general-use format for representing biological sample by observation contingency
tables. BIOM is a recognized standard for the Earth Microbiome Project and is a
Genomics Standards Consortium supported project.
The BIOM format is designed for general use in broad areas of comparative
-omics. For example, in marker-gene surveys, the primary use of this format is
to represent OTU tables: the observations in this case are OTUs and the matrix
contains counts corresponding to the number of times each OTU is observed in
each sample. With respect to metagenome data, this format would be used to
represent metagenome tables: the observations in this case might correspond to
SEED subsystems, and the matrix would contain counts corresponding to the number
of times each subsystem is observed in each metagenome. Similarly, with respect
to genome data, this format may be used to represent a set of genomes: the
observations in this case again might correspond to SEED subsystems, and the
counts would correspond to the number of times each subsystem is observed in
each genome.
WWW: http://biom-format.org/
PR: 209193
Submitted by: Joseph Mingrone
- Update to version 2.3.0
- Including RCE vulnerability fix
- Version includes previously added patches
Security: CVE-2016-1541
Approved by: feld (mentor, ports-secteam)
MFH: 2016Q2
Thick database bindings for MySQL, PostgreSQL and SQLite written in Ada.
This is the first release of AdaBase, an abstraction library that provides
a consistent interface to multiple database servers. Currently only one
driver for MySQL is provided, but additional ones for SQLite and
PostgreSQL are planned for the near term. It's extensible, so support
for others such as Firebird, Oracle and MSSQL would be easily possible.
AdaBase offers unique features over similar frameworks. For starters,
it's limited to database support rather than including many other unwanted
components in a "kitchen sink" fashion, and unneeded drivers can be
excluded from the library as desired. It's got a developer and commerce
friend license (ICS), it comes with good documentation and working
examples, and the bindings are thick enough where database server backends
can be interchangeable.
AdaBase may seem familiar to some users as it was partially inspired by
PHP's PDO database framework and is a sequel of sorts to an earlier
project by the same author, Pascal Data Objects.
WWW: http://jrmarino.github.io/AdaBase/
MLVPN allow to bond your internet links to increase bandwidth, secure your
internet connection by actively monitoring your links and removing the faulty
ones, without loosing your TCP connections and secure your internet connection
to the aggregation server using cryptography.
WWW: https://zehome.github.io/MLVPN/
Approved by: mat
Differential Revision: https://reviews.freebsd.org/D6034
This fix was added in r408318, but now this change is redundant after this
argument is defined by default in ports Templates/config.site (r414724).
Approved by: just-fix-it (continuation of r408318)
Zip-ada moved to version 50_f1 using a PORTREVISION bump and portscout
doesn't know how to deal with it. Just ignore the version to clear the
false positive.
