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- Currently, this service is unavailable. It is anticipated that it will be deployed again in 2012.413 bytes (59 words) - 15:14, 24 November 2011
- ...on about installing the dependencies is not provided in this document, and it is recommended that you make use of your system's package management tools, ...on/env.sh</tt> in the <tt>bsadmin</tt> distribution and then incorporating it into your environment within a <tt>.bashrc</tt> or equivalent file as follo3 KB (393 words) - 13:36, 14 July 2010
- ...ocument, potentially with information about the location of such mentions, it is much more convenient to produce a display which integrates such results1 KB (182 words) - 13:48, 14 July 2010
- ...r the first time installation of the plugin, if the user tries to activate it there will be an error message. The user will be instructed to restart Cyto Reasons for this: The plugin requires the installation location of it self, before downloading the data component. PluginManager.getPluginURLs()1 KB (160 words) - 09:14, 18 June 2010
- It may be necessary to initialise a "database cluster" for Bioscape. This is t ...rectory given in the above commands will save you the effort of specifying it later with other5 KB (714 words) - 13:38, 14 July 2010
- <li>Compile the source code. It might be necessary to edit the <tt>build.xml</tt> file, changing the partic It may then be run as follows:5 KB (822 words) - 18:37, 17 November 2011
- However, it should be possible to mitigate these problems by adopting a number of techn ...n forms, For example, "AN" could be a valid component of a gene name; thus it is not desirable to filter out this form of the stop word "an", since such6 KB (954 words) - 13:45, 14 July 2010
- ==What is canonicalization and how does it alter iRefIndex and iRefWeb data? == ...7-1) but it is not always the -1 variant of the canonical accession (i.e., it could be O43497-4). The protein isoform that is chosen to be the canonical6 KB (981 words) - 16:44, 14 March 2013
- # Each concept has a probability associated with it (defining the probability of "encountering an instance" of that concept). ...umes all possible concepts, the probability of encountering an instance of it is 1.6 KB (928 words) - 18:01, 29 February 2012
- print "add 3 to $z: $z + 3\n"; #did it work? #for each letter in the sequence check if it is the base G12 KB (1,936 words) - 15:22, 22 November 2011
- With this information available to Bioscape, it becomes possible to see each result set in the same document and to perform Using BioCreative results, it is possible to take a selection of Bioscape results and to assess them acco10 KB (1,540 words) - 16:48, 15 July 2010
- It will be necessary to change the date details included in the above filename ...nerally split to expose the prefix and identifier, name or value following it.5 KB (720 words) - 14:51, 19 September 2011
- .... Once the ligand is outside the compartment, its state (yellow) prevents it from assembling with the importing receptor (black) for a second time. ...er to life, the universe, and everything. Amongst the people who worked on it was Slartibartfast, a coastal designer who won an award for his work on Nor5 KB (770 words) - 15:09, 24 November 2011
- ...r types, it is highly likely to "bloat" the term dictionary and bring with it undesirable resource and performance characteristics. ...consider allocating ranges of usable identifiers within the system. Thus, it becomes possible to process a number of sections of a literature collection6 KB (874 words) - 13:45, 14 July 2010
- iRefR is an R package that provides access to [[iRefIndex]]. It allows the user to load any version of the consolidated protein interaction1 KB (198 words) - 16:08, 2 December 2011
- Notepad is found in the same menu, but it can be easier to open Notepad by typing the <tt>notepad</tt> command in the ...makes sure that the new file is created in the right place. In this case, it is called <tt>example1.plx</tt>. If you started Notepad from the menu, when4 KB (596 words) - 11:20, 9 May 2012
- When dealing with multiple instances of MySQL it can be useful to remember the <tt>--defaults-file</tt> option to the MySQL ...and delimited/tabular dumps. Although the latter is arguably more elegant, it does not offer much help with the task of restoring the tables in the corre7 KB (1,088 words) - 16:05, 26 October 2012
- ...plugin called iRefIndex installed, it is recommended that you first delete it''', selecting the "Manage Plugins" option in the "Plugins" menu. This will # When the plugin is started for the first time, it will download the publicly available dataset.15 KB (2,297 words) - 16:09, 6 July 2011
- ...plugin called iRefIndex installed, it is recommended that you first delete it''', selecting the "Manage Plugins" option in the "Plugins" menu. This will # When the plugin is started for the first time, it will download the dataset.18 KB (2,800 words) - 20:08, 14 March 2013
- ...ogram needs Python 2.5 or later since it uses the <tt>hashlib</tt> module. It could probably be made compatible with earlier Python versions if necessary6 KB (1,046 words) - 13:04, 20 October 2011
- ...hIKey - a form of checksum or hash of the chemical structure of the drug - it is not equivalent or directly comparable to the ROG (redundant object group ...idB) may be either a protein or a small molecule. Where uidB is a protein, it will always have a UniProt accession as an identifier: interactors not havi6 KB (888 words) - 14:46, 25 August 2011
- Data is distributed in the hope that it will be useful, but WITHOUT ANY ...omim identifier usually refers to a record describing a disease phenotype; it is a descriptive entry that does not refer to a unique locus.5 KB (771 words) - 09:25, 30 June 2010
- ...sult, this human interaction ends up in the mouse MITAB (because HPRD says it was mouse). BioGRID correctly curates the paper as about mouse. ...plete provenance info (this will become the main MITAB file we release and it will support PSICQUIC services and we will drop non-canonicalised version i4 KB (649 words) - 14:38, 7 November 2011
- ...d data into tabular data to be stored in a database. In the above example, it is apparent that the experiment, interaction and interactor details reside ...ke an existing mapper file which supports the same subformat and to modify it to understand the new data source. For example, the InnateDB data resembles40 KB (4,270 words) - 16:04, 26 October 2012
- It will be necessary to change the date details included in the above filename ...nerally split to expose the prefix and identifier, name or value following it.6 KB (879 words) - 16:52, 29 November 2011
- This is a planning template for the next release. It does not correspond to a released product. In case of controlled terms to be standard conform it should look like this:11 KB (1,675 words) - 11:47, 26 February 2014
- with the <tt>not_wordnet</tt> method. It is the task of subsequent processing of the ...xtual search results. For example, where only human genes are of interest, it is necessary to firstly identify such genes and to assign a positive score13 KB (1,932 words) - 13:43, 14 July 2010
- ...ch as the individual sentences in each document. By identifying sentences, it then becomes easier to determine whether results occur together in the same ...ch terms, the same matching criteria still apply within Bioscape. However, it can be undesirable to permit such case-insensitive matches for certain kind24 KB (3,501 words) - 13:46, 14 July 2010
- It should be emailed to ian.donaldson at biotek.uio.no preferably as a PDF doc Download, install (if necessary) and learn how to use it.17 KB (2,539 words) - 11:32, 22 August 2012
- When there are many search terms, it is convenient to construct a batch file containing a list of all terms. Thi It is possible to include multiple attributes in the same file. To do this, ea7 KB (1,128 words) - 15:41, 6 July 2011
- This interface is currently discontinued until a new location is arranged for it.4 KB (589 words) - 17:23, 28 December 2019
- ...p://www.ebi.ac.uk/intact/site/index.jsf IntAct], [http://mint.bio.uniroma2.it/mint/Welcome.do MINT], [http://mips.gsf.de/genre/proj/mpact MPact], [http:/ As such, it is important that these databases have the means to effectively exchange an9 KB (1,251 words) - 12:27, 17 October 2011
- A sample configuration file is located in the <tt>config</tt> directory. It can be copied, modified and supplied to the program. ...and run in the [[iRefIndex Build Process]]. For a completed build process it '''should not''' need to be run again, but an option does exist to explicit11 KB (1,698 words) - 13:34, 16 February 2012
- AH2_ARATH returns CAH2_ARATH. It should return 0 results. '''FAIL'''. Imagine if the user accidently had s AHP2_ARATH.2 returns results. It should return 0 results. '''FAIL'''.20 KB (3,064 words) - 12:43, 15 June 2010
- ...e referenced explicitly in various parts of the software. For such values, it is most convenient to5 KB (827 words) - 13:48, 14 July 2010
- | 2 nodes (POL_HV1H2 and POL_HV1B1 interacting with it) ...ntation of results from the term isn't particularly easy to accomplish, or it isn't obvious how to accomplish this successfully, because the iRefScape pa24 KB (3,634 words) - 17:32, 24 November 2011
- ...tection method name used inappropriately as a interaction type name - here it is difficult to say what the inequality between a, b, ab and WT is. ...||immunoblotting might be used as a method of interaction detection though it is usually a method for participant identification - cases should be review31 KB (4,505 words) - 12:50, 7 April 2011
- ...p://www.ebi.ac.uk/intact/site/index.jsf IntAct], [http://mint.bio.uniroma2.it/mint/Welcome.do MINT], [http://mips.gsf.de/genre/proj/mpact MPact], [http:/ As such, it is important that these databases have the means to effectively exchange an11 KB (1,496 words) - 08:22, 23 April 2015
- ...' (letter or number) with a word from the explanatory text. Here, although it is tempting to only take the first letter (or digit) from each word, other Sometimes, it can be inferred which kind of bioentity is being written about in the text.12 KB (1,525 words) - 13:46, 14 July 2010
- ...p://www.ebi.ac.uk/intact/site/index.jsf IntAct], [http://mint.bio.uniroma2.it/mint/Welcome.do MINT], [http://mips.gsf.de/genre/proj/mpact MPact], [http:/ As such, it is important that these databases have the means to effectively exchange an11 KB (1,556 words) - 12:52, 22 April 2015
- Download the file into the newly created data directory and unpack it as follows: ....Z</tt> should be replaced by the actual release number) and download/copy it to the newly created data directory for BioGRID.47 KB (7,595 words) - 15:50, 4 October 2011
- '''granulocyte-macrophage colony-stimulating factor (GM-CSF)''' made it possible to increase dose However, in order to eliminate obvious bad suggestions for genes, it is also21 KB (2,669 words) - 13:44, 14 July 2010
- ...format that was proposed for use in iRefIndex 7.0 and subsequent releases; it does not correspond to any released product and is considered '''obsolete'' ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim29 KB (4,420 words) - 13:29, 27 October 2010
- ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim ...d then list these binary interactions in the MITAB. This would be wrong. It implies interactions that may not exist and hides the fact that the entry i30 KB (4,488 words) - 12:47, 9 November 2011
- * <tt>download</tt> - the retrieval of data from the location where it is published6 KB (979 words) - 13:39, 14 July 2010
- When the plugin is started for the first time, it will download the publicly available data set. ...Taxonomy] for more details on taxonomy identifiers. For most search types, it is acceptable to leave this field set to <tt>Any</tt>.36 KB (5,904 words) - 16:13, 6 July 2011
- ...format that was proposed for use in iRefIndex 7.0 and subsequent releases; it does not correspond to any released product and is considered '''obsolete'' ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim54 KB (8,103 words) - 12:20, 19 October 2010
- ...format that was proposed for use in iRefIndex 7.0 and subsequent releases; it does not correspond to any released product and is considered '''obsolete'' ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim52 KB (7,816 words) - 13:44, 27 October 2010
- When the plugin is started for the first time, it will download the publicly available data set. ...Taxonomy] for more details on taxonomy identifiers. For most search types, it is acceptable to leave this field set to <tt>Any</tt>.33 KB (5,470 words) - 16:18, 6 July 2011
- It will be made available for releases of iRefIndex starting with release 7.0. ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim51 KB (7,623 words) - 15:44, 25 October 2010
- ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim Here A is chosen as the "hub" of the spoke model since it was the "bait" protein. For experimental systems that do not have "baits"49 KB (7,401 words) - 12:34, 17 October 2011
- In case of controlled terms to be standard conform it should look like this: ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim51 KB (7,688 words) - 10:45, 27 May 2013
- .../) and now only releases data in PSI-MITAB format (ftp://mint.bio.uniroma2.it/pub/release/mitab26/). The most recent MINT release at the time of writing In case of controlled terms to be standard conform it should look like this:52 KB (7,804 words) - 09:47, 21 June 2013
- In case of controlled terms to be standard conform it should look like this: ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim52 KB (7,812 words) - 12:00, 5 April 2013
- In case of controlled terms to be standard conform it should look like this: ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim53 KB (7,878 words) - 10:30, 13 December 2013
- ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim Here A is chosen as the "hub" of the spoke model since it was the "bait" protein. For experimental systems that do not have "baits"52 KB (7,771 words) - 16:03, 10 March 2018
- The assignment is due by Friday, October 29th. It should be emailed to ian.donaldson at biotek.uio.no preferably as a PDF doc ...tion to your problem area, clearly state your hypothesis and how you think it might be addressed by each of the methods. Provide justifications for your19 KB (2,793 words) - 22:48, 14 June 2011
- ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim Here A is chosen as the "hub" of the spoke model since it was the "bait" protein. For experimental systems that do not have "baits"52 KB (7,785 words) - 09:48, 9 October 2019
- ...p://www.ebi.ac.uk/intact/site/index.jsf IntAct], [http://mint.bio.uniroma2.it/mint/Welcome.do MINT], [http://mips.gsf.de/genre/proj/mpact MPact], [http:/ As such, it is important that these databases have the means to effectively exchange an14 KB (2,049 words) - 12:30, 17 October 2011
- ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim Here A is chosen as the "hub" of the spoke model since it was the "bait" protein. For experimental systems that do not have "baits"52 KB (7,774 words) - 10:25, 20 August 2021
- ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim Here A is chosen as the "hub" of the spoke model since it was the "bait" protein. For experimental systems that do not have "baits"52 KB (7,778 words) - 19:31, 30 June 2020
- There is no formal requirement for number of words - your notes should make it clear that you understood the main points of the lecture. You may also wis6 KB (822 words) - 09:27, 25 October 2012
- ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim Here A is chosen as the "hub" of the spoke model since it was the "bait" protein. For experimental systems that do not have "baits"53 KB (7,933 words) - 10:41, 4 December 2012
- In case of controlled terms to be standard conform it should look like this: ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim55 KB (8,209 words) - 09:44, 23 July 2016
- ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim Here A is chosen as the "hub" of the spoke model since it was the "bait" protein. For experimental systems that do not have "baits"56 KB (8,235 words) - 06:27, 29 August 2023
- ...MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experim Here A is chosen as the "hub" of the spoke model since it was the "bait" protein. For experimental systems that do not have "baits"56 KB (8,227 words) - 12:11, 9 August 2023
- After parsing it is important to make sure there is no overlap in the UID:12 KB (1,682 words) - 10:21, 14 December 2010
- ...node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"9 KB (1,459 words) - 15:45, 6 July 2011
- When the plugin is started for the first time, it will download the publicly available data set. ...Taxonomy] for more details on taxonomy identifiers. For most search types, it is acceptable to leave this field set to <tt>Any</tt>.45 KB (7,264 words) - 11:10, 19 March 2013
- ...audhry || Scientific fraud and other irregularities - What can we do about it?9 KB (1,185 words) - 23:06, 24 November 2011
- ...an> : Single digit matching was blocked in beta 0.85 and now I have enable it. Noe even if the user enters a 0 or a 1 as query the complete search operat ...rlier feature calculate node degree related to selected nodes and replaced it between nodes the generalization is lost. I believe we could achieve what y28 KB (4,119 words) - 14:30, 18 June 2010
- ...an> : Single digit matching was blocked in beta 0.85 and now I have enable it. Noe even if the user enters a 0 or a 1 as query the complete search operat ...rlier feature calculate node degree related to selected nodes and replaced it between nodes the generalization is lost. I believe we could achieve what y28 KB (4,119 words) - 00:10, 19 June 2010
- Data is distributed in the hope that it will be useful, but WITHOUT ANY17 KB (2,607 words) - 08:48, 20 January 2011
- Data is distributed in the hope that it will be useful, but WITHOUT ANY18 KB (2,645 words) - 17:38, 9 November 2011
- or one of the other publications listed above if it is more appropriate.19 KB (2,634 words) - 15:25, 15 March 2013
- ...an interaction was mapped to a ROGID, that interaction is not included (as it would not have a RIGID). If a protein occurred only in interactions that we20 KB (1,610 words) - 16:30, 12 January 2011
