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Downloads and Upgrades: JMP Genomics and JMP Clinical; Biopython 1.60; Reactome 41; and More

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The SAS Institute is releasing new versions of its JMP Genomics and JMP Clinical software.

JMP Genomics 6, released earlier this month, provides a genomic analysis toolkit that runs on the JMP 10 platform. It features enhanced routines for importing and normalizing data; new algorithms for rare variant analysis; RNA-seq workflow capabilities that boost downstream analysis of data from next-gen studies; and tools to improve agronomic crops, such as a new Basic Linkage Mapping workflow that simplifies genetic linkage map construction.

JMP Clinical 4, which is scheduled for release in early August, includes workflows, templates, and reporting tools intended to make it easier for clinicians without statistical training or programming experience to analyze safety and efficacy data from clinical trials.

The developers further claim that the tool will promote collaboration between clinicians and biostatisticians through a simplified interface for sharing ad hoc reviews, safety workflows, and more via e-mail, shared folders, or clinical data repositories. Finally, it can be used to generate configurable patient profiles and patient narratives for the Clinical Study Report required by the US Food and Drug Administration.


Biopython 1.60 is now available.

In addition to bug fixes, the release includes a new module that supports the reading and writing of files in the Blocked GNU Zip Format.

Additionally, its GenBank/EMBL parser now gives a warning on unrecognized feature locations and continues parsing where previously it would abort with an exception; and in the Phylo module, the "draw" function for plotting tree objects has become much more flexible and includes improved support for matplotlib conventions and new parameters for specifying branch and taxon labels among other updates.


The genome bioinformatics group at the University of California, Santa Cruz, has released a new browser for the dog genome assembly, Canis familiaris produced by the Broad Institute.


Oracle has released a new version of the Oracle Health Sciences Translational Research Center, a tool that supports secondary use of electronic health records, administrative, and omics data in biomarker identification studies for drug discovery, clinical development, and translational research.

The newest version of the tool includes updated query capabilities that improve users' ability to search for phenotype and genotype attributes in order to identify target patient populations. Users can also create gene-centric searches, which lets them pull out 'omics data for particular gene sets of interest within larger datasets.

Other updates include improved genomic visualization tools; and new pre-built adapters for RNA sequencing, SIFT, and Polyphen data sets


Reactome 41 is available here.

The release a new topic; cellular response to stress. Topics with new or revised events include the immune system, metabolism, signal transduction, extracellular matrix organization, and gene expression. New disease pathways include abnormal metabolism in phenylketonuria; latent infection of Homo sapiens with Mycobacterium tuberculosis; and signaling by FGFR in disease.


This week, Sophic launched the first version of its cancer biomarker knowledge environment SCan-MarK Explorer.

The new software-as-a-service tool combines a database of manually curated breast, ovarian, colon, non-Hodgkin’s lymphoma, and melanoma biomarker targets with BioXM, an integrated knowledge management system that uses data models, ontologies, thesauri, and vocabularies to help scientists find and map biomarker knowledge networks. The interface lets researchers visualize networks of valid semantic and scientific relationships that connect cancer biomarker objects, pathways, near-neighbors, analyzed sequence data, mutations, and drug compound information.


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The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.