https://adciwiki.cytognomix.com/ 2026-04-23T20:21:29+00:00 https://adciwiki.cytognomix.com/ https://adciwiki.cytognomix.com/lib/tpl/dokuwiki/images/favicon.ico text/html 2021-02-09T16:25:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:comparekriging&rev=1612887946&do=diff Compare a Kriging result with a previous one After obtaining a Kriging result in the current iteration, the next step is to compare it with a Kriging result from the previous iteration (see the overall workflow). Remember that the difference between the current iteration and the previous one is the current sample set, which is contained in the current iteration but not in the previous one. To compare with a previous Kriging result, click the 'Compare to previous Kriging result' menu item under … text/html 2021-02-09T16:23:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:createasampleforaperson&rev=1612887781&do=diff Create a sample for a person A sample is a compressed file of the .tgz (.tar.gzip) format, containing a number of metaphase images from the person. It is the basic unit for estimating the radiation dose that the person was exposed to. To create a sample, click the ‘New samples’ menu item within the ‘Sample sets’ menu. text/html 2021-02-09T16:23:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:createasampleset&rev=1612887802&do=diff Create a sample set A sample set is a set of samples, physically corresponding to one directory on the BGQ server. Typically, it contains samples of a set of persons within a geographical area (e.g. a city) where the nuclear event occurred, which were collected by responders in one iteration (see the overall workflow). It is the basic unit for submitting a job to the BGQ supercomputer to process samples. text/html 2021-02-09T16:23:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:createascenario&rev=1612887821&do=diff Create a scenario A scenario is a higher-level structure above the sample set, typically corresponding to a geographical area where a large-scale nuclear event occurred and containing all of the sample sets collected by responders in all iterations (see the overall workflow). text/html 2021-02-09T16:26:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:densifyakrigingresultofasampleset&rev=1612887965&do=diff Densify a Kriging result The densification algorithm identifies the critical points in a Kriging result. Therefore, the densification result indicates the approximate locations of the people whose samples will be collected by responders in the next iteration. text/html 2021-02-09T16:24:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:displaysamplelocationsanddosesofasampleset&rev=1612887898&do=diff Display sample locations and doses of a scenario on a map In one iteration (see the overall workflow), after processing the current sample set and performing dose estimation, the next step is to display the geographic locations and ADCI-estimated doses of all samples contained in all sample sets of the scenario. To achieve this, first select the scenario in the scenario tree, then click the ‘Display sample locations’ menu item under the ‘Geoprocessing’ menu. text/html 2021-02-09T16:23:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:editdescriptions&rev=1612887838&do=diff Edit descriptions of a scenario, sample sets and samples After finishing creating a scenario and adding a sample set to it, you may want to further change their descriptions (e.g. entering physical doses and coordinates for individuals). To do this, click the 'Edit scenario descriptions' menu item under the 'Scenario' menu. text/html 2021-02-09T16:20:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:getstarted&rev=1612887648&do=diff Get started ADCI-BGQ is a plug-in in the ADCI software, enabling you to take advantage of the IBM Blue Gene/Q (BGQ) supercomputer located in Toronto, Canada to significantly expedite processing samples and estimating radiation doses. Install JRE text/html 2021-02-09T16:22:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:maingui&rev=1612887762&do=diff Main GUI The GUI of ADCI-BGQ consists of two windows, the login window and the main window. Login window The login window is what you will first see after starting ADCI-BGQ. In this window, you enter the user name and password of your account, then click the ‘Login’ button. text/html 2021-02-09T16:25:20+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:performkrigingonasampleset&rev=1612887920&do=diff Perform Kriging on a scenario Given the values of a number of discrete, individual locations, the Kriging algorithm interpolates the value of each location in a region containing these input locations. Due to resource constraints (e.g. number of responders), it is not realistic to collect a sample from every person who was potentially radiated and needs treatment in the region where the nuclear scenario occurred. Therefore, the Kriging result of a scenario illustrates a fast estimation on the i… text/html 2021-02-09T16:24:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:processasampleset&rev=1612887880&do=diff Process a sample set To process a sample set and perform dose estimation, select it in the left tree and click the ‘Process sample set’ menu item under the ‘Run’ menu. The sample set can either belong to a scenario or be isolated. Prepare text/html 2021-02-16T19:00:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:startpage&rev=1613502027&do=diff ADCI-BGQ (in progress) Get started Overall workflow Main GUI Create a sample for a person Create a sample set Create a scenario Edit descriptions of a scenario, sample sets and samples Process a sample set Display sample locations and doses of a scenario on a map Perform Kriging on a scenario Compare a Kriging result with a previous one Densify a Kriging result text/html 2021-02-09T16:22:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://adciwiki.cytognomix.com/doku.php?id=bgq:workflow&rev=1612887743&do=diff Overall workflow The following figure shows the entire iterative process to handle a large-scale nuclear event using the ADCI-BGQ plug-in. The steps performed by ADCI-BGQ are enclosed in the dashed rectangle, which will be described in detail below.