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  1. Content type: Software review

    The Portable Document Format (PDF) is the most commonly used file format for online scientific publications. The absence of effective means to extract text from these PDF files in a layout-aware manner present...

    Authors: Cartic Ramakrishnan, Abhishek Patnia, Eduard Hovy and Gully APC Burns

    Citation: Source Code for Biology and Medicine 2012 7:7

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  2. Content type: Software review

    In scientific computing, Fortran was the dominant implementation language throughout most of the second part of the 20th century. The many tools accumulated during this time have been difficult to integrate wi...

    Authors: Ralf W Grosse-Kunstleve, Thomas C Terwilliger, Nicholas K Sauter and Paul D Adams

    Citation: Source Code for Biology and Medicine 2012 7:5

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  3. Content type: Software review

    The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, used in a wide range of genetic analyses. The SAMtools utilities...

    Authors: Ricardo H Ramirez-Gonzalez, Raoul Bonnal, Mario Caccamo and Daniel MacLean

    Citation: Source Code for Biology and Medicine 2012 7:6

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  4. Content type: Software review

    The assembly of next-generation short-read sequencing data can result in a fragmented non-contiguous set of genomic sequences. Therefore a common step in a genome project is to join neighbouring sequence regio...

    Authors: Michael D Barton and Hazel A Barton

    Citation: Source Code for Biology and Medicine 2012 7:4

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  5. Content type: Editorial

    Authors: Cameron Neylon, Jan Aerts, C Titus Brown, Simon J Coles, Les Hatton, Daniel Lemire, K Jarrod Millman, Peter Murray-Rust, Fernando Perez, Neil Saunders, Nigam Shah, Arfon Smith, Gaël Varoquaux and Egon Willighagen

    Citation: Source Code for Biology and Medicine 2012 7:2

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  6. Content type: Research

    There is a significant demand for creating pipelines or workflows in the life science discipline that chain a number of discrete compute and data intensive analysis tasks into sophisticated analysis procedures...

    Authors: Adam A Hunter, Andrew B Macgregor, Tamas O Szabo, Crispin A Wellington and Matthew I Bellgard

    Citation: Source Code for Biology and Medicine 2012 7:1

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  7. Content type: Software review

    Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are face...

    Authors: Caroline Baroukh, Sherry L Jenkins, Ruth Dannenfelser and Avi Ma'ayan

    Citation: Source Code for Biology and Medicine 2011 6:15

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  8. Content type: Software review

    With ever-increasing numbers of microbial genomes being sequenced, efficient tools are needed to perform strain-level identification of any newly sequenced genome. Here, we present the SNP identification for s...

    Authors: Ravi Vijaya Satya, Nela Zavaljevski and Jaques Reifman

    Citation: Source Code for Biology and Medicine 2011 6:14

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  9. Content type: Software review

    Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata....

    Authors: Marc E Colosimo, Matthew W Peterson, Scott Mardis and Lynette Hirschman

    Citation: Source Code for Biology and Medicine 2011 6:13

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  10. Content type: Software review

    We previously developed the DBRF-MEGN (d ifference-b ased r egulation f inding-m inimum e quivalent g ene n etwork) method, which deduces the most parsimonious signed directed graphs (SDGs) consistent with expres...

    Authors: Koji Kyoda, Kotaro Baba, Hiroaki Kitano and Shuichi Onami

    Citation: Source Code for Biology and Medicine 2011 6:12

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  11. Content type: Software review

    Recent developments in sequencing technologies have given the opportunity to sequence many bacterial genomes with limited cost and labor, compared to previous techniques. However, a limiting step of genome seq...

    Authors: Marco Galardini, Emanuele G Biondi, Marco Bazzicalupo and Alessio Mengoni

    Citation: Source Code for Biology and Medicine 2011 6:11

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  12. Content type: Software review

    Use of missing genotype imputations and haplotype reconstructions are valuable in genome-wide association studies (GWASs). By modeling the patterns of linkage disequilibrium in a reference panel, genotypes not...

    Authors: Kazuharu Misawa and Naoyuki Kamatani

    Citation: Source Code for Biology and Medicine 2011 6:10

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  13. Content type: Software review

    Laboratory Information Management Systems (LIMS) are an increasingly important part of modern laboratory infrastructure. As typically very sophisticated software products, LIMS often require considerable resou...

    Authors: Timothy G Bath, Selcuk Bozdag, Vackar Afzal and Daniel Crowther

    Citation: Source Code for Biology and Medicine 2011 6:9

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  14. Content type: Software review

    Creating a user friendly web based application which executes an R script allows physicians, epidemiologists, and others unfamiliar with the statistical language to perform powerful statistical analyses easily...

    Authors: Richard Newton, Andrew Deonarine and Lorenz Wernisch

    Citation: Source Code for Biology and Medicine 2011 6:6

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  15. Content type: Brief reports

    With the advent of high throughput genomics and high-resolution imaging techniques, there is a growing necessity in biology and medicine for parallel computing, and with the low cost of computing, it is now co...

    Authors: Kenneth S Kompass, Thomas J Hoffmann and John S Witte

    Citation: Source Code for Biology and Medicine 2011 6:4

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  16. Content type: Brief reports

    Cluster analysis methods have been extensively researched, but the adoption of new methods is often hindered by technical barriers in their implementation and use. WebGimm is a free cluster analysis web-servic...

    Authors: Vineet K Joshi, Johannes M Freudenberg, Zhen Hu and Mario Medvedovic

    Citation: Source Code for Biology and Medicine 2011 6:3

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  17. Content type: Software review

    Next Generation Sequencing (NGS) technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a refere...

    Authors: Guorong Xu, Nan Deng, Zhiyu Zhao, Thair Judeh, Erik Flemington and Dongxiao Zhu

    Citation: Source Code for Biology and Medicine 2011 6:2

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  18. Content type: Software review

    Protein-protein interactions are crucially important for cellular processes. Knowledge of these interactions improves the understanding of cell cycle, metabolism, signaling, transport, and secretion. Informati...

    Authors: Chandra Sekhar Pedamallu and Janos Posfai

    Citation: Source Code for Biology and Medicine 2010 5:8

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  19. Content type: Brief reports

    Gaggle Tool Creator (GTC) is a web application which provides access to public annotation, interaction, orthology, and genomic data for hundreds of organisms, and enables instant analysis of the data using man...

    Authors: Dan Tenenbaum, J Christopher Bare and Nitin S Baliga

    Citation: Source Code for Biology and Medicine 2010 5:7

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  20. Content type: Software review

    The use of haplotype-based association tests can improve the power of genome-wide association studies. Since the observed genotypes are unordered pairs of alleles, haplotype phase must be inferred. However, es...

    Authors: Kazuharu Misawa and Naoyuki Kamatani

    Citation: Source Code for Biology and Medicine 2010 5:5

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  21. Content type: Methodology

    Michigan's Department of Community Health (MDCH) is responsible for managing hospitals through the utilization of a Certificate of Need (CON) Commission. Regulation is achieved by limiting the number of beds a...

    Authors: Shaun A Langley, Steven P Fuller, Joseph P Messina, Ashton M Shortridge and Sue C Grady

    Citation: Source Code for Biology and Medicine 2010 5:4

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  22. Content type: Software review

    Meta-analysis is a major theme in biomedical research. In the present paper we introduce a package for R and Bioconductor that provides useful tools for performing this type of work. One idea behind the develo...

    Authors: Karl G Kugler, Laurin AJ Mueller and Armin Graber

    Citation: Source Code for Biology and Medicine 2010 5:3

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  23. Content type: Software review

    The manual counting of cells by microscopy is a commonly used technique across biological disciplines. Traditionally, hand tally counters have been used to track event counts. Although this method is adequate,...

    Authors: Charles C Kim and Joseph L DeRisi

    Citation: Source Code for Biology and Medicine 2010 5:1

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  24. Content type: Methodology

    Visualization tools allow researchers to obtain a global view of the interrelationships between the probes or experiments of a gene expression (e.g. microarray) data set. Some existing methods include hierarchica...

    Authors: Raymond Wan, Larisa Kiseleva, Hajime Harada, Hiroshi Mamitsuka and Paul Horton

    Citation: Source Code for Biology and Medicine 2009 4:8

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  25. Content type: Software review

    Since more than a million single-nucleotide polymorphisms (SNPs) are analyzed in any given genome-wide association study (GWAS), performing multiple comparisons can be problematic. To cope with multiple-compar...

    Authors: Kazuharu Misawa and Naoyuki Kamatani

    Citation: Source Code for Biology and Medicine 2009 4:7

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  26. Content type: Software review

    Due to the advanced techniques in sequencing and fragment analysis, DNA sequencers and analyzers produce vast amounts of data within short time. To administrate the large data volume conveniently, efficient da...

    Authors: Justina Krawczyk, Alexander Goesmann, Ralf Nolte, Martin Werber and Bernd Weisshaar

    Citation: Source Code for Biology and Medicine 2009 4:4

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  27. Content type: Methodology

    In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitemen...

    Authors: Jeremy N Block, David J Zielinski, Vincent B Chen, Ian W Davis, E Claire Vinson, Rachael Brady, Jane S Richardson and David C Richardson

    Citation: Source Code for Biology and Medicine 2009 4:3

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  28. Content type: Methodology

    Information about protein interaction networks is fundamental to understanding protein function and cellular processes. Interaction patterns among proteins can suggest new drug targets and aid in the design of...

    Authors: Fiona Browne, Haiying Wang, Huiru Zheng and Francisco Azuaje

    Citation: Source Code for Biology and Medicine 2009 4:2

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  29. Content type: Software review

    Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region for use in BLAST-based similarity searches in th...

    Authors: R Henrik Nilsson, Gunilla Bok, Martin Ryberg, Erik Kristiansson and Nils Hallenberg

    Citation: Source Code for Biology and Medicine 2009 4:1

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  30. Content type: Research

    The main problem in many model-building situations is to choose from a large set of covariates those that should be included in the "best" model. A decision to keep a variable in the model might be based on th...

    Authors: Zoran Bursac, C Heath Gauss, David Keith Williams and David W Hosmer

    Citation: Source Code for Biology and Medicine 2008 3:17

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  31. Content type: Methodology

    Modern life sciences research increasingly relies on computational solutions, from large scale data analyses to theoretical modeling. Within the theoretical models Boolean networks occupy an increasing role as...

    Authors: István Albert, Juilee Thakar, Song Li, Ranran Zhang and Réka Albert

    Citation: Source Code for Biology and Medicine 2008 3:16

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  32. Content type: Software review

    Genomics and proteomics analyses regularly involve the simultaneous test of hundreds of hypotheses, either on numerical or categorical data. To correct for the occurrence of false positives, validation tests b...

    Authors: Anyela Camargo, Francisco Azuaje, Haiying Wang and Huiru Zheng

    Citation: Source Code for Biology and Medicine 2008 3:15

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  33. Content type: Software review

    Microarrays are becoming a very popular tool for microbial detection and diagnostics. Although these diagnostic arrays are much simpler when compared to the traditional transcriptome arrays, due to the high th...

    Authors: Joy Scaria, Aswathy Sreedharan and Yung-Fu Chang

    Citation: Source Code for Biology and Medicine 2008 3:14

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  34. Content type: Research

    Biological imaging is an emerging field, covering a wide range of applications in biological and clinical research. However, while machinery for automated experimenting and data acquisition has been developing...

    Authors: Lior Shamir, Nikita Orlov, D Mark Eckley, Tomasz Macura, Josiah Johnston and Ilya G Goldberg

    Citation: Source Code for Biology and Medicine 2008 3:13

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  35. Content type: Methodology

    CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous ...

    Authors: Alexei A Podtelezhnikov and David L Wild

    Citation: Source Code for Biology and Medicine 2008 3:12

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  36. Content type: Software review

    Ultrasound scanning uses the medical imaging format, DICOM, for electronically storing the images and data associated with a particular scan. Large health care facilities typically use a picture archiving and ...

    Authors: Will Stott, Andy Ryan, Ian J Jacobs, Usha Menon, Conrad Bessant and Christopher Jones

    Citation: Source Code for Biology and Medicine 2008 3:11

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  37. Content type: Software review

    Flow is an open source software application for clinical and experimental researchers to perform exploratory data analysis, clustering and annotation of flow cytometric data. Flow is an extensible system that off...

    Authors: Jacob Frelinger, Thomas B Kepler and Cliburn Chan

    Citation: Source Code for Biology and Medicine 2008 3:10

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  38. Content type: Brief reports

    FASH (Fourier Alignment Sequence Heuristics) is a web application, based on the Fast Fourier Transform, for finding remote homologs within a long nucleic acid sequence. Given a query sequence and a long text-s...

    Authors: Isana Veksler-Lublinksy, Danny Barash, Chai Avisar, Einav Troim, Paul Chew and Klara Kedem

    Citation: Source Code for Biology and Medicine 2008 3:9

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  39. Content type: Brief reports

    Here we report the improved results of a new siRNA design program and analysis tool called siRNA_profile that reveals an additional criterion for bioinformatic search of highly functional siRNA sequences.

    Authors: Pirkko Muhonen, Ranga N Parthasarathy, Anthony J Janckila, Kalman G Büki and H Kalervo Väänänen

    Citation: Source Code for Biology and Medicine 2008 3:8

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  40. Content type: Research

    As the demands for competency-based education grow, the need for standards-based tools to allow for publishing and discovery of competency-based learning content is more pressing. This project focused on devel...

    Authors: Ravi Teja Bhupatiraju, William R Hersh, Valerie Smothers, Michael Fordis and Peter S Greene

    Citation: Source Code for Biology and Medicine 2008 3:7

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