New in 9.11:
Because the program uses the approximation of 4 calories per gram
for carbohydrate and protein to analyze meals according to the
"Daily Value" -- although real food has various values for calories
per gram -- the program now refigures fat percentage values at each
analysis so that when calories, carbs, and protein are each at
exactly 100%, fat will be also.
New in 9.10:
This release fixes a buffer overflow in the food selection function
which caused the program to not find certain foods even though they
existed in the database.
New in 9.9:
A bug has been fixed in which during food selection, the program
lost the value of the food name key. Also, some of the program's
reference values for the essential fatty acids have been modified.
New in 9.8:
The program now defaults to either grams or ounces, depending on
the weight unit the user enters to specify servings. A bug in
handling customary meal names that are too long has been fixed.
New in 9.7:
The program computes essential fatty acid reference values based
on the user's diet. Prior releases aimed toward a particular balance
of Omega-6 and Omega-3. This release allows the user to specify
the balance between Omega-6 and Omega-3 without having to determine
the amount of the individual fatty acids.
New in 9.6:
The program is now capable of understanding food names in simple
English, such as "fried chicken" and "mashed potatoes." This is
accomplished by including the list of abbreviations the USDA uses
and by successively searching for each tokenized term, whatever
the order in the USDA name.
9.5:
The last release introduced a bug when adding customary meals to
regular meals. The program now adds the foods without the additional
prompt screen.
9.4:
This release changes the method of searching for foods to a substring
search. The narrowing-down of food categories to a unique food is
the same as in prior releases.
This release fixes a bug in the graphs where the "Daily Value" was
such a small percentage of the values graphed that the DV line
indicator exceeded the graph width.
gcc3. While here, update to version 2.12 (previous version was erraneously
named 2.1, when it should have been 2.10) which is the only distfile
available on the ftp site.
Changelog seems to say:
- Fix bug on long-orfs.cc to avoid occasional array out-of-bounds
error (detected on Mac OS X).
9.2:
The upper limit of the polyunsaturated reference value for linoleic
acid has been reduced to 4% of calories, while that for alpha
linolenic acid has been raised to 2%. An internal constant for the
percentage of total fat that is fatty acids has been replaced by
a function that figures it for each analysis.
9.1:
The program is no longer limited to three meals a day, and can now
be set for 1 to 19 meals per day. A list of the meals not yet
recorded for a selected day is displayed as a mnemonic during the
"Record Meals" function.
brook at biology dot nmsu dot edu and his team at NMSU.
XYLEM is a package of tools designed to exploit the Unix environment to enable
the user to identify, extract and manipulate data from major databases such as
GenBank, EMBL and PIR.
brook at biology dot nmsu dot edu and his team at NMSU.
Glimmer (Gene Locator and Interpolated Markov Modeler) is a system for finding
genes in microbial DNA, especially the genomes of bacteria and archaea.
Glimmer uses interpolated Markov models (IMMs) to identify the coding regions
and distinguish them from noncoding DNA. The IMM approach uses a combination
of Markov models from 1st through 8th-order, weighting each model according to
its predictive power.
brook at biology dot nmsu dot edu and his team at NMSU.
GeneSplicer is a fast, flexible system for detecting splice sites in the
genomic DNA of various eukaryotes. The system has been trained and tested
successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human,
Drosophila, and rice.
brook at biology dot nmsu dot edu and his team at NMSU.
FLUCTUATE fits the model which has a single population which has been
growing (or shrinking) according to an exponential growth law. It
estimates 4Nu and g, where N is the effective population size, u is
the neutral mutation rate per site, and g is the growth rate of the
population.
brook at biology dot nmsu dot edu and his team at NMSU.
COALESCE fits the model which has a single population of constant size, and
estimates 4Nu, where N is the effective population size and u is the neutral
mutation rate per site.
brook at biology dot nmsu dot edu and his team at NMSU.
SeWeR is SEquence Analysis using WEb Resources. It has web based Sequence
Analysis. SeWeR is an integrated portal to common web-based services in
bioinformatics.
brook at biology dot nmsu dot edu and his team at NMSU.
ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate
program for performing least squares fits of two protein structures. It
performs a very simple and basic function, but allows as much flexibility as
possible in performing this procedure. Thus one can specify subsets of atoms
to be considered, specify zones to be fitted by number, sequence, or by
sequence alignment.
brook at biology dot nmsu dot edu and his team at NMSU.
Mummer is a system for aligning whole genome sequences. Using an efficient
data structure called a suffix tree, the system is able rapidly to align
sequences containing millions of nucleotides whether in complete or draft
form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s
of contigs from a shotgun sequencing project with ease, and will align them to
another set of contigs or a genome using the NUCmer program included with the
system.
brook at biology dot nmsu dot edu and his team at NMSU.
HMMER is an implementation of profile HMM methods for sensitive database
searches using multiple sequence alignments as queries. HMMER takes
multiple sequence alignement as input and builds statistical model
called "Hidden Markov Model" which can be used as a query into a
sequence database to find and/or align additional homologues of the
sequence family.
brook at biology dot nmsu dot edu and his team at NMSU.
GP is a set of small utilities written in ANSI C to manipulate
DNA sequences in a Unix fashion, fit for combining within shell
and cgi scripts.
Given a GCG multiple sequence alignment file (a GCG MSF file), which a
includes a sequence of known structure, the program pdbalign maps the
sequence variability onto the known structure. The central premise is
of course, that for a closely related family of proteins (sequence ID
> 40%) the 3-D structures will not be significantly different.pdbdist
calculates the distance from each atom in the pdb file to each atom in
the ligand and records the minimum in the temperature field for that
atom record.distalign reads the output from pdbdist and also the
original GCG MSF file and produces an MSF file annotated with a
measure of sequence variability and the distance of the residue at
that position (of the sequence of known structure) from the ligand.
brook at biology dot nmsu dot edu and his team at NMSU.
Given a GCG multiple sequence alignment file (a GCG MSF file), which a
includes a sequence of known structure, the program pdbalign maps the
sequence variability onto the known structure. The central premise is
of course, that for a closely related family of proteins (sequence ID
> 40%) the 3-D structures will not be significantly different.pdbdist
calculates the distance from each atom in the pdb file to each atom in
the ligand and records the minimum in the temperature field for that
atom record.distalign reads the output from pdbdist and also the
original GCG MSF file and produces an MSF file annotated with a
measure of sequence variability and the distance of the residue at
that position (of the sequence of known structure) from the ligand.
USE_GCC2 or USE_GCC3 where appropriate.
the functionality of the old gcc.buildlink2.mk has been rolled into
compiler.mk now, which is automatically used.
more changes to come later...
New features in chemtool 1.6
- universal import mode based on BABEL (both openbabel and babel supported)
- Formula weight calculator now handles all main group elements and the first
row of transition elements, and accepts greek phi as phenyl substituent.
- Movable hexagonal or square grid backdrop
- Improved SVG export, optional preview bitmaps in EPS export, optional EMF
export
- Cursor key support for pixel-precise drawing and moving
- The cleanup function now corrects bonds that deviate from ideal
horizontal or vertical orientation by a single pixel
- Color support (bonds and text can be red,green,blue,cyan,magenta or yellow).
- Default bond length now configurable, additional grid positions at two and
three times this length added
- Added a brief help text to accompany the 'About' window in the 'Help' menu.
- Added alternate text font (Times Roman)
- An attachment site can be marked before saving a molecule or fragment,
which act as reference point for adding this fragment to other molecules
(previously, this had to be the first atom in a file). Attachment sites are
marked in the preview window by a small x.
- Background color can now be chosen for screen display and EPS export, and
drawing whiteout boxes under labels is now an option ( off by default !).
- Text at 8,10,12,14,17,20 and 24pt can now coexist in a drawing.
- Increased allowed label length to 100.
- Improved rendering of dashed wedge and dotted lines
- Improved text kerning in xfig-based print and export.
- It is now possible to place an auto-incrementing counter at the cursor
position for numbering sites.
- Changed double bond drawing code to no longer switch sides depending
on drawing (or rotation) angle. (As a result of this, some older drawings
will need fixing)
- Rescaling a molecule now also scales its labels. Downscaling beyond
zero size (causing strange inversions) is no longer possible.
- Renamed the "Orbitals" template menu to "Symbols" and added "plus",
"minus" and a rearrangement arrow to it.
- Added two new bond types, a triple bond with all three lines equal,
and a quadruple bond.
