An overview of the consequences of uneven resource distribution and its impact on countries that have resources and lack resources. From the About.com Geography GuideSite. RD2: Resource Distribution 2. Resource Distribution 2. This is a rewrite of the Resource Distribution addon by Shanjaq.! Don't expect anything anytime soon, nothing will be ready for testing for a very long time. Ideas for RDx. 5 air gens on one net is the same as the air gen formula * 5). English: How to download SVN/Git Addons (Wiremod, Stargate (CAP), Spacebuild, CAF, RD3, LS3) for Gmod.Maybe just develop core code outside GMod using standard lua binaries and port for GMod for release. Resource Distribution 2. The Garry's Mod community is a tremendous source of content and has added. Brief How-To for Garry's Mod Files Garry's Mod STORE COMMUNITY ABOUT. When I first started using Gmod I was absolutely CLUELESS about where things went, and unfortunately not every download came with. MAKER Tutorial 2. GMODThis MAKER tutorial was taught by Barry Moore as part of the 2. GMOD Summer School. See the GMOD Cloud Tutorial for information on how to get this AMI. However, MAKER is also designed to be scalable and is thus appropriate for projects of any size including use by large sequence centers. MAKER can be used for de novo annotation of newly sequenced genomes, for updating existing annotations to reflect new evidence, or just to combine annotations, evidence, and quality control statistics for use with other GMOD programs like GBrowse, JBrowse, Chado, and Apollo. California Davis) Pub. Med. Atta cephalotes - leaf- cutter ant (C Currie, Univ. Wisconsin, Madison) Pub. Med. Linepithema humile - Argentine ant (CD Smith, San Francisco State Univ.) Pub. Med. Pogonomyrmex barbatus - red harvester Ant (J Gadau, Arizona State Univ.) Pub. Med. Conus bullatus - cone snail (B Olivera Univ. Utah) Pub. Med. Petromyzon marinus - Sea lamprey (W Li, Michigan State) - Manuscript in preparation. Fusarium circinatum - pine pitch canker (B Wingfield, Univ. Pretoria) - Manuscript in preparation. Cardiocondyla obscurior - tramp ant (J Gadau, Arizona State Univ.) - Manuscript in preparation. Columba livia - pigeon (M Shapiro, Univ. Utah) - Manuscript in preparation. Megachile routundata alfalfa leafcutter bee () - Manuscript in preparation. Latimeria menadoensis - coelacanth () - Manuscript in preparation. Nannochloropsis - micro algae (SH Shiu, Michigan State Univ.) - Manuscript in preparation. Arabidopsis thale cress re- annotation (E Huala, TAIR) - Manuscript in preparation. Cronartium quercuum - rust fungus (JM Davis, Univ. Florida) - Annotation in progress. Ophiophagus hannah - King cobra (T. Colorado) - Annotation in progress. Python molurus - Burmese python (T. Colorado) - Annotation in progress. Lactuca sativa - Lettuce (RW Michelmore) - Annotation in progress. M Mitreva, Washington Univ). Diabrotica virgifera - corn rootworm beetle (H Robertson, Univ. Illinois). Oryza sativa - rice re- annotation (R Buell, MSU). Zea mays - maize re- annotation (C Lawrence, Maize. GDP). Cephus cinctus - wheat stem sawfly (H Robertson, Univ. Illinois). Rhagoletis pomonella - apple maggot fly (H Robertson, Univ. Illinois). Introduction to Genome Annotation. What Are Annotations? Annotations are descriptions of different features of the genome, and they can be structural or functional in nature. This assists in curation, quality control and management of genome annotations. The first question that occurs to most of us when a genome is sequenced is, . And while most researchers probably don't give annotations a lot of thought, they use them everyday. If an annotation is correct, then these experiments should succeed; however, if an annotation is incorrect then the experiments that are based on that annotation are bound to fail. Which brings up a major point. Incorrect and incomplete genome annotations poison every experiment that uses them. Quality control and evidence management are therefore essential components to the annotation process. Single- molecule sequencing technologies such as those in development by Pacific Bio. Sciences and Oxford Nanopore have demonstrated that very long, very low cost sequence reads are possible - although none of these technologies has fully matured. If the hype is to be believed, then whole genome sequencing will become . Unfortunately, however, advances in annotation technology have not kept pace with genome sequencing, and annotation is rapidly becoming a major bottleneck affecting modern genomics research. MAKER does not predict genes, rather MAKER leverages existing software tools (some of which are gene predictors) and integrates their output to produce what MAKER finds to be the best possible gene model for a given location based on evidence alignments. However there are significant differences that are discussed below. Classic Model Genomes. Not all genomes are created equal - each comes with its own set of issues that are not necessarily found in classic model organism genomes. These include difficulties associated with repeat identification, gene finder training, and other complex analyses. Emerging model organisms are often studied by small research communities which may lack the infrastructure and bioinformatics expertise necessary to 'roll- ther- own' annotation solution. Emerging Genomes. If you have looked at a comparison of gene predictor performance on classic model organisms such as C. It is important to keep in mind, however, that ab initio gene predictors have been specifically optimized to perform well on model organisms such as Drosophila and C. Gene prediction in classic model organisms is relatively simple because there are already a large number of experimentally determined and verified gene models, but with emerging model organisms, we are lucky to have a handful of gene models to train with. As a result ab initio gene predictors generally perform very poorly on emerging genomes. Pfam domain content of gene models determined using rpsblast. By using ab inito gene predictors within the MAKER pipeline you get several key benefits. MAKER provides gene models together with an evidence trail - useful for manual curation and quality control. Navigate your browser to. The AWS EC2 Management Console. Search for the AMI named MAKER. INSTALL gives a brief overview of MAKER and prerequisite installation. Let's take a look at this. But for the sake of documentation.. Xcode) from your installation. If you are on a 3. Rosetta from your instalation. If you are using a 6. Make sure to. install fink as 6. Go to the ../maker/src/ directory and run 'perl Build. PL' to configure. Accept default configuration options by just pressing enter. If anything fails, either use the ./Build file commands to retry the. Use ./Build status to see. You can edit this file. You need to have perl 5. You can verify this by. Type 'perl - MCPAN - e shell' to access the CPAN shell. You may. have to answer some configuration questions if this is your first time. CPAN. You can normally just hit enter to accept defaults. Type 'install DBI' to install the first module, then type. DBD: :SQLite' to install the next, and so on. Alternatively you can download moadules from http: //www. Install Bio. Perl 1. Download the Core Package from. MAKER uses will). Download and unpack the most recent Bio. Perl package to a directory of your. Git to access the most current version of Bio. Perl. See. http: //www. Git. Type perl - MCPAN - e shell into the command line to set up CPAN on your. CPAN helps install perl dependencies. For the most part just accept any default options. Type install Bundle: :CPAN on the cpan command line. Once again just press. Type install Module: :Build on the cpan command line. Once again just. press enter to accept default installation options. Type install Bundle: :Bio. Perl on the cpan command line. Once again press. Unpack the downloaded bioperl tar file to the directory of your choice or. Git to get the most up to date version. Then use the terminal. Build. PL in the command line, then. Build test, then if all tests pass, type ./Build install. This. will install Bio. Perl where perl is installed. Press enter to accept all. Install either Wu. Blast or NCBI- BLAST using instruction in 3a and 3b. Install Wu. Blast 2. Alternatively install NCBI- BLAST in 3b). Wu. Blast has become AB- Blast and is no longer freely available, so if you. Wu. Blast, you can use NCBI. BLAST or BLAST+ instead). Unpack the tar file into the directory of your choice (i. Add the following in your . Add the location where you installed Wu. Blast to your PATH variable in. Install NCBI- BLAST 2. X or higher (Alternatively install Wu. Blast in 3a). a. Unpack the tar file into the directory of your choice (i. Add the location where you installed NCBI- BLAST to your PATH variable in. Download from http: //homepage. Unpack the SNAP tar file into the directory of your choice (ie /usr/local). Add the following to your . Navigate to the directory where snap was unpacked (i. Add the location where you installed SNAP to your PATH variable in. Download from http: //www. The most current version of Repeat. Masker requires a program called TRF. The TRF download will contain a single executable file. You will need to. Make TRF executable by typing chmod +x+u trf. You can then move this file. I just put it in the /Repeat. Masker directory. Unpack Repeat. Masker to the directory of your choice (i. If you do not have Wu. Blast installed, you will need to install RMBlast. Now in the Repeat. Masker directory type perl ./configure in the command. You will be asked to identify the location of perl, wublast, and. The script expects the paths to the folders containing the. Add the location where you installed Repeat. Masker to your PATH variable in. You must register at http: //www. Repbase. repeat database, Repeat Masker edition, for Repeat. Masker to work. Unpack the contents of the Rep. Base tarball into the Repeat. Masker/Libraries. Install Exonerate 1. Download from. http: //www. Exonerate has pre- comiled binaries for many systems; however, for Mac OS- X. You need to have Glib 2. The easiest way to do this on a Mac. For 6. 4- bit systems. Change to the directory containing the Exonerate package to be compiled. To install exonerate in the directory /usr/local/exonerate, type. Add the location where you installed exonerate to your PATH variable in. Download from http: //www. Unpack the MAKER tar file into the directory of your choice (i. Go to the MAKER src/ directory. Configure using - -> perl Build. PL. D. Install using - -> ./Build install. Remember to add the following to your . Add the location where you installed MAKER to your PATH variable in. You can now run a test of MAKER by following the instructions in the MAKER. README file. If you want to install the MPI version of MAKER, you need to have Perl. Install standard MAKER and verify that it runs. Install MPICH2 with the - -enable- sharedlibs flag set to the. OS (See MPICH2 documentation). Use cd to change to the maker/src subdirectory in the MAKER.
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