014, 10:12:00 UTC · Comment
gene@home: Parameters tuning reloaded
We have scheduled more than 10000 (ten thousands! :) ) workunits for a second phase of parameters tuning.
We are trying different parameters' values, hence the time estimation could be not always correct.
As usual use the forum if there are any problems.
Have a nice work!
Thank you all! 8 May 2014, 9:38:09 UTC · Comment
gene@home: Presentation @ ICT-Days 2014
The gene@home project has been briefly presented at the Transversal Technologies Section of the ICT-Days http://2014.ictdays.it/ held in Trento at the beginning of April 2014, here is the presentation http://gene.disi.unitn.it/test/documents/geneAThome.ICT.Days.2014.pdf 17 Apr 2014, 16:06:38 UTC · Comment
gene@home: Parameters tuning
We started a new test phase where we are tuning the application parameters. We are currently expanding a flowering process of the Arabidopsis thaliana.
As usual use the forum for reporting problems.
Thank you. 3 Apr 2014, 12:13:35 UTC · Comment
gene@home: Solved not unique download filename
we should have solved the issues arise yesterday related to the not unique filename generated by the work generator.
We also update the application in order to get a bette stderr from the executions.
Let us know if there are still problems,
Thank you all for the support! 25 Mar 2014, 16:56:23 UTC · Comment
gene@home: Testing the new system
We just put on the queue about 1000 workunits for testing the new system. The work generator was completely rewritten and also the application has been modified a lot. We hope that we solved (almost) all the problems we found in the past. Let's see. A more detailed changelog will shortly follow. As usual, feedback will be very appreciated. Thanks all for helping us in this projects. 24 Mar 2014, 17:51:47 UTC · Comment
gene@home: Temporarily out of work.
We finished our first batch of workunits. We need some time before starting a new one. Please hold on and stay tuned. 22 Jan 2014, 11:11:30 UTC · Comment
gene@home: System restarted with new application
I just restarted the system, new work is available. A new version of the application (version 4) has also been deployed. Someone of the application group will soon post a changelog describing changes made. 20 Jan 2014, 14:11:20 UTC · Comment
Validation problems (update) - phase 1
The validation problem has been (theoretically) solved.
The problem: We noticed that results coming from Windows computers were slightly different than results coming from other machines, thus not validating, when compared with each other, even if the results are BOTH correct.
The solution: We enabled homogeneous redundancy for the above (two) classes of computers. This way we may just use the standard bitwise validator for doing the job.
Timing: Done. Let's check if it works.
All received workunits were checked for errors and eventually validated (with a bonus) 9 Jan 2014, 17:58:21 UTC · Comment
New work available (intermittently)
The answer is NO, we didn't solve yet our size/validation problems. I just decided to put more work on the queue for two reasons, gathering more statistics and producing some (hopefully) useful data for the post processing group. Returned workunits will not be validated until we solve the problem we have.
BTW I upgraded the whole system to the the latest snapshot. 2 Jan 2014, 14:05:45 UTC · Comment
Temporary stop of the validator/task generator
In short: Soon the task generator and the validator will be stopped, and they will remain down until we find a fix the validation problems we are having.
Long version: The validation issue is prolonging for too much time and we don't want you to waste your cpu cycles on something that will probably result in a validation error, so we decided to temporarily stop the task generator and the validator of the project.
Stopping the task generator will allow us to clear our queue cleanly, while stopping the validator should allow us to freeze the currently running tasks, and process them with the working validator later on. The credits for the tasks should remain freezed until we will start up the project again.
Sorry for the problems we are having in this period, we are working hard in order to fix them.
Thank you all for helping in this odissey :)
26 Dec 2013, 23:13:27 UTC · Comment
Server Down - Uploading new experiments [UPDATE: up again]
The server will be down for approximately 10 minutes in order for me to upload the new longer workunits with the "final" round of experiments.
I will post here when everything is done. 23 Dec 2013, 22:48:46 UTC · Comment
Application version v0,02
A new version of the application, that should have no more suspend/checkpoint problems, has been released. Please test it thoroughly. 23 Dec 2013, 13:44:33 UTC · Comment
Please do not try to suspend/resume the workunits. The checkpoint system works but the validator marks such a wu as invalid. We are checking this out and will release an application without this problem as soon as possible. 20 Dec 2013, 10:10:35 UTC · Comment
Test phase (stage 1) has just started
Applications are (almost) ready for the most common platforms and some invitation codes have already been given away to members of the Boinc.Italy community. Hope that everything will go smoothly and that we will be able to fix any of the problems or annoyances we may find.
Thank you all. 19 Dec 2013, 15:37:02 UTC · Comment
We are (almost) ready to start a test phase (stage 1)
We still have to fix a lot of little things (hopefully this will not be too complex to do...). When we will be ready, we will send invitation codes to a restricted number of people willing to actively participate (just test and give feedback, nothing really difficult). Stay tuned! 12 Dec 2013, 17:26:59 UTC · Comment