http://helix.nih.gov Helix Systems at NIH en Fri, 01 Jan 2010 00:00:00 EST Thu, 23 May 2013 00:00:04 EDT http://cyber.law.harvard.edu/rss/rss.html staff@helix.nih.gov staff@helix.nih.gov http://helix.nih.gov/images/mini_helix_blue.png http://helix.nih.gov 88 31 Helix Systems at NIH http://helix.nih.gov/News/index.php?409 Environment Modules are a convenient way for users to dynamically set paths, library paths, and other required environment variables for an application. Instead of typing shell-dependent commands, for example, a user could now type:<br><br> module load ThisApp<br><br> to set up all environment variables for the program ThisApp, and:<br><br> module unload ThisApp<br><br> to unset all those environment variables. <br><br> Almost all the scientific applications, libraries, and interpreters such as Perl, Python and Java on Helix & Biowulf now use modules. Details are on the application webpages. <br><br> If you are not familiar with the use of modules, please see <A href="http://helix.nih.gov/Applications/modules.html">http://helix.nih.gov/Applications/modules.html</a> for an introduction.<br><br> Please contact staff@helix.nih.gov with any questions. Thu, 14 Feb 2013 16:42:02 EST http://helix.nih.gov/News/index.php?404 This email is for Biowulf users who have their /data directories on the /gs2 filesystem. If you use the "gpfs" property for your 'qsub' or 'swarm' jobs, this means you.<br><br> Biowulf staff will have to take the gs2 filesystem OFFLINE to repair filesystem damage incurred last week.<br><br> This means that when the filesystem is taken offline, any jobs currently accessing that filesystem will be terminated, and that jobs submitted requiring that filesystem will be rejected.<br><br> The software vendor informs us that it will take anywhere between 8 and 48 hours to repair the filesystem. <br><br> Jobs accessing or submitting to the /gs2 filesystem will be terminated starting TODAY at 10 am. Email will be sent to biowulf users when /gs2 is again available.<br><br> We apologize for this disruption to your work, but delaying this repair could have serious consequences for the integrity of data on /gs2.<br><br> Wed, 05 Dec 2012 09:06:51 EST http://helix.nih.gov/News/index.php?403 The Helix/Biowulf staff will present a series of classes in Jan 2013 Classes are free but registration is required. Helix/Biowulf users will have priority enrollment, and new users are highly encouraged to attend.<br><br> Introduction to Linux ---------------------- <a href="http://training.cit.nih.gov/?SS880">http://training.cit.nih.gov/?SS880</a> Date & Time: Wed, Jan 9, 9 am - 4 pm Location: Bldg 12A, Rm B51. This class is intended as a starting point for individuals new to Linux and UNIX. The class will center on basic UNIX/Linux concepts: logging in, navigating the file system, commands for interacting with files, running and viewing processes, checking disk space and other common tasks. The class will also cover the use of some services specific to Helix/Biowulf usage.<br><br> Bash Shell Scripting for Helix and Biowulf ------------------------------------------ <a href="http://training.cit.nih.gov/?SS890">http://training.cit.nih.gov/?SS890</a> Date & Time: Wed, Jan 16, 10 am - 4 pm Location: Bldg 12A, Rm B51. The default shell on many Linux systems is bash. Bash shell scripting provides a method for automating common tasks on Linux systems (such as Helix and Biowulf), including transferring and parsing files, creating qsub and swarm scripts, pipelining tasks, and monitoring jobs. This class will give a hands-on tutorial on how to create and use bash shell scripts in a Linux environment.<br><br> NIH Biowulf Cluster: Scientific Computing ----------------------------------------- <A href="http://training.cit.nih.gov/?SS610">http://training.cit.nih.gov/?SS610</a> Date & Time: Wed, Jan 23, 9 am - 4 pm Location: Bldg 12A, Rm B51 Morning: Introduction to the Biowulf Linux cluster, cluster concepts, accounts, logging in, storage options, interactive vs. batch jobs, how to set up and submit a simple batch job, batch queues, available software, and job monitoring. Afternoon: Hardware and network configuration, types of nodes, selection of nodes using properties, system software, parallel programs, programming tools.<br><br> Wed, 28 Nov 2012 14:25:29 EST http://helix.nih.gov/News/index.php?405 The /gs2 filesystem is again available and users who submit qsub or swarm jobs with the "gpfs" property may resume doing so.<br><br> File system repair took about 8 hours with damage believed to be limited to one user's directory entry for a single file. Biowulf staff will continue analysis of repair log files to confirm the scope of damage.<br><br> Wed, 05 Dec 2012 20:55:49 EST http://helix.nih.gov/News/index.php?406 The Biowulf staff is pleased to announce the addition of 24 large memory (256 GB) nodes to the cluster. These nodes will be for jobs that require more than 72 GB, and in contrast to most nodes in the cluster will be shareable by more than one job.<br><br> To allocate these nodes to your job, use the "mem=" option to the 'qsub' command, for example:<br><br> qsub -l nodes=1,mem=128gb myjob.bat<br><br> mem must be equal or greater than 72gb and less than or equal 250gb. Jobs requesting more than 250gb will continue to allocate the single 512GB node.<br><br> Multi-process or multi-threaded jobs should use the "ncpus=" option to 'qsub', for example:<br><br> qsub -l nodes=1,mem=192gb,ncpus=24 myjob.bat<br><br> ncpus must be 32 or less.<br><br> The 'freen' command now reports the largest block of available memory on the 256GB nodes:<br><br> -------------------- 256 GB nodes ---------- Available memory: Min - 72 GB, Max - 250 GB<br><br> Tue, 11 Dec 2012 15:02:56 EST http://helix.nih.gov/News/index.php?417 The Helix Systems staff maintains a small collection of 1000 genomes data (vcf files) in /fdb/1000genomes/. We are considering maintaining a copy of the BAM files (alignments) from 1000 Genomes.<br><br> These files are very large (currently 132 TB total, and growing), and since disk space is always in short supply, we need to seriously consider their value to the Helix/Biowulf user community before downloading them.<br><br> * Have you ever used the 1000 Genomes BAM files? * Do you currently have a copy of any of the 1000 Genomes data on your Helix/Biowulf account? * Do you plan to use the 1000 Genomes BAM files? If so, when?<br><br> Thanks for your input! Helix Systems Staff. <br><br> Wed, 27 Mar 2013 11:18:25 EDT http://helix.nih.gov/News/index.php?418 For NIH Helix & Biowulf users who have Linux or Mac systems in their labs, there is a new file transfer program available for the Helix Systems.<br><br> 'bbcp' is a high-performance version of scp which can provide significantly increased file transfer performance over scp. You can use 'bbcp' on Biowulf or Helix to transfer files to your local Linux or Mac system; you can also download a version of 'bbcp' for your local system and use it there.<br><br> For details on using 'bbcp' on Biowulf see the section entitled "Commandline File Transfer: Macs & Unix/Linux: bbcp" at <A href="http://helix.nih.gov/Documentation/transfer.html">http://helix.nih.gov/Documentation/transfer.html</a><br><br> Wed, 17 Apr 2013 11:50:38 EDT http://helix.nih.gov/News/index.php?415 The Helix/Biowulf staff will present a series of classes in April 2013. Classes are free but registration is required. Helix/Biowulf users will have priority enrollment, and new users are highly encouraged to attend.<br><br> Introduction to Linux ---------------------- <A href="http://training.cit.nih.gov/class_details.aspx?cId=NIHCIT-SS880">http://training.cit.nih.gov/class_details.aspx?cId=NIHCIT-SS880</a> Date & Time: Wed, Apr 10, 9 am - 4 pm Location: Bldg 12A, Rm B51. This class is intended as a starting point for individuals new to Linux and UNIX. The class will center on basic UNIX/Linux concepts: logging in, navigating the file system, commands for interacting with files, running and viewing processes, checking disk space and other common tasks. The class will also cover the use of some services specific to Helix/Biowulf usage.<br><br> Bash Shell Scripting for Helix and Biowulf ------------------------------------------ <A href="http://training.cit.nih.gov/class_details.aspx?cId=NIHCIT-SS890">http://training.cit.nih.gov/class_details.aspx?cId=NIHCIT-SS890</a> Date & Time: Wed, Apr 17, 10 am - 4 pm Location: Bldg 12A, Rm B51. The default shell on many Linux systems is bash. Bash shell scripting provides a method for automating common tasks on Linux systems (such as Helix and Biowulf), including transferring and parsing files, creating qsub and swarm scripts, pipelining tasks, and monitoring jobs. This class will give a hands-on tutorial on how to create and use bash shell scripts in a Linux environment.<br><br> NIH Biowulf Cluster: Scientific Computing ----------------------------------------- <A href="http://training.cit.nih.gov/class_details.aspx?cId=NIHCIT-SS610">http://training.cit.nih.gov/class_details.aspx?cId=NIHCIT-SS610</a> Date & Time: Wed, Apr 24, 9 am - 4 pm Location: Bldg 12A, Rm B51 Morning: Introduction to the Biowulf Linux cluster, cluster concepts, accounts, logging in, storage options, interactive vs. batch jobs, how to set up and submit a simple batch job, batch queues, available software, and job monitoring. Afternoon: Hardware and network configuration, types of nodes, selection of nodes using properties, system software, parallel programs, programming tools.<br><br> Tue, 12 Mar 2013 09:17:32 EDT http://helix.nih.gov/News/index.php?416 The Helix Systems staff is pleased to announce a utility tool that lets users monitor their usage of CPU and storage on Biowulf and Helix.<br><br> To view your usage, go to <A href="https://helixweb.nih.gov/usage/">https://helixweb.nih.gov/usage/</a><br><br> You will need to authenticate with your NIH login username and password. This utility is only available within the NIH network. <br><br> The website also displays papers that cited Helix and Biowulf during this period. If you have additional papers that are not listed, please let us know by sending email to staff@helix.nih.gov<br><br> Helix Systems Staff. Mon, 18 Mar 2013 07:57:12 EDT http://pubs.acs.org/doi/pdf/10.1021/pr301139y Recent publication citing Helix/Biowulf resources:<br><br><u>Improving Peptide Identification Sensitivity in Shotgun Proteomics by Stratification of Search Space</u><br><br>Gelio Alves and Yi-Kuo Yu DOI: 10.1021/pr301139y (2013) <i>J. Proteome Research</i> <b></b>: Tue, 21 May 2013 08:25:53 EDT http://onlinelibrary.wiley.com/doi/10.1111/trf.12193/full Recent publication citing Helix/Biowulf resources:<br><br><u>Degenerate polymerase chain reaction strategy with DNA microarray for detection of multiple and various subtypes of virus during blood screening</u><br><br>K. Takizawa, T. Nakashima, T Mizukami et al. DOI: 10.1111/trf.12193 (2013) <i>Transfusion</i> <b></b>: Fri, 03 May 2013 09:09:44 EDT http://www.sciencedirect.com/science/article/pii/S0165027012004608 Recent publication citing Helix/Biowulf resources:<br><br><u>The effect of spatial smoothing on fMRI decoding of columnar-level organization with linear support vector machine</u><br><br>Masaya Misaki, Wen-Ming Luh, Peter A. Bandettini doi://10.1016/j.jneumeth.2012.11.004 (2012) <i>J. Neuroscience Methods</i> <b></b>: Mon, 26 Nov 2012 07:57:33 EST http://circgenetics.ahajournals.org/content/early/2012/11/19/CIRCGENETICS.112.962787.short Recent publication citing Helix/Biowulf resources:<br><br><u>The Impact of Ancestry and Common Genetic Variants on QT Interval in African Americans</u><br><br>JG Smith, CL Avery, DS Evans, MA Nalls et al. doi: 10.1161/&#8203;CIRCGENETICS.112.962787 (2012) <i>Circulation: Cardiovascular Genetics</i> <b></b>: Mon, 26 Nov 2012 08:00:09 EST http://pubs.acs.org/doi/abs/10.1021/jp309119h Recent publication citing Helix/Biowulf resources:<br><br><u>A Systematic Approach for Development of an OPLS-Like Force Field and Its Application to Hydrofluorocarbons</u><br><br>Eugene Paulechka , Kenneth Kroenlein , Andrei Kazakov , and Michael Frenkel DOI: 10.1021/jp309119h (2012) <i>J. Phys. Chem. B</i> <b></b>: Mon, 26 Nov 2012 08:19:29 EST http://www.sciencedirect.com/science/article/pii/S0092867412012974 Recent publication citing Helix/Biowulf resources:<br><br><u>STATs Shape the Active Enhancer Landscape of T Cell Populations</u><br><br>Golnaz Vahedi, Hayato Takahashi, Shingo Nakayamada, Hong-wei Sun, Vittorio Sartorelli, Yuka Kanno, John J. O'Shea doi://10.1016/j.cell.2012.09.044, (2012) <i>Cell</i> <b></b>: Sat, 08 Dec 2012 09:04:04 EST http://www.sciencedirect.com/science/article/pii/S1547527112013422 Recent publication citing Helix/Biowulf resources:<br><br><u>Common genetic variation near the Connexin-43 gene is associated with resting heart rate in African Americans: A Genome-wide Association Study of 13,372 participants</u><br><br>R Deo, MA Nalls, CL Avery, JG Smith et al. doi://10.1016/j.hrthm.2012.11.014 (2012) <i>Heart Rhythm</i> <b></b>: Thu, 29 Nov 2012 08:26:02 EST http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0050411 Recent publication citing Helix/Biowulf resources:<br><br><u>Evaluation of Gene Association Methods for Coexpression Network Construction and Biological Knowledge Discovery</u><br><br>Sapna Kumari, Jeff Nie, Huann-Sheng Chen, Hao Ma, Ron Stewart, Xiang Li, Meng-Zhu Lu, William M. Taylor, Hairong Wei doi:10.1371/journal.pone.0050411 (2012) <i>PLoS One</i> <b></b>: Tue, 04 Dec 2012 07:44:57 EST http://www.sciencedirect.com/science/article/pii/S0969212612004121 Recent publication citing Helix/Biowulf resources:<br><br><u>Protein Secondary Structure Determination by Constrained Single-Particle Cryo-Electron Tomography</u><br><br>Alberto Bartesaghi, Federico Lecumberry, Guillermo Sapiro, Sriram Subramaniam (2012) <i>Structure</i> <b>20(12)</b>: 2003-2013 Tue, 27 Nov 2012 08:41:37 EST http://pubs.acs.org/doi/abs/10.1021/jp308984e Recent publication citing Helix/Biowulf resources:<br><br><u>Structural Ensemble of an Intrinsically Disordered Polypeptide</u><br><br>Jeetain Mittal , Tae Hyeon Yoo , George Georgiou , and Thomas Michael Truskett DOI: 10.1021/jp308984e (2012) <i>J. Phys. Chem. B</i> <b></b>: Mon, 10 Dec 2012 08:07:16 EST http://pubs.acs.org/doi/abs/10.1021/ct300916f Recent publication citing Helix/Biowulf resources:<br><br><u>Mechanisms for the Insertion of Toxic, Fibril-like &beta;-Amyloid Oligomers into the Membrane</u><br><br>Hyunbum Jang , Laura Connelly , Fernando Teran Arce , Srinivasan Ramachandran , Bruce L. Kagan , Ratnesh Lal , and Ruth Nussinov DOI: 10.1021/ct300916f (2012) <i>J. Chem. Theory Compt. </i> <b></b>: Tue, 11 Dec 2012 08:15:43 EST http://onlinelibrary.wiley.com/doi/10.1002/rcm.6451/full Recent publication citing Helix/Biowulf resources:<br><br><u>Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. II. Results for hexapeptides with non-polar side chains</u><br><br>O. I. Obolensky, Wells W. Wu, Rong-Fong Shen, Yi-Kuo Yu DOI: 10.1002/rcm.6451 (2012) <i>Rapid Comm. in Mass. Spec.</i> <b></b>: Tue, 18 Dec 2012 07:44:42 EST http://onlinelibrary.wiley.com/doi/10.1002/ana.23838/abstract Recent publication citing Helix/Biowulf resources:<br><br><u>Ischaemic stroke is associated with the ABO locus: The euroclot study</u><br><br>FMK WIlliams, AM Carter, PG Hysi et al EuroCLOT Investigators, the Wellcome Trust Case Control Consortium 2 (WTCCC2), MORGAM, MetaStroke and the International Stroke Genetics Consortium DOI: 10.1002/ana.23838 (2012) <i>Annals of Neurology</i> <b></b>: Tue, 18 Dec 2012 07:47:44 EST http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=6374364&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6374364 Recent publication citing Helix/Biowulf resources:<br><br><u>On the edge of web-based multiple sequence alignment services</u><br><br>Nguyen, Ken D. (2012) <i>Tsinghua Science and Technology</i> <b>17(6)</b>: 629-637 Tue, 18 Dec 2012 09:02:27 EST http://www.plosone.org/article/authors/info%3Adoi%2F10.1371%2Fjournal.pone.0034060 Recent publication citing Helix/Biowulf resources:<br><br><u>RNA Interference Mediated Inhibition of Dengue Virus Multiplication and Entry in HepG2 Cells</u><br><br>MA Alhoot, SM Wang, SD Sekaran RNA Interference Mediated Inhibition of Dengue Virus Multiplication and Entry in HepG2 Cells (2012) <i>PLoS One</i> <b></b>: Thu, 27 Dec 2012 08:37:35 EST http://digitalcommons.usu.edu/etd/1393/ Recent publication citing Helix/Biowulf resources:<br><br><u>Structural and Mechanistic Investigations of Phosphothreonine Lyase Class of Enzymes</u><br><br>Alok Gopalkrishna Shenoy (2012) <i>Graduate Thesis, Utah State University</i> <b></b>: Tue, 04 Dec 2012 09:21:42 EST http://www.tandfonline.com/doi/full/10.1080/07391102.2012.742460 Recent publication citing Helix/Biowulf resources:<br><br><u>Effect of compatible and noncompatible osmolytes on the enzymatic activity and thermal stability of bovine liver catalase</u><br><br>H. Sepasi Tehrani, A.A. Moosavi-Movahedia, H. Ghourchian, F. Ahmad, A. Kiany, M.S. Atri, Sh Ariaeenejad, K. Kavousi & A.A. Sabourya DOI:10.1080/07391102.2012.742460 (2012) <i>J. Biomol. Struct. Dynamics</i> <b></b>: Fri, 04 Jan 2013 09:23:50 EST http://www.pnas.org/content/early/2012/12/20/1214810110.short Recent publication citing Helix/Biowulf resources:<br><br><u>Molecular structures of trimeric HIV-1 Env in complex with small antibody derivatives</u><br><br>Joel R. Meyerson, Erin E. H. Tran, Oleg Kuybeda, Weizao Chen, Dimiter S. Dimitrov, Andrea Gorlani, Theo Verrips, Jeffrey D. Lifson, and Sriram Subramaniam doi:10.1073/pnas.1214810110 (2012) <i>PNAS</i> <b></b>: Mon, 07 Jan 2013 09:02:11 EST http://www.sciencedirect.com/science/article/pii/S0300908412004889 Recent publication citing Helix/Biowulf resources:<br><br><u>Screening system for orthogonal suppressor tRNAs based on the species-specific toxicity of suppressor tRNAs</u><br><br>Hong Tian, Danni Deng, Jie Huang, Dongning Yao, Xiaowei Xu, Xiangdong Gao doi://10.1016/j.biochi.2012.12.010 (2012) <i>Biochimie</i> <b></b>: Fri, 07 Dec 2012 09:05:55 EST http://www.sciencedirect.com/science/article/pii/S2211124712004317 Recent publication citing Helix/Biowulf resources:<br><br><u>RPA Accumulation during Class Switch Recombination Represents 5'-3' DNA-End Resection during the S-G2/M Phase of the Cell Cycle</u><br><br>Arito Yamane, Davide F. Robbiani, Wolfgang Resch, Anne Bothmer, Hirotaka Nakahashi, Thiago Oliveira, Philipp C. Rommel, Eric J. Brown, Andre Nussenzweig, Michel C. Nussenzweig, Rafael Casellas doi://10.1016/j.celrep.2012.12.006, (2012) <i>Cell Reports</i> <b></b>: Tue, 08 Jan 2013 07:35:03 EST http://onlinelibrary.wiley.com/doi/10.1111/jpi.12034/abstract Recent publication citing Helix/Biowulf resources:<br><br><u>Melatonin inhibits matrix metalloproteinase-9 activity by binding to its active site</u><br><br>Deep Sankar Rudra, Uttam Pal, Nakul Chandra Maiti, Russel J. Reiter, Snehasikta Swarnakar DOI: 10.1111/jpi.12034 (2012) <i>J. Pineal Research</i> <b></b>: Mon, 14 Jan 2013 09:08:34 EST http://hmg.oxfordjournals.org/content/early/2013/01/12/hmg.ddt010.short Recent publication citing Helix/Biowulf resources:<br><br><u>Genetic variation associated with circulating monocyte count in the eMERGE Network</u><br><br>DR Crosslin, A McDavid, N Weston et al doi: 10.1093/hmg/ddt010 (2013) <i>Hum. Mol. Genetics</i> <b></b>: Tue, 22 Jan 2013 08:00:10 EST http://www.sciencedirect.com/science/article/pii/S0092867413000081 Recent publication citing Helix/Biowulf resources:<br><br><u>Identification of Early Replicating Fragile Sites that Contribute to Genome Instability</u><br><br>JH Barlow, RB Faryabi, E Callen, N Wong, A Malhowski, H Tang Chen, G Gutierrez-Cruz, H-W Sun, P McKinnon, G Wright, R Casellas, DF Robbiani, L Staudt, O Fernandez-Capetillo, A Nussenzweig doi://10.1016/j.cell.2013.01.006 (2013) <i>Cell</i> <b></b>: Tue, 29 Jan 2013 07:56:51 EST http://www.sciencedirect.com/science/article/pii/S0005272813000121 Recent publication citing Helix/Biowulf resources:<br><br><u>Alternative Complex III from phototrophic bacteria and its electron acceptor auracyanin</u><br><br>Erica L.W. Majumder, Jeremy D. King, Robert E. Blankenship doi://10.1016/j.bbabio.2013.01.008 (2013) <i>Biochimica et Biophysica Acta (BBA) - Bioenergetics</i> <b></b>: Fri, 01 Feb 2013 09:33:47 EST http://onlinelibrary.wiley.com/doi/10.1111/ahg.12000/full Recent publication citing Helix/Biowulf resources:<br><br><u>Initial Assessment of the Pathogenic Mechanisms of the Recently Identified Alzheimer Risk Loci</u><br><br>P Holton, M Ryten, MA Nalls et al. DOI: 10.1111/ahg.12000 (2013) <i>Annals of Human Genetics</i> <b></b>: Tue, 05 Feb 2013 09:10:50 EST http://onlinelibrary.wiley.com/doi/10.1002/ana.23838/full Recent publication citing Helix/Biowulf resources:<br><br><u>Ischemic stroke is associated with the ABO locus: The EuroCLOT study</u><br><br>FMK Williams, AM Carter, PG Hysi et al and EuroCLOT Investigators, the Wellcome Trust Case Control Consortium 2, MORGAM, MetaStroke and the International Stroke Genetics Consortium DOI: 10.1002/ana.23838 (2013) <i>Annals of Neurology</i> <b></b>: Mon, 11 Feb 2013 08:18:29 EST http://www.nature.com/ncomms/journal/v4/n2/abs/ncomms2438.html Recent publication citing Helix/Biowulf resources:<br><br><u>Genome-wide profiles of CtBP link metabolism with genome stability and epithelial reprogramming in breast cancer</u><br><br>Li-Jun Di, Jung S. Byun, Madeline M. Wong, Clay Wakano, Tara Taylor, Sven Bilke, Songjoon Baek, Kent Hunter, Howard Yang, Maxwell Lee, Cecilia Zvosec, Galina Khramtsova, Fan Cheng, Charles M. Perou, C. Ryan Miller, Rachel Raab, Olufunmilayo I. Olopade & Kevin Gardner doi:10.1038/ncomms2438 (2013) <i>Nature Communications</i> <b></b>: Mon, 11 Feb 2013 08:28:58 EST http://www.jneurosci.org/content/33/7/2889.short Recent publication citing Helix/Biowulf resources:<br><br><u>The Convergence of Maturational Change and Structural Covariance in Human Cortical Networks</u><br><br>Aaron Alexander-Bloch, Armin Raznahan, Ed Bullmore, and Jay Giedd doi: 10.1523/&#8203;JNEUROSCI.3554-12.2013 (2013) <i>J. Neuroscience </i> <b></b>: Tue, 19 Feb 2013 08:26:54 EST http://jnnp.bmj.com/content/early/2013/02/12/jnnp-2012-304475.abstract Recent publication citing Helix/Biowulf resources:<br><br><u>The Val158Met COMT polymorphism is a modifier of the age at onset in Parkinson's disease with a sexual dimorphism</u><br><br>S Klebe, J-L Golmard, MA Nalls et al, French Parkinson's Disease Genetics Study Group and the International Parkinson's Disease Genomics Consortium doi:10.1136/jnnp-2012-304475 (2013) <i>J Neurol Neurosurg Psychiatry </i> <b></b>: Tue, 19 Feb 2013 08:35:06 EST http://www.pnas.org/content/early/2013/02/01/1218066110.short Recent publication citing Helix/Biowulf resources:<br><br><u>Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly</u><br><br>C Park, X Chen, J-R Yang, J Zhang doi: 10.1073/pnas.1218066110 (2013) <i>PNAS</i> <b></b>: Tue, 19 Feb 2013 10:39:01 EST http://onlinelibrary.wiley.com/doi/10.1002/pmic.201100540/abstract Recent publication citing Helix/Biowulf resources:<br><br><u>Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome</u><br><br>Yu Xu, Hong Wang, Ruth Nussinov, Buyong Ma DOI: 10.1002/pmic.201100540 (2013) <i>Proteomics</i> <b></b>: Mon, 25 Feb 2013 07:56:56 EST http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570896/ Recent publication citing Helix/Biowulf resources:<br><br><u>Control of breathing by interacting pontine and pulmonary feedback loops</u><br><br>Yaroslav I. Molkov, Bartholomew J. Bacak, Thomas E. Dick, and Ilya A. Rybak (2013) <i>Frontiers in Neural Circuits</i> <b>7</b>: 16 Mon, 25 Feb 2013 08:00:24 EST http://pubs.rsc.org/en/content/articlelanding/2013/cp/c3cp00017f Recent publication citing Helix/Biowulf resources:<br><br><u>Alzheimer's disease: Which type of amyloid-preventing drug agents to employ?</u><br><br>Hyunbum Jang , Laura Connelly , Fernando Teran Arce , Srinivasan Ramachandran , Ratnesh Lal , Bruce L Kagan and Ruth Nussinov DOI: 10.1039/C3CP00017F (2013) <i>Phys. Chem. Chem. Phys.</i> <b></b>: Tue, 26 Feb 2013 09:06:20 EST http://pubs.rsc.org/en/content/articlelanding/2013/cp/c3cp00058c Recent publication citing Helix/Biowulf resources:<br><br><u>Electrostatic spectral tuning mechanism of the green fluorescent protein</u><br><br>Ville R. I. Kaila , Robert Send and Dage Sundholm DOI: 10.1039/C3CP00058C (2013) <i>Phys. Chem. Chem. Phys.</i> <b></b>: Tue, 26 Feb 2013 09:08:20 EST http://www.sciencedirect.com/science/article/pii/S1047847713000439 Recent publication citing Helix/Biowulf resources:<br><br><u>Sequence dependence of C-end rule peptides in binding and activation of neuropilin-1 receptor</u><br><br>David Zanuy, Rohith Kotla, Ruth Nussinov, Tambet Teesalu, Kazuki N. Sugahara, Carlos Alem&agrave;n, Nurit Haspel doi://10.1016/j.jsb.2013.02.006 (2013) <i>J. Struct. Biol. </i> <b></b>: Mon, 04 Mar 2013 07:49:13 EST http://onlinelibrary.wiley.com/doi/10.1002/sim.5763/full Recent publication citing Helix/Biowulf resources:<br><br><u>Antedependence models for nonstationary categorical longitudinal data with ignorable missingness likelihood-based inference</u><br><br>Yunlong Xie, Dale Zimmerman DOI: 10.1002/sim.5763 (2013) <i>Statistics in Medicine</i> <b></b>: Mon, 04 Mar 2013 07:51:50 EST http://stroke.ahajournals.org/content/44/3/612.abstract Recent publication citing Helix/Biowulf resources:<br><br><u>Common Variants Within Oxidative Phosphorylation Genes Influence Risk of Ischemic Stroke and Intracerebral Hemorrhage</u><br><br>CD Anderson, A Biffi, MA Nalls, et al. & the International Stroke Genetics Consortium doi: 10.1161/&#8203;STROKEAHA.112.672089 (2013) <i>Stroke</i> <b></b>: Mon, 04 Mar 2013 09:25:07 EST http://hmg.oxfordjournals.org/content/early/2013/02/26/hmg.ddt087.short Recent publication citing Helix/Biowulf resources:<br><br><u>Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network</u><br><br>Z Chen, H Tang, R Qayyum, UM Schick, MA Nalls et al. doi: 10.1093/hmg/ddt087 (2013) <i>Human Molecular Genetics</i> <b></b>: Tue, 05 Mar 2013 09:16:58 EST http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001492 Recent publication citing Helix/Biowulf resources:<br><br><u>The Molecular Mechanism of Substrate Engagement and Immunosuppressant Inhibition of Calcineurin</u><br><br>Simina Grigoriu, Rachel Bond, Pilar Cossio, Jennifer A. Chen, Nina Ly, Gerhard Hummer, Rebecca Page, Martha S. Cyert, Wolfgang Peti doi:10.1371/journal.pbio.1001492 (2013) <i>PLoS Biology</i> <b></b>: Tue, 05 Mar 2013 09:20:19 EST http://link.springer.com/protocol/10.1007/978-1-62703-293-3_12 Recent publication citing Helix/Biowulf resources:<br><br><u>Gene Synthesis by Assembly of Deoxyuridine-Containing Oligonucleotides</u><br><br>Romualdas Vaisvila, Jurate Bitinaite (2013) <i>Methods in Molecular Biology</i> <b>978</b>: 165-171 Thu, 07 Mar 2013 09:03:02 EST http://jvi.asm.org/content/87/5/2767.short Recent publication citing Helix/Biowulf resources:<br><br><u>Both Genome Segments Contribute to the Pathogenicity of Very Virulent Infectious Bursal Disease Virus</u><br><br>Olivier Escaffre, Cyril Le Nou&euml;n, Michel Amelot, Xavier Ambroggio, Kristen M. Ogden, Olivier Guionie, Didier Toquin, Hermann M&uuml;ller, Mohammed R. Islam and Nicolas Eterradossi doi: 10.1128/JVI.02360-12 (2012) <i>J. Virology</i> <b></b>: Fri, 15 Mar 2013 14:48:58 EDT http://www.pnas.org/content/early/2013/02/28/1214913110.short Recent publication citing Helix/Biowulf resources:<br><br><u>Structure and accessibility of HA trimers on intact 2009 H1N1 pandemic influenza virus to stem region-specific neutralizing antibodies</u><br><br>AK Harris, JR Meyerson, Y Matsuoka, O Kuybeda, A Moran, D Bliss, SR Das, JW Yewdell, G Sapiro, K Subbarao, and S Subramaniam doi: 10.1073/pnas.1214913110 (2013) <i>PNAS</i> <b></b>: Fri, 15 Mar 2013 15:01:32 EDT http://link.springer.com/article/10.1007/s10822-012-9623-5 Recent publication citing Helix/Biowulf resources:<br><br><u>Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing</u><br><br>David Zanuy, Francisco J. Sayago, Guillem Revilla-L&ograve;pez, Gema Ballano, Lilach Agemy, Venkata Ramana Kotamraju, Ana I. Jim&egrave;nez, Carlos Cativiela, Ruth Nussinov, April M. Sawvel, Galen Stucky, Erkki Ruoslahti, Carlos Alem&agrave;n doi:10.1007/s10822-012-9623-5 (2013) <i>J. Computer-Aided Mol. Design</i> <b></b>: Mon, 18 Mar 2013 08:42:39 EDT http://www.sciencedirect.com/science/article/pii/S1570963913000873 Recent publication citing Helix/Biowulf resources:<br><br><u>X-Ray crystallographic structural characteristics of Arabidopsis hemoglobin I and their functional implications</u><br><br>Nitika Mukhi, Sonali Dhindwal, Sheetal Uppal, Pravindra Kumar, Jagreet Kaur, Suman Kundu doi://10.1016/j.bbapap.2013.02.024 (2013) <i>Biochim. et Biophys. Acta</i> <b></b>: Mon, 18 Mar 2013 09:21:54 EDT http://www.biomedcentral.com/1471-2164/13/610/ Recent publication citing Helix/Biowulf resources:<br><br><u>Cell population-specific expression analysis of human cerebellum</u><br><br>A Kuhn, A Kumar, A Beilina, A Dillman, MR Cookson, AB Singleton doi:10.1186/1471-2164-13-610 (2012) <i>BMC Genomics</i> <b></b>: Mon, 18 Mar 2013 09:33:00 EDT http://www.nature.com/nsmb/journal/v20/n3/full/nsmb.2517.html#/affil-auth Recent publication citing Helix/Biowulf resources:<br><br><u>Transcription-dependent dynamic supercoiling is a short-range genomic force</u><br><br>Fedor Kouzine, Ashutosh Gupta, Laura Baranello, Damian Wojtowicz, Khadija Ben-Aissa, Juhong Liu, Teresa M Przytycka & David Levens doi:10.1038/nsmb.2517 (2013) <i>Nature Structural & Molecular Biology</i> <b></b>: Mon, 18 Mar 2013 09:38:55 EDT http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588598/ Recent publication citing Helix/Biowulf resources:<br><br><u>An efficient dynamic programming algorithm for phosphorylation site assignment of large-scale mass spectrometry data</u><br><br>Fahad Saeed, Trairak Pisitkun, Jason D. Hoffert, Guanghui Wang, Marjan Gucek, and Mark A. Knepper doi://10.1109/BIBMW.2012.6470210 (2012) <i>Proceedings of IEEE Int Conf Bioinformatics Biomed</i> <b></b>: Tue, 19 Mar 2013 13:30:45 EDT http://www.sciencedirect.com/science/article/pii/S1096495913000304 Recent publication citing Helix/Biowulf resources:<br><br><u>A novel taurocyamine kinase found in the protist Phytophthora infestans</u><br><br>Kouji Uda, Michihiro Hoshijima, Tomohiko Suzuki doi://10.1016/j.cbpb.2013.03.003 (2013) <i>Comp. Biochem. Phys. Part B: Biochem & Mol. Bio. </i> <b></b>: Sun, 17 Mar 2013 13:33:57 EDT http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11716.html Recent publication citing Helix/Biowulf resources:<br><br><u>RNAi triggered by specialized machinery silences developmental genes and retrotransposons</u><br><br>Soichiro Yamanaka, Sameet Mehta, Francisca E. Reyes-Turcu, Fanglei Zhuang, Ryan T. Fuchs, Yikang Rong, Gregory B. Robb & Shiv I. S. Grewal doi:10.1038/nature11716 (2013) <i>Nature</i> <b></b>: Thu, 21 Mar 2013 08:11:53 EDT http://www.nature.com/mtna/journal/v2/n3/abs/mtna20135a.html Recent publication citing Helix/Biowulf resources:<br><br><u>In Silico, In Vitro, and In Vivo Studies Indicate the Potential Use of Bolaamphiphiles for Therapeutic siRNAs Delivery</u><br><br>Taejin Kim, Kirill A. Afonin, Mathias Viard, Alexey Y Koyfman, Selene Sparks, Eliahu Heldman, Sarina Grinberg, Charles Linder, Robert P Blumenthal and Bruce A Shapiro doi:10.1038/mtna.2013.5 (2013) <i>Mol. Therapy - Nuc. Acids</i> <b></b>: Wed, 27 Mar 2013 08:50:53 EDT http://www.biomedcentral.com/content/pdf/1472-6750-13-26.pdf Recent publication citing Helix/Biowulf resources:<br><br><u>The alkaline pectate lyase PEL168 of Bacillus subtilis heterologously expressed in Pichia pastoris is more stable and efficient for degumming ramie fiber</u><br><br>Chengjie Zhang, Jia Yao,Cheng Zhou,Liangwei Mao, Guimin Zhang, Yanhe Ma doi:10.1186/1472-6750-13-26 (2013) <i>BMC Biotechnology</i> <b></b>: Wed, 27 Mar 2013 12:21:20 EDT http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0059285 Recent publication citing Helix/Biowulf resources:<br><br><u>Global Analysis of Neuronal Phosphoproteome Regulation by Chondroitin Sulfate Proteoglycans</u><br><br>Panpan Yu, Trairak Pisitkun, Guanghui Wang, Rong Wang, Yasuhiro Katagiri, Marjan Gucek, Mark A. Knepper, Herbert M. Geller doi:10.1371/journal.pone.0059285 (2013) <i>PLoS One</i> <b></b>: Wed, 27 Mar 2013 12:30:18 EDT http://jcp.aip.org/resource/1/jcpsa6/v138/i17/p174110_s1 Recent publication citing Helix/Biowulf resources:<br><br><u>A simplified representation of anisotropic charge distributions within proteins</u><br><br>Travis Hoppe doi://10.1063/1.4803099 (2013) <i>J. Chem. Phys.</i> <b></b>: Tue, 14 May 2013 14:08:58 EDT http://onlinelibrary.wiley.com/doi/10.1002/bit.24907/abstract Recent publication citing Helix/Biowulf resources:<br><br><u>Effects of pre-existing anti-carrier immunity and antigenic element multiplicity on efficacy of a modular virus-like particle vaccine</u><br><br>Yap P. Chuan, Tania Rivera-Hernandez, Nani Wibowo, Natalie K. Connors, Yang Wu, Fiona K. Hughes, Linda H. L. Lua, Anton P. J. Middelberg DOI: 10.1002/bit.24907 (2013) <i>Biotech. & Bioengg. </i> <b></b>: Tue, 09 Apr 2013 11:38:02 EDT http://pubs.acs.org/doi/abs/10.1021/ci300625c Recent publication citing Helix/Biowulf resources:<br><br><u>Pharmacophore and 3D-QSAR Characterization of 6-arylquinazolin-4-amines as Cdc2-like kinase 4 (Clk4) and Dual Specificity Tyrosine-phosphorylation-regulated Kinase 1A (Dyrk1A) Inhibitors</u><br><br>Yongmei Pan , Yanli Wang, and Stephen H. Bryant DOI: 10.1021/ci300625c (2013) <i>J. Chem. Inf. Model. </i> <b></b>: Tue, 09 Apr 2013 11:41:27 EDT http://onlinelibrary.wiley.com/doi/10.1002/sim.5784/full Recent publication citing Helix/Biowulf resources:<br><br><u>A crossed random effects modeling approach for estimating diagnostic accuracy from ordinal ratings without a gold standard</u><br><br>Yunlong Xie, Zhen Chen, Paul S. Albert DOI: 10.1002/sim.5784 (2013) <i>Statistics in Medicine</i> <b></b>: Tue, 09 Apr 2013 12:47:25 EDT http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3544163/ Recent publication citing Helix/Biowulf resources:<br><br><u>On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in SN2 Reactions</u><br><br>Edina Rosta and Arieh Warshal doi: 10.1021/ct2009329 (2012) <i>J Chem Theory Comput. </i> <b></b>: Tue, 09 Apr 2013 12:55:46 EDT http://www.pnas.org/content/early/2013/04/04/1215770110.short Recent publication citing Helix/Biowulf resources:<br><br><u>Molecular mechanisms for the subversion of MyD88 signaling by TcpC from virulent uropathogenic Escherichia coli</u><br><br>GA Snyder, C Cirl, J Jiang et al doi: 10.1073/pnas.1215770110 (2013) <i>PNAS</i> <b></b>: Mon, 15 Apr 2013 09:18:35 EDT http://biostatistics.oxfordjournals.org/content/early/2013/04/09/biostatistics.kxt008.short Recent publication citing Helix/Biowulf resources:<br><br><u>Controlling the local false discovery rate in the adaptive Lasso</u><br><br>Joshua N Sampson & Nilanjan Chatterjee doi: 10.1093/biostatistics/kxt008 (2013) <i>Biostatistics</i> <b></b>: Mon, 15 Apr 2013 09:21:47 EDT http://ije.oxfordjournals.org/content/42/2/475.short Recent publication citing Helix/Biowulf resources:<br><br><u>Apolipoprotein E genotype, cardiovascular biomarkers and risk of stroke: Systematic review and meta-analysis of 14 015 stroke cases and pooled analysis of primary biomarker data from up to 60 883 individuals</u><br><br>TA Khan, T Shah, D Prieto et al. doi: 10.1093/ije/dyt034 (2013) <i>Int. J. Epidemiol. </i> <b></b>: Mon, 15 Apr 2013 10:04:15 EDT http://link.springer.com/article/10.1007/s10157-013-0789-5 Recent publication citing Helix/Biowulf resources:<br><br><u>Vasopressin and the regulation of aquaporin-2</u><br><br>Justin L. L. Wilson, Carlos A. Miranda, Mark A. Knepper doi://10.1007/s10157-013-0789-5 (2013) <i>Clinical and Experimental Nephrology</i> <b></b>: Fri, 19 Apr 2013 09:09:09 EDT http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623917/ Recent publication citing Helix/Biowulf resources:<br><br><u>Reconciling Mediating and Slaving Roles of Water in Protein Conformational Dynamics</u><br><br>Li Zhao, Wenzhao Li, and Pu Tian doi://10.1371/journal.pone.0060553 (2013) <i>PLoS One</i> <b></b>: Fri, 19 Apr 2013 09:12:44 EDT http://jvi.asm.org/content/early/2013/04/10/JVI.03284-12.short Recent publication citing Helix/Biowulf resources:<br><br><u>HIV-1 envelope glycoprotein trimers display open quaternary conformation when bound to the gp41 MPER-directed broadly neutralizing antibody Z13e1</u><br><br>Audray K. Harris, Alberto Bartesaghi, Jacqueline L. S. Milne and Sriram Subramaniam doi: 10.1128/&#8203;JVI.03284-12 (2013) <i>J. Virology</i> <b></b>: Tue, 23 Apr 2013 08:42:42 EDT http://genome.cshlp.org/content/early/2013/04/16/gr.146654.112.abstract Recent publication citing Helix/Biowulf resources:<br><br><u>CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that are active in vivo</u><br><br>Ishminder K Mann, Raghunath Chatterjee, Jianfei Zhao, Ximiao He, Mathew T Weirauch, Timothy R Hughes and Charles Vinson doi://10.1101/gr.146654.112 (2013) <i>Genome Research</i> <b></b>: Tue, 23 Apr 2013 08:47:20 EDT http://hmg.oxfordjournals.org/content/early/2013/04/17/hmg.ddt181.short Recent publication citing Helix/Biowulf resources:<br><br><u>Genome-wide association study of age at menarche in African-American women</u><br><br>EW Demerath, C-T Liu, N Franceschini et al. doi: 10.1093/hmg/ddt181 (2013) <i>Human Molecular Genetics</i> <b></b>: Mon, 29 Apr 2013 09:34:11 EDT http://biostatistics.oxfordjournals.org/content/early/2013/04/30/biostatistics.kxt016.abstract Recent publication citing Helix/Biowulf resources:<br><br><u>Pointwise confidence intervals for a survival distribution with small samples or heavy censoring</u><br><br>Michael P. Fay, Erica H. Brittain and Michael A. Proschan doi: 10.1093/biostatistics/kxt016 (2013) <i>Biostatistics</i> <b></b>: Mon, 06 May 2013 09:04:05 EDT http://genome.cshlp.org/content/early/2013/04/28/gr.146654.112.abstract Recent publication citing Helix/Biowulf resources:<br><br><u>CG methylated microarrays identify a novel methylated sequence bound by the CEBPB| ATF4 heterodimer that is active in vivo</u><br><br>Ishminder K. Mann, Raghunath Chatterjee, Jianfei Zhao et al. doi:10.1101/gr.146654.112 (2013) <i>Genome Research</i> <b></b>: Tue, 07 May 2013 09:17:36 EDT http://www.sciencedirect.com/science/article/pii/S0022283613002751 Recent publication citing Helix/Biowulf resources:<br><br><u>Three-Dimensional Structure of CAP-Gly Domain of Mammalian Dynactin Determined by Magic Angle Spinning NMR Spectroscopy: Conformational Plasticity and Interactions with End Binding Protein EB1</u><br><br>S. Yan, G. Hou, CD Schwieters, S Ahmed, JC Williams T Polenova doi://10.1016/j.jmb.2013.04.027 (2013) <i>J. Mol. Biol. </i> <b></b>: Tue, 07 May 2013 09:20:37 EDT http://helix.nih.gov/Applications/index.php?update=2012-11-27#PyRosetta Scientific Software Update:<br><br>The PyRosetta package has been updated to version r52071.<br><br>PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions. Tue, 27 Nov 2012 11:46:02 EST http://helix.nih.gov/Applications/index.php?update=2012-11-28#bedtools Scientific Software Update:<br><br>The bedtools package has been updated to version 2.17.0.<br><br>The BEDTools utilities allow one to address common genomics tasks such finding feature overlaps and computing coverage. In addition, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. Wed, 28 Nov 2012 12:06:48 EST http://helix.nih.gov/Applications/index.php?update=2012-11-29#lifescope Scientific Software Update:<br><br>The lifescope package has been updated to version 2.5.1.<br><br>a modular data analysis bioinformatics tool for performing off&#8208;instrument secondary and tertiary analyses on sequence data generated by Life Technologies instruments Thu, 29 Nov 2012 07:52:00 EST http://helix.nih.gov/Applications/index.php?update=2012-11-29#TORTOISE Scientific Software Update:<br><br>The TORTOISE package has been updated to version 1.4.0.<br><br>(Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble) The TORTOISE software package is for processing diffusion MRI data. Thu, 29 Nov 2012 11:02:50 EST http://helix.nih.gov/Applications/index.php?update=2012-12-09#abyss Scientific Software Update:<br><br>The abyss package has been updated to version 1.3.4.<br><br>Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. The parallel version is implemented using MPI and is capable of assembling larger genomes. Sun, 09 Dec 2012 14:41:46 EST http://helix.nih.gov/Applications/index.php?update=2012-12-10#apt Scientific Software Update:<br><br>The apt package has been updated to version 1.15.0.<br><br>apt - Affymetrix Power Tools - is a set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChipR arrays. Mon, 10 Dec 2012 10:50:05 EST http://helix.nih.gov/Applications/index.php?update=2012-12-10#Solar Scientific Software Update:<br><br>The Solar package has been updated to version 6.6.2.<br><br>SOLAR is a program for multipoint, oligogenic, variance component linkage analysis in pedigrees of arbitrary size and complexity (Almasy L; Blangero J, 1998). Mon, 10 Dec 2012 10:50:33 EST http://helix.nih.gov/Applications/index.php?update=2012-12-11#lumpy-sv Scientific Software Update:<br><br>The lumpy-sv package has been updated to version 0.1.<br><br>Lumpy-sv is a software for finding and categorizing structural variation in genome sequencing data Tue, 11 Dec 2012 09:07:07 EST http://helix.nih.gov/Applications/index.php?update=2012-12-12#Bluefish Scientific Software Update:<br><br>The Bluefish package has been updated to version 2.2.3.<br><br>Bluefish is a powerful editor targeted towards programmers and webdesigners, with many options to write websites, scripts and programming code. Wed, 12 Dec 2012 14:16:37 EST http://helix.nih.gov/Applications/index.php?update=2012-12-12#Comsol Scientific Software Update:<br><br>The Comsol package has been updated to version 4.3a.<br><br>The COMSOL Multiphysics engineering simulation software environment facilitates all steps in the modeling process − defining your geometry, meshing, specifying your physics, solving, and then visualizing your results. Wed, 12 Dec 2012 14:21:35 EST http://helix.nih.gov/Applications/index.php?update=2012-12-13#qctool Scientific Software Update:<br><br>The qctool package has been updated to version 1.3.<br><br>QCTOOL is a command-line utility program for basic quality control of gwas datasets. Thu, 13 Dec 2012 11:09:01 EST http://helix.nih.gov/Applications/index.php?update=2012-12-15#vcftools Scientific Software Update:<br><br>The vcftools package has been updated to version 0.1.10.<br><br>VCFtools contains a Perl API (Vcf.pm) and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc. Sat, 15 Dec 2012 20:45:43 EST http://helix.nih.gov/Applications/index.php?update=2012-12-19#fastqc Scientific Software Update:<br><br>The fastqc package has been updated to version 0.10.1.<br><br>It provide quality control functions to next gen sequencing data. Wed, 19 Dec 2012 09:02:01 EST http://helix.nih.gov/Applications/index.php?update=2012-12-19#shrimp Scientific Software Update:<br><br>The shrimp package has been updated to version 2.2.3.<br><br>SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation. Wed, 19 Dec 2012 09:25:03 EST http://helix.nih.gov/Applications/index.php?update=2012-12-26#trans-abyss Scientific Software Update:<br><br>The trans-abyss package has been updated to version 1.4.4.<br><br>Trans-ABySS is a software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. Wed, 26 Dec 2012 13:15:37 EST http://helix.nih.gov/Applications/index.php?update=2012-12-31#STAR Scientific Software Update:<br><br>The STAR package has been updated to version 2.3.0.<br><br>STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Mon, 31 Dec 2012 12:30:16 EST http://helix.nih.gov/Applications/index.php?update=2013-01-02#fusionmap Scientific Software Update:<br><br>The fusionmap package has been updated to version 2012-01-01.<br><br>FusionMap is an efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. Wed, 02 Jan 2013 12:13:32 EST http://helix.nih.gov/Applications/index.php?update=2013-01-08#NestedMICA Scientific Software Update:<br><br>The NestedMICA package has been updated to version 0.8.0.<br><br>NestedMICA is a method for discovering over-represented short motifs in large sets of strings. Typical applications include finding candidate transcription factor binding sites in DNA sequences. Tue, 08 Jan 2013 11:22:11 EST http://helix.nih.gov/Applications/index.php?update=2013-01-08#GAMESS Scientific Software Update:<br><br>The GAMESS package has been updated to version 01May12-R2.<br><br>GAMESS is a general ab initio quantum chemistry package. Tue, 08 Jan 2013 11:59:42 EST http://helix.nih.gov/Applications/index.php?update=2013-01-10#Grace Scientific Software Update:<br><br>The Grace package has been updated to version 5.99.0.<br><br>Grace is a WYSIWYG 2D plotting tool for the X-Window system. It is a successor to Xmgr. Thu, 10 Jan 2013 13:55:35 EST http://helix.nih.gov/Applications/index.php?update=2013-01-14#Meme & Mast Scientific Software Update:<br><br>The Meme & Mast package has been updated to version 4.9.0.<br><br>MEME and MAST are usde to discover motifs in groups of DNA/protein sequences or databases. Mon, 14 Jan 2013 12:25:29 EST http://helix.nih.gov/Applications/index.php?update=2013-01-15#RepeatMasker Scientific Software Update:<br><br>The RepeatMasker package has been updated to version 4.0.0.<br><br>RepeatMasker screens DNA sequences of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions Tue, 15 Jan 2013 08:48:23 EST http://helix.nih.gov/Applications/index.php?update=2013-01-16#consed Scientific Software Update:<br><br>The consed package has been updated to version 23.0.<br><br>Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Wed, 16 Jan 2013 09:19:35 EST http://helix.nih.gov/Applications/index.php?update=2013-01-16#CSD Scientific Software Update:<br><br>The CSD package has been updated to version 5.34.<br><br>The Cambridge Structural Database is the world repository of small molecule crystal structures. Wed, 16 Jan 2013 14:08:00 EST http://helix.nih.gov/Applications/index.php?update=2013-01-28#mira Scientific Software Update:<br><br>The mira package has been updated to version 3.4.1.1.<br><br>MIRA is a Whole Genome Shotgun and EST Sequence Assembler. It is able to perform true hybrid de-novo assemblies and mapping assemblies of data from the 454 and Illumina/Solexa sequencing machines, either on their own or together with Sanger type sequencing data (hybrid mapping assemblies). Mon, 28 Jan 2013 14:21:18 EST http://helix.nih.gov/Applications/index.php?update=2013-01-30#phred Scientific Software Update:<br><br>The phred package has been updated to version 071220.<br><br>Phred reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. Phrap is a program for assembling shotgun DNA sequence data. Cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. Wed, 30 Jan 2013 14:47:12 EST http://helix.nih.gov/Applications/index.php?update=2013-01-30#phrap Scientific Software Update:<br><br>The phrap package has been updated to version 1.090518.<br><br>Phred reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. Phrap is a program for assembling shotgun DNA sequence data. Cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. Wed, 30 Jan 2013 14:47:44 EST http://helix.nih.gov/Applications/index.php?update=2013-02-01#shapeit Scientific Software Update:<br><br>The shapeit package has been updated to version 2.r644.<br><br>SHAPEIT is a fast and accurate haplotype inference software Fri, 01 Feb 2013 15:20:32 EST http://helix.nih.gov/Applications/index.php?update=2013-02-04#BSOFT Scientific Software Update:<br><br>The BSOFT package has been updated to version 1.8.6.<br><br>Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages. Mon, 04 Feb 2013 10:21:47 EST http://helix.nih.gov/Applications/index.php?update=2013-02-04#viennarna Scientific Software Update:<br><br>The viennarna package has been updated to version 2.1.1.<br><br>RNA Secondary Structure Prediction and Comparison Mon, 04 Feb 2013 10:55:00 EST http://helix.nih.gov/Applications/index.php?update=2013-02-04#opticall Scientific Software Update:<br><br>The opticall package has been updated to version 0.6.4.<br><br>optiCall is designed to make accurate genotype calls across the minor allele frequency spectrum. Using intensity information from across multiple individuals and multiple SNPs when calling genotypes, allows it to call both rare and common variants accurately. Mon, 04 Feb 2013 15:04:19 EST http://helix.nih.gov/Applications/index.php?update=2013-02-05#Chimera Scientific Software Update:<br><br>The Chimera package has been updated to version 1.7.0.<br><br>Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. Tue, 05 Feb 2013 13:09:41 EST http://helix.nih.gov/Applications/index.php?update=2013-02-06#Mathematica Scientific Software Update:<br><br>The Mathematica package has been updated to version 9.0.<br><br>Mathematica is an interactive system for doing mathematical computation. It performs numerical, symbolic and graphical computations, and incorporates a high-level programming language. Wed, 06 Feb 2013 12:39:16 EST http://helix.nih.gov/Applications/index.php?update=2013-02-11#ChunkChromosome Scientific Software Update:<br><br>The ChunkChromosome package has been updated to version 2012-08-28.<br><br>ChunkChromosome is a helper utility for minimac and MaCH. It can be used to facilitate analyses of very large datasets in overlapping slices. Mon, 11 Feb 2013 07:55:52 EST http://helix.nih.gov/Applications/index.php?update=2013-02-18#quip Scientific Software Update:<br><br>The quip package has been updated to version 1.1.3.<br><br>Quip compresses next-generation sequencing data with extreme prejudice. It supports input and output in the FASTQ and SAM/BAM formats. Mon, 18 Feb 2013 14:11:53 EST http://helix.nih.gov/Applications/index.php?update=2013-02-19#PARADIGM Scientific Software Update:<br><br>The PARADIGM package has been updated to version 1.0.<br><br>PARADIGM (PAthway Representation and Analysis by DIrect reference on Graphical Models) is a factor graph framework for pathway inference on high-throughput genomic data. Tue, 19 Feb 2013 10:46:22 EST http://helix.nih.gov/Applications/index.php?update=2013-02-21#defuse Scientific Software Update:<br><br>The defuse package has been updated to version 0.6.1.<br><br>deFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion. Thu, 21 Feb 2013 11:22:41 EST http://helix.nih.gov/Applications/index.php?update=2013-02-21#quantisnp Scientific Software Update:<br><br>The quantisnp package has been updated to version 2.<br><br>To detect rare or de novo copy number alterations in normal DNA samples. Thu, 21 Feb 2013 14:57:21 EST http://helix.nih.gov/Applications/index.php?update=2013-02-26#SIFT Scientific Software Update:<br><br>The SIFT package has been updated to version 5.0.3.<br><br>SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. Tue, 26 Feb 2013 14:30:21 EST http://helix.nih.gov/Applications/index.php?update=2013-02-26#rseqc Scientific Software Update:<br><br>The rseqc package has been updated to version 2.3.1.<br><br>comprehensively evaluate RNA-seq datasets generated from clinical tissues or other well annotated organisms such as mouse, fly and yeast. Tue, 26 Feb 2013 14:42:23 EST http://helix.nih.gov/Applications/index.php?update=2013-02-28#mirdeep2 Scientific Software Update:<br><br>The mirdeep2 package has been updated to version 2.0.0.5.<br><br>miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. Thu, 28 Feb 2013 11:28:29 EST http://helix.nih.gov/Applications/index.php?update=2013-03-01#trimmomatic Scientific Software Update:<br><br>The trimmomatic package has been updated to version 0.25.<br><br>Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data. Fri, 01 Mar 2013 09:00:44 EST http://helix.nih.gov/Applications/index.php?update=2013-03-01#bowtie2 Scientific Software Update:<br><br>The bowtie2 package has been updated to version 2.1.0.<br><br>A version of bowtie that's particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes Fri, 01 Mar 2013 13:20:01 EST http://helix.nih.gov/Applications/index.php?update=2013-03-01#rum Scientific Software Update:<br><br>The rum package has been updated to version 2.0.4.<br><br>RUM is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data. Fri, 01 Mar 2013 13:42:55 EST http://helix.nih.gov/Applications/index.php?update=2013-03-04#freebayes Scientific Software Update:<br><br>The freebayes package has been updated to version 0.9.9.<br><br> Mon, 04 Mar 2013 13:03:34 EST http://helix.nih.gov/Applications/index.php?update=2013-03-04#ogap Scientific Software Update:<br><br>The ogap package has been updated to version .<br><br>Realigns alignments meeting specified criteria (number of gaps, mismatches) using Smith-Waterman parameters optimized to open gaps and eliminate mismatches and writes the stream of alignments as BAM on stdout. Mon, 04 Mar 2013 14:00:07 EST http://helix.nih.gov/Applications/index.php?update=2013-03-05#Gaussian Scientific Software Update:<br><br>The Gaussian package has been updated to version g09 C.01.<br><br>Gaussian is a connected system of programs for performing semiempirical and ab initio molecular orbital (MO) calculations. Tue, 05 Mar 2013 12:34:44 EST http://helix.nih.gov/Applications/index.php?update=2013-03-07#ANNOVAR Scientific Software Update:<br><br>The ANNOVAR package has been updated to version 2013-02-21.<br><br>ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes. Thu, 07 Mar 2013 17:14:27 EST http://helix.nih.gov/Applications/index.php?update=2013-03-13#Neuron Scientific Software Update:<br><br>The Neuron package has been updated to version 7.2.<br><br>NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties. Wed, 13 Mar 2013 09:54:56 EDT http://helix.nih.gov/Applications/index.php?update=2013-03-13#soap Scientific Software Update:<br><br>The soap package has been updated to version soap3-dp-2.3.116-cud.<br><br>SOAP is a program package which provides full solution to next generation sequencing data analysis. Wed, 13 Mar 2013 10:59:17 EDT http://helix.nih.gov/Applications/index.php?update=2013-03-13#SciTE Scientific Software Update:<br><br>The SciTE package has been updated to version 3.2.5.<br><br>SciTE or SCIntilla based Text Editor is a cross-platform text editor. Lightweight and built for speed, it is designed mainly for source editing, and performs syntax highlighting and inline function reference for many different languages. Wed, 13 Mar 2013 13:28:40 EDT http://helix.nih.gov/Applications/index.php?update=2013-03-18#fcgene Scientific Software Update:<br><br>The fcgene package has been updated to version 1.0.4.<br><br>FCgene is a Format Converting tool for genotyped Data (e.g.PLINK-MACH,MACH-PLINK) Mon, 18 Mar 2013 11:59:02 EDT http://helix.nih.gov/Applications/index.php?update=2013-03-18#Coot Scientific Software Update:<br><br>The Coot package has been updated to version 0.6.2.<br><br>Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. Mon, 18 Mar 2013 15:21:59 EDT http://helix.nih.gov/Applications/index.php?update=2013-03-18#GCTA Scientific Software Update:<br><br>The GCTA package has been updated to version 1.11.<br><br>GCTA (Genome-wide Complex Trait Analysis) is designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits. Mon, 18 Mar 2013 15:55:56 EDT http://helix.nih.gov/Applications/index.php?update=2013-03-19#Impute Scientific Software Update:<br><br>The Impute package has been updated to version 2.3.0.<br><br>Impute is a program for estimating ("imputing") unobserved genotypes in SNP association studies. Tue, 19 Mar 2013 10:51:16 EDT http://helix.nih.gov/Applications/index.php?update=2013-03-22#muTect Scientific Software Update:<br><br>The muTect package has been updated to version 1.1.4.<br><br>MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. Fri, 22 Mar 2013 11:58:33 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-01#bedops Scientific Software Update:<br><br>The bedops package has been updated to version 2.0.0b.<br><br>A suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets — BEDOPS aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data. Mon, 01 Apr 2013 11:32:20 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-02#sratoolkit Scientific Software Update:<br><br>The sratoolkit package has been updated to version 2.3.1.<br><br>Sequence Read Archive Toolkit Tue, 02 Apr 2013 11:42:38 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-03#LOOS Scientific Software Update:<br><br>The LOOS package has been updated to version 2.0.3b.<br><br>LOOS (Lightweight Object-Oriented Structure library) is a code library for developing new molecular dynamics analysis applications. It also has a large number of stand-alone tools for manipulating and analyzing trajectories and molecules. Wed, 03 Apr 2013 11:25:17 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-03#PartekGS Scientific Software Update:<br><br>The PartekGS package has been updated to version 6.6-LINUX64-6.13.040.<br><br>Partek GS provides rigorous and easy-to-use statistical tests for differential expression of genes or exons, and a flexible and powerful statistical test to detect alternative splicing based on a powerful mixed model analyis of variance. Wed, 03 Apr 2013 13:59:38 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-08#express Scientific Software Update:<br><br>The express package has been updated to version 1.3.1.<br><br>eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Mon, 08 Apr 2013 09:51:45 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-08#bamUtil Scientific Software Update:<br><br>The bamUtil package has been updated to version 1.0.7.<br><br>bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam. Mon, 08 Apr 2013 10:19:57 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-08#BEAST Scientific Software Update:<br><br>The BEAST package has been updated to version 1.7.5.<br><br>BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences. Mon, 08 Apr 2013 16:04:34 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-08#Mach2qtl Scientific Software Update:<br><br>The Mach2qtl package has been updated to version V112.<br><br>QTL analysis based on imputed dosages/posterior_probabilities Mon, 08 Apr 2013 16:04:51 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-08#OpenBabel Scientific Software Update:<br><br>The OpenBabel package has been updated to version 2.3.2.<br><br>Open Babel is a chemical toolbox designed to speak the many languages of chemical data. Mon, 08 Apr 2013 16:05:08 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-09#metAMOS Scientific Software Update:<br><br>The metAMOS package has been updated to version 1.1.<br><br>metAMOS is an integrated assembly and analysis pipeline for metagenomic data. Tue, 09 Apr 2013 11:21:01 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-12#clustalo Scientific Software Update:<br><br>The clustalo package has been updated to version 1.1.0.<br><br>Clustal-Omega is a general purpose multiple sequence alignment (MSA) program for proteins and DNA/RNA. It produces high quality MSAs and is capable of handling data-sets of hundreds of thousands of sequences in reasonable time. Fri, 12 Apr 2013 09:35:53 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-15#cgatools Scientific Software Update:<br><br>The cgatools package has been updated to version 1.7.1.5.<br><br>The Complete Genomics Analysis Tools (cgatools) is an open source project to provide tools for downstream analysis of Complete Genomics data. The general areas of functionality include genome comparison, format conversion, and reference tools. Mon, 15 Apr 2013 11:07:52 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-15#mosaik Scientific Software Update:<br><br>The mosaik package has been updated to version 2.1.73.<br><br>MOSAIK is a reference-guided assembler that can work with FASTA,FASTQ,Illumina Bustard & Gerald, or SRF file formats and outputs phrap ace and GigaBayes gig formats. Mon, 15 Apr 2013 12:23:56 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-15#circos Scientific Software Update:<br><br>The circos package has been updated to version 0.63-4.<br><br>Circos is a software package for visualizing data and information. It visualizes data in a circular layout. It's useful for visualizing genomic data. Mon, 15 Apr 2013 12:52:47 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-15#macs Scientific Software Update:<br><br>The macs package has been updated to version 2.0.10-20130412.<br><br>Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. Mon, 15 Apr 2013 15:04:14 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-16#VarSifter Scientific Software Update:<br><br>The VarSifter package has been updated to version 1.6.<br><br>VarSifter is a graphical Java program designed to display, sort, filter, and generally sift variation data from massively parallel sequencing experiments. It is designed to read exome-scale variation data in either a tab-delimited text file with header, or an uncompressed VCF file. Tue, 16 Apr 2013 08:10:03 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-17#cufflinks Scientific Software Update:<br><br>The cufflinks package has been updated to version 2.1.1.<br><br>Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. Wed, 17 Apr 2013 09:19:11 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-17#tophat Scientific Software Update:<br><br>The tophat package has been updated to version 2.0.8b.<br><br>TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. Wed, 17 Apr 2013 11:58:02 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-17#biotoolbox Scientific Software Update:<br><br>The biotoolbox package has been updated to version 1.10.2.<br><br>A collection of various Perl scripts that utilize BioPerl modules for use in bioinformatics analysis. Tools are included for processing microarray data, next generation sequencing data, data file format conversion, querying datasets, and general high level analysis of datasets. Wed, 17 Apr 2013 12:30:55 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-18#IGV Scientific Software Update:<br><br>The IGV package has been updated to version 2.3.0.<br><br>The Integrative Genomics Viewer is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. Thu, 18 Apr 2013 11:04:40 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-18#IGVTools Scientific Software Update:<br><br>The IGVTools package has been updated to version 2.2.2.<br><br>IGVTools provides utilities for working with ascii file formats used by the Integrated Genome Viewer. The files can be sorted, tiled, indexed, and counted. Thu, 18 Apr 2013 11:04:51 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-18#breakdancer Scientific Software Update:<br><br>The breakdancer package has been updated to version 1.1.2.<br><br>provides genome-wide detection of structural variants from next generation paired-end sequencing reads. Thu, 18 Apr 2013 11:42:11 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-19#cutadapt Scientific Software Update:<br><br>The cutadapt package has been updated to version 1.2.1.<br><br>cutadapt removes adapter sequences from DNA high-throughput sequencing data. This is usually necessary when the read length of the machine is longer than the molecule that is sequenced, such as in microRNA data. Fri, 19 Apr 2013 09:45:08 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-19#bamtools Scientific Software Update:<br><br>The bamtools package has been updated to version 2.2.3.<br><br>BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files. Fri, 19 Apr 2013 12:25:07 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-19#Huygens Scientific Software Update:<br><br>The Huygens package has been updated to version 4.3.1-p2.<br><br>Huygens is an image restoration, deconvolution, resolution and noise reduction. It can process images from all current optical microscopes, including wide-field, confocal, Nipkow (scanning disk confocal), multiple-photon, and 4Pi microscopes. Fri, 19 Apr 2013 17:11:19 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-23#homer Scientific Software Update:<br><br>The homer package has been updated to version 4.2.<br><br>HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. Tue, 23 Apr 2013 12:15:32 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-23#ssaha2 Scientific Software Update:<br><br>The ssaha2 package has been updated to version 2.5.5.<br><br>SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package. Tue, 23 Apr 2013 12:56:23 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-24#bwa Scientific Software Update:<br><br>The bwa package has been updated to version 0.7.4.<br><br>BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. Wed, 24 Apr 2013 07:46:35 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-24#Genome Browser Scientific Software Update:<br><br>The Genome Browser package has been updated to version 282.<br><br>The Genome Browser Mirror Fragments at Helix Systems is a mirror of the UCSC Genome Browser. The URL is http://genome.cit.nih.gov. Users can also access the MySQL databases and supporting files directly. Wed, 24 Apr 2013 09:55:27 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-26#somaticsniper Scientific Software Update:<br><br>The somaticsniper package has been updated to version 1.0.2.2-1.<br><br>identify single nucleotide positions that are di&#64256;erent between tumor and normal Fri, 26 Apr 2013 09:37:03 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-29#Random Jungle Scientific Software Update:<br><br>The Random Jungle package has been updated to version 2.0.0.<br><br>Random Jungle is a fast implementation of RandomForest that can be used for analyzing big Genome Wide Association data. Mon, 29 Apr 2013 08:26:06 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-29#AFNI Scientific Software Update:<br><br>The AFNI package has been updated to version 7-Feb-2013.<br><br>AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. Mon, 29 Apr 2013 08:50:28 EDT http://helix.nih.gov/Applications/index.php?update=2013-04-29#bowtie Scientific Software Update:<br><br>The bowtie package has been updated to version 1.0.0.<br><br>bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. Mon, 29 Apr 2013 09:43:38 EDT http://helix.nih.gov/Applications/index.php?update=2013-05-01#R Scientific Software Update:<br><br>The R package has been updated to version 3.0.0.<br><br>R (the R Project) is a language and environment for statistical computing and graphics. R is similar to S, and provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, ...). Wed, 01 May 2013 10:20:27 EDT http://helix.nih.gov/Applications/index.php?update=2013-05-06#CCP4 Scientific Software Update:<br><br>The CCP4 package has been updated to version 6.3.0.1.<br><br>CCP4 is a suite of programs for protein crystallography and structural biology. Mon, 06 May 2013 17:15:05 EDT http://helix.nih.gov/Applications/index.php?update=2013-05-06#QIIME Scientific Software Update:<br><br>The QIIME package has been updated to version 1.6.0.<br><br>QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). Mon, 06 May 2013 17:18:09 EDT http://helix.nih.gov/Applications/index.php?update=2013-05-07#gmap-gsnap Scientific Software Update:<br><br>The gmap-gsnap package has been updated to version 2013-04-30.<br><br> Tue, 07 May 2013 12:00:00 EDT http://helix.nih.gov/Applications/index.php?update=2013-05-08#Phenix Scientific Software Update:<br><br>The Phenix package has been updated to version 1.8.2-1309.<br><br>PHENIX is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods. Wed, 08 May 2013 13:05:04 EDT http://helix.nih.gov/Applications/index.php?update=2013-05-08#ranseqc Scientific Software Update:<br><br>The ranseqc package has been updated to version 1.1.7.<br><br> Wed, 08 May 2013 13:27:34 EDT http://helix.nih.gov/Applications/index.php?update=2013-05-08#LibreOffice (OpenOffice) Scientific Software Update:<br><br>The LibreOffice (OpenOffice) package has been updated to version 4.0.2.2.<br><br>OpenOffice is the leading open-source office software suite for word processing, spreadsheets, presentations, graphics, databases and more. Wed, 08 May 2013 15:48:23 EDT http://helix.nih.gov/Applications/index.php?update=2013-05-09#GROMACS Scientific Software Update:<br><br>The GROMACS package has been updated to version 4.6.1.<br><br>GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. Thu, 09 May 2013 08:16:04 EDT http://helix.nih.gov/Applications/index.php?update=2013-05-14#samtools Scientific Software Update:<br><br>The samtools package has been updated to version 0.1.19.<br><br>SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Tue, 14 May 2013 10:21:47 EDT http://helix.nih.gov/Applications/index.php?update=2013-05-14#novocraft Scientific Software Update:<br><br>The novocraft package has been updated to version 3.00.04.<br><br>Package includes aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties. Tue, 14 May 2013 10:32:36 EDT http://helix.nih.gov/Applications/index.php?update=2013-05-14#ngsplot Scientific Software Update:<br><br>The ngsplot package has been updated to version 1.68.<br><br>ngsplot is an easy-to-use global visualization tool for next-generation sequencing data. Tue, 14 May 2013 11:13:33 EDT http://helix.nih.gov/Applications/index.php?update=2013-05-17#snpEff Scientific Software Update:<br><br>The snpEff package has been updated to version 3.2a.<br><br>snpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes). Fri, 17 May 2013 11:38:06 EDT