Overview • User interface • Special tasks ↑ | ↓ Site scan setup • Labeling conditions
MMM describes spin labels by a set of alternative conformations, rotamers, which can be attached without serious clashes with atoms of other residues or cofactors. The individual rotamers are assigned Boltzmann populations corresponding to an estimate of the sum of their internal energy and interaction energy with the protein. All simulations of experiments on spin labels are then based on the population weighted average over the ensemble of rotamers. Since version 2010 clashes with water are automatically disregarded.
For further information, please read the publications on this approach. Full-text links:
Rotamer library and attachment
Spin labels can also be localized with respect to a reference structure or with respect to each other (networks).
The conformations allowed for an isolated spin label and their relative energies are stored in rotamer libraries. Currently such libraries exist for methanethiosulfonate spin label (MTSL) and iodoacetamido-PROXYL (IA-PROXYL) for cryogenic temperature and ambient temperature. As the cryogenic temperature, 175 K was selected, close enough to the glass transition temperatures of water/glycerol mixtures as a solvent for soluble proteins and lipid bilayers. Temperature scaling of the Boltzmann distribution is possible, but with the system not being ergodic, is only an approximation and should be restricted to small temperature intervals.
Some further libraries, based on the same rotamers but with different relative probabilities of these rotamers, have been created for tests. These libraries can be used after unlocking advanced features with the Lock/Unlock (toggle button)).
Interaction with atoms of the protein is estimated as dominated by packing effects (only pairwise Lenard-Jones potentials for label and protein atoms) and uses a distance cutoff to speed up computation. The protein backbone and conformations of native side groups are currently considered as static.
MMM has a two-step process of attaching labels. First spin label rotamers are computed for a set of selected residues or selected chains and after that they are attached to the model structure.
The reason is that rotamers computed in site scans do not interfer with each other, but they do interfer with labels that are already attached. A one-step labeling procedure would thus require to attach all desired labels at once.
In a site scan rotamer distributions are computed and stored and a HTML report of favourable labeling sites is prepared, but the structure remains unchanged. If you later select residues that were already computed in a site scan and click the labeling toolbutton the rotamers are attached at once (in seconds). If you have prepared and stored a model with a complete site scan, you can always reload it and attach the desired labels. Furthermore, you can attach rotamers from a site scan consecutively without any interference (the distributions were all computed for the virgin structure).
The main results from the site scan (number of significantly populated rotamers, partition function, r.m.s.d. of the N-O midpoint coordinate) are stored as residue annotations with the keyword
Select the residues for labeling by any selection method, for instance in the hierarchy window, by clicking on the structure in the model window or by the select command. Now click the labeling toolbutton. A window
MMM now checks for each selected residue if rotamer computations for that label and that temperature were already done. If so, the label is attached, if not, a warning message is shown in the message board of the main window.
Labels will not be displayed automatically. Use the graphics toolbutton for display.
rotamers computed
. Hence, you can find all residues for which rotamers were computed via the keyword finder and can obtain these statistics via the Show annotation
button.
Set labeling conditions
opens. Pick the Label
from the corresponding listbox and select the temperature with the cryogenic
or ambient
radiobutton. Direct temperature input in the corresponding edit field is also possible, but should be used with care and only if you understand the concept of rotamer computations well.
spin label attached
. Hence, you can find all labeled residues via the keyword finder and can obtain the corresponding rotamer statistics via the Show annotation
button.
A protein structure downloaded from PDB may need some modification before labeling to get the most realistic results. First, mutations to non-native amino acids, such as selenocysteine (CSE) or selenomethionine (MSE), may have been used to solve the phase problem in x-ray crystallography. The protein that is used in EPR experiments most likely has the native amino acids instead. You can fix this with the Build/Replace non-standard residues menu item. This replaces selenium by sulfur in MSE and CSE and reduces the Se-C bond lengths to the typical values of S-C bond lengths. The residues are renamed to MET or CYS. The same function can also replace existing spin labels, if you use a crystal structure that has already spin labels attached. This is required as MMM labels only native amino acids. Spin labels are replaced by cysteine.
Second, some amino acids may have missing sidechains. Although it is proper in crystallography not to specify sidechains if the corresponding electron density is missing, just ignoring these sidechains is not the best choice for subsequent spin label rotamer computations. The problem can be identified in sequence display in the hierarchy window, where residues with missing atoms are displayed by green letters, or by the Edit/Find by keyword menu item (keyword: missing atoms). You can (try to) repair all sidechains with the Build/Repair sidechains menu item. This requires that you have the third-party software SCWRL4 installed, which we strongly recommend. All residues will be repaired for which at least all backbone atoms exist. The function reports in the Message Borad of the main window whether all residues could be repaired. If not, you should check if incomplete residues are spatially close to your spin labels.
Third, your protein may have been mutated to make it amenable to spin labeling. Typically, this involves removal of all or most native cysteines. You should perform the same mutations on the structural model in MMM, using the Biochemistry/Mutation menu item. This also requires that you have the third-party software SCWRL4 installed and that all backbone atoms of the mutated residues are specified in the structure.
A site scan pertains to selected chains or coordinate sets of chains (in NMR structures with several chain models) or to selected residues. If nothing is selected, the current chain (displayed in the title of the main window) is labelled. To scan a chain or several chains, select them by any selection method, for instance in the hierarchy window, by clicking on the structure in the model window or by the select command. Now select the EPR/Site scan/selected chains or current chain
menu item. A Site scan setup
window opens that allows you to determine the labeling pattern. If there are alternative chain models (coordinate sets) for a selected chain, you are previously asked to determine which one should be labeled.
To scan selected residues, select them by any selection method, for instance in the hierarchy window, by clicking on the structure in the model window or by the select command. Now select the EPR/Site scan/selected residues
menu item. A Site scan setup
window opens that allows you to exclude certain residue types from the scan (this is handy for domain scans, if you are reluctant to label charged residues).
Here you can select Residue types
that you want to label or want to exclude from labeling. Each of the 20 native amino acids can be selected or unselected by checkbox. There are also two predefined labeling patterns. The conservative
pattern selects native Cys, Ile, Leu, Met, Ser, Thr, and Val residues, i.e., those residue types for which mutation to Cys is least likely to affect structure and function. The pattern all
selects all amino acids, including non-native amino acids. For chain scans, conservative
is the default choice, for selected residue scans all
is the default choice.
If your system has a symmetry axis or pseudo-symmetry axis and you have applied the Symmetry
command in the Edit
menu before, the z axis is a unique axis
. The same applies if you have defined a bilayer with the z axis being the bilayer normal. In these cases you may want to activate the z axis is a unique axis
checkbox, as spatial distribution of the label in z direction is of interest.
After a site scan, rotamer distributions of label pairs can be used for Distance analysis
. Such analysis can suggest label pairs that are suitable for CW EPR or DEER distance measurements. You can select by radiobuttons whether you want ditance analysis to be performed within the same chain (intrachain all
) for residue pairs in different chains (interchain all
) only for residues with the same number in different chains (interchain equivalent
, useful for homooligomers) or if you want to create homooligomer distance distributions by symmetry.
With the latter option you need to scan only one of the equivalent chains in a homooligomer. This requires that the z axis is the symmetry axis and that you know how many protein molecules make up the homooligomer (Multiplicity
).
If you want to analyze rotamer statistics with your own program or need populations of all rotamers in the library with original rotamer numbers, you can request a clear text file of rotamer statistics output by activating the Save statistics
checkbox. If you scan several chains at once, separate statistics files are written for individual chains. The file name(s) will be derived from the name of the HTML output file (see below) and statistics files will only be written if the HTML file is also written. For the format of this file, see Clear text output.
You can also save the coordinates of all rotamers for all labeled residues in individual (pseudo-)PDB files. This is not needed in application work and can create a large number of very long files. If you must do this, activate the Save PDB rotamers
checkbox. There is a warning about the storage requirements. See Pseudo PDB format for rotamers for the format description.
Click the OK
button to proceed or the Cancel
button to cancel the computation.
For each chain you can set labeling conditions separately. This allows to scan with different labels for different chains. A window Set labeling conditions
opens
(see also Labeling conditions window). Pick the Label
from the corresponding listbox and select the temperature with the cryogenic
or ambient
radiobutton. Direct temperature input in the corresponding edit field is also possible, but should be used with care and only if you understand the concept of rotamer computations well.
After the labeling conditions for all chains are set, a file dialog opens that allows to select a file name for the HTML output file with results of the site scan analysis (spatial restrictions of spin labels at the selected sites, distance analysis). Decide on a file name or click Cancel
to perform a site scan without HTML output.
Progress is reported in the message board of the main window and, for individual residues, in a status bar. The message board tells how many residues are already completed and also reports on the number of significantly populated rotamers and the uncertainty of the NO bond midpoint for each individual residue (labeling site).
If necessary, you can stop the computation by closing the status bar tha reports on progress for individual residues (click the cross in the top right corner). A question dialog appears that will let you Stop
or Resume
the computation. Note that the remainder of the site scan will be skipped if you decide to Stop
. Analysis of the site scan will also be skipped and no HTML output stored.
After the site scan is completed, you are asked whether to open the HTML result file in a web browser. If you decide not to, the file will still be stored for later use.
After a site scan, rotamer distributions are stored, but labels are not attached to the structure. It is strongly recommended to save the mode (File/Save as..
menu item) before actually attaching any labels.
There are several possible sources of error:
Further reliability tests become possible, if you have experimental distance distributions and want to understand the deviation between prediction and experiment. For this, you can use the Any rotamers? and Range analysis features in the DEER window.
Residues that are spin labeled or for which rotamers were computed are automatically annotated and tagged with the keyword
If only one set of residues is scanned with the same rotamer library or only a single chain is scanned, one statistics file is written. It is stored in the same directory as the HTML file and the name is derived from the name of the HTML file without extension by appending
The format of the clear text output file is explained by an example:
1st line of file:
lists the library file used during the whole site scan.
The following lines are separated into records, one record per successfully scanned residue. For a library that contains n possible rotamers, each record has n+3 lines. The record lines are:
1st line of record:
gives the residue address, the calibration temperature of the library and the label type as clear text.
2nd line of record:
gives the total number of rotamers (column 1), the number of significant rotamers (column 2), the actual labeling temperature (column 3), the "forgive factor" (column 4), and the label type as a number column (5, 1 corresponds to MTSL, 2 to IA-PROXYL).
3rd line of record:
The first three columns give the Cα coordinate of the residue (in Å), column 4 the net external potential and column 5 the partition function.
The following n lines in the record (here 108 lines) provide information on the individual rotamers. All of them have the following format:
The first three columns give the midpoint coordinate of the N-O bond (in Å), column 4 the relative population due to only the external potential and column 5 the total population (total populations are normalized, they add up to unity).
This file can be read by Matlab with a single load command.
In the PDB mindset rotamers correspond to alternate locations of sidechain atoms. Alternate locations are tagged by a single upper-case letter, hence only up to 26 rotamers can be stored in a PDB file that conforms to the official format specification. In fact, if MMM saves a PDB file with attached rotamers, the 26 leading rotamers (with the largest populations) are saved, all others are skipped. The MMM model has information on all rotamers, but in rare cases you might want to have a PDB file with all rotamers in the same coordinate frame as the protein structure. This may be useful for methodological work on rotamers with other visualization programs that understand PDB format.
For this purpose, a pseudo PDB format is defined in which the number of a rotamer in the original library is stored as the residue number. Hence, the set of rotamers corresponds to a chain A with all residues sharing the same positions of the N, CA, and C atoms. Only atom records (HETATM) and bond records (CONECT) are specified. The HEADER line (example):
specifies the rotamer library and the TITLE line
the MMM address of the labeled residue, the label type (here IA1 = iodoacetamido PROXYL) and the labeling temperature. A REMARK 4 is written to specify that this is a non-standard format:
spin labels
. Hence, a list of all spin labeled residues in a structure can be obtained with the keyword finder window, which is accessible via the Edit/Find by keyword menu item.
_1.dat
. If several chains are scanned, separate statistics files are written for the individual chains. They are consecutively numbered (_1.dat
, _2.dat
, ...).
%% Rotamer site scan with library IA1_175K_090814
% [2BHW](A){1}106 labeled at calibration temperature 175.0 (label IA1)
108 37 175.0 0.50 2
56.292 45.484 61.913 145.834 1.38553
49.863 41.213 59.022 0.014 0.01741
HEADER SPIN LABELING WITH LIBRARY IA1_175K_090814
TITLE [2BHW](A){1}160 LABELED WITH IA1 AT 175 K
REMARK 4 MMM ROTAMERS (PSEUDO-PDB FORMAT) RESIDUE NUMBERS ARE ROTAMER IDS
A fake B factor is specified that corresponds to 1 Å r.m.s.d. of all atom positions.
The format can be read again by MMM (use the File/Add.../From PDB.../local file
menu item) and is recognized as a special format. The structure tag is constructed based on the address of the labeled residue and the keyword rotamers
. Backbone bond generation and DSSP secondary structure assignment (if installed) are suppressed. When displaying low population rotamers (population < = 0.005), you have to change transparency, otherwise they are invisible.
As the format is non-standard, there is some risk that other visualization programs do not process it properly. We have tested Swiss-PdbViewer 4.0.1 and Accelrys DS Visualizer Accelrys DS Visualizer v<IP_ADDRESS>47. Both these programs appear to work properly (within their own limits) with this format.


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It follows 2 digit format
For Example:- I did my task in 45m and it takes 01h20m in preparation.


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ntpq
Section: Maintenance Commands (8)Index Return to Main Contents
NAME
ntpq - standard NTP query programSYNOPSIS
ntpq [-46dinp] [-c command] [host] [...]DESCRIPTION
The ntpq utility program is used to monitor NTP daemon ntpd operations and determine performance. It uses the standard NTP mode 6 control message formats defined in Appendix B of the NTPv3 specification RFC1305. The same formats are used in NTPv4, although some of the variables have changed and new ones added. The description on this page is for the NTPv4 variables.
The program can be run either in interactive mode or controlled using command line arguments. Requests to read and write arbitrary variables can be assembled, with raw and pretty-printed output options being available. The ntpq can also obtain and print a list of peers in a common format by sending multiple queries to the server.
If one or more request options is included on the command line when ntpq is executed, each of the requests will be sent to the NTP servers running on each of the hosts given as command line arguments, or on localhost by default. If no request options are given, ntpq will attempt to read commands from the standard input and execute these on the NTP server running on the first host given on the command line, again defaulting to localhost when no other host is specified. ntpq will prompt for commands if the standard input is a terminal device.
ntpq uses NTP mode 6 packets to communicate with the NTP server, and hence can be used to query any compatible server on the network which permits it. Note that since NTP is a UDP protocol this communication will be somewhat unreliable, especially over large distances in terms of network topology. ntpq makes one attempt to retransmit requests, and will time requests out if the remote host is not heard from within a suitable timeout time.
Note that in contexts where a host name is expected, a -4 qualifier preceding the host name forces DNS resolution to the IPv4 namespace, while a -6 qualifier forces DNS resolution to the IPv6 namespace.
For examples and usage, see the NTP Debugging Techniques page.
Command line options are described following. Specifying a command line option other than -i or -n will cause the specified query (queries) to be sent to the indicated host(s) immediately. Otherwise, ntpq will attempt to read interactive format commands from the standard input.
-
- -4
- Force DNS resolution of following host names on the command line to the IPv4 namespace.
- -6
- Force DNS resolution of following host names on the command line to the IPv6 namespace.
- -c
- The following argument is interpreted as an interactive format command and is added to the list of commands to be executed on the specified host(s). Multiple -c options may be given.
- -d
- Turn on debugging mode.
- -i
- Force ntpq to operate in interactive mode. Prompts will be written to the standard output and commands read from the standard input.
- -n
- Output all host addresses in dotted-quad numeric format rather than converting to the canonical host names.
- -p
- Print a list of the peers known to the server as well as a summary of their state. This is equivalent to the peers interactive command.
INTERNAL COMMANDS
Interactive format commands consist of a keyword followed by zero to four arguments. Only enough characters of the full keyword to uniquely identify the command need be typed. The output of a command is normally sent to the standard output, but optionally the output of individual commands may be sent to a file by appending a >, followed by a file name, to the command line. A number of interactive format commands are executed entirely within the ntpq program itself and do not result in NTP mode 6 requests being sent to a server. These are described following.
-
- ? [command_keyword]
- helpl [command_keyword]
- A ? by itself will print a list of all the command keywords known to this incarnation of ntpq[char46] A ? followed by a command keyword will print function and usage information about the command. This command is probably a better source of information about ntpq than this manual page.
- addvars variable_name [ = value] [...]
- rmvars variable_name [...]
- clearvars
- The data carried by NTP mode 6 messages consists of a list of items of the form variable_name = value, where the = value is ignored, and can be omitted, in requests to the server to read variables. ntpq maintains an internal list in which data to be included in control messages can be assembled, and sent using the readlist and writelist commands described below. The addvars command allows variables and their optional values to be added to the list. If more than one variable is to be added, the list should be comma-separated and not contain white space. The rmvars command can be used to remove individual variables from the list, while the clearlist command removes all variables from the list.
- cooked
- Causes output from query commands to be "cooked", so that variables which are recognized by ntpq will have their values reformatted for human consumption. Variables which ntpq thinks should have a decodable value but didn't are marked with a trailing ?[char46]
- debug more | less | off
- Turns internal query program debugging on and off.
- delay milliseconds
- Specify a time interval to be added to timestamps included in requests which require authentication. This is used to enable (unreliable) server reconfiguration over long delay network paths or between machines whose clocks are unsynchronized. Actually the server does not now require timestamps in authenticated requests, so this command may be obsolete.
- host hostname
- Set the host to which future queries will be sent. Hostname may be either a host name or a numeric address.
- hostnames [yes | no]
- If yes is specified, host names are printed in information displays. If no is specified, numeric addresses are printed instead. The default is yes, unless modified using the command line -n switch.
- keyid keyid
- This command specifies the key number to be used to authenticate configuration requests. This must correspond to a key number the server has been configured to use for this purpose.
- ntpversion 1 | 2 | 3 | 4
- Sets the NTP version number which ntpq claims in packets. Defaults to 2, Note that mode 6 control messages (and modes, for that matter) didn't exist in NTP version 1.
- passwd
- This command prompts for a password (which will not be echoed) which will be used to authenticate configuration requests. The password must correspond to the key configured for NTP server for this purpose.
- quit
- Exit ntpq[char46]
- raw
- Causes all output from query commands is printed as received from the remote server. The only formatting/interpretation done on the data is to transform non-ASCII data into a printable (but barely understandable) form.
- timeout millseconds
- Specify a timeout period for responses to server queries. The default is about 5000 milliseconds. Note that since ntpq retries each query once after a timeout, the total waiting time for a timeout will be twice the timeout value set.
CONTROL MESSAGE COMMANDS
Each association known to an NTP server has a 16 bit integer association identifier. NTP control messages which carry peer variables must identify the peer the values correspond to by including its association ID. An association ID of 0 is special, and indicates the variables are system variables, whose names are drawn from a separate name space.
Control message commands result in one or more NTP mode 6 messages being sent to the server, and cause the data returned to be printed in some format. Most commands currently implemented send a single message and expect a single response. The current exceptions are the peers command, which will send a preprogrammed series of messages to obtain the data it needs, and the mreadlist and mreadvar commands, which will iterate over a range of associations.
-
- associations
- Obtains and prints a list of association identifiers and peer statuses for in-spec peers of the server being queried. The list is printed in columns. The first of these is an index numbering the associations from 1 for internal use, the second the actual association identifier returned by the server and the third the status word for the peer. This is followed by a number of columns containing data decoded from the status word. See the peers command for a decode of the condition field. Note that the data returned by the associations command is cached internally in ntpq[char46] The index is then of use when dealing with stupid servers which use association identifiers which are hard for humans to type, in that for any subsequent commands which require an association identifier as an argument, the form &index may be used as an alternative.
- clockvar [assocID] [variable_name [ = value [...]] [...]
- cv [assocID] [variable_name [ = value [...] ][...]
- Requests that a list of the server's clock variables be sent. Servers which have a radio clock or other external synchronization will respond positively to this. If the association identifier is omitted or zero the request is for the variables of the system clock and will generally get a positive response from all servers with a clock. If the server treats clocks as pseudo-peers, and hence can possibly have more than one clock connected at once, referencing the appropriate peer association ID will show the variables of a particular clock. Omitting the variable list will cause the server to return a default variable display.
- lassociations
- Obtains and prints a list of association identifiers and peer statuses for all associations for which the server is maintaining state. This command differs from the associations command only for servers which retain state for out-of-spec client associations (i.e., fuzzballs). Such associations are normally omitted from the display when the associations command is used, but are included in the output of lassociations[char46]
- lpassociations
- Print data for all associations, including out-of-spec client associations, from the internally cached list of associations. This command differs from passociations only when dealing with fuzzballs.
- lpeers
- Like R peers, except a summary of all associations for which the server is maintaining state is printed. This can produce a much longer list of peers from fuzzball servers.
- mreadlist assocID assocID
- mrl assocID assocID
- Like the readlist command, except the query is done for each of a range of (nonzero) association IDs. This range is determined from the association list cached by the most recent associations command.
- mreadvar assocID assocID [ variable_name [ = value[ ... ]
- mrv assocID assocID [ variable_name [ = value[ ... ]
- Like the readvar command, except the query is done for each of a range of (nonzero) association IDs. This range is determined from the association list cached by the most recent associations command.
- opeers
- An old form of the peers command with the reference ID replaced by the local interface address.
- passociations
- Displays association data concerning in-spec peers from the internally cached list of associations. This command performs identically to the associations except that it displays the internally stored data rather than making a new query.
- peers
- Obtains a current list peers of the server, along with a summary of each peer's state. Summary information includes the address of the remote peer, the reference ID (<IP_ADDRESS> if this is unknown), the stratum of the remote peer, the type of the peer (local, unicast, multicast or broadcast), when the last packet was received, the polling interval, in seconds, the reachability register, in octal, and the current estimated delay, offset and dispersion of the peer, all in milliseconds. The character at the left margin of each line shows the synchronization status of the association and is a valuable diagnostic tool. The encoding and meaning of this character, called the tally code, is given later in this page.
- pstatus assocID
- Sends a read status request to the server for the given association. The names and values of the peer variables returned will be printed. Note that the status word from the header is displayed preceding the variables, both in hexadecimal and in pidgeon English.
- readlist [ assocID ]
- rl [ assocID ]
- Requests that the values of the variables in the internal variable list be returned by the server. If the association ID is omitted or is 0 the variables are assumed to be system variables. Otherwise they are treated as peer variables. If the internal variable list is empty a request is sent without data, which should induce the remote server to return a default display.
- readvar assocID variable_name [ = value ] [ ...]
- rv assocID [ variable_name [ = value ] [...]
- Requests that the values of the specified variables be returned by the server by sending a read variables request. If the association ID is omitted or is given as zero the variables are system variables, otherwise they are peer variables and the values returned will be those of the corresponding peer. Omitting the variable list will send a request with no data which should induce the server to return a default display. The encoding and meaning of the variables derived from NTPv3 is given in RFC-1305; the encoding and meaning of the additional NTPv4 variables are given later in this page.
- writevar assocID variable_name [ = value [ ...]
- Like the readvar request, except the specified variables are written instead of read.
- writelist [ assocID ]
- Like the readlist request, except the internal list variables are written instead of read.
TALLY CODES
The character in the left margin in the peers billboard, called the tally code, shows the fate of each association in the clock selection process. Following is a list of these characters, the pigeon used in the rv command, and a short explanation of the condition revealed.
-
- space reject
- The peer is discarded as unreachable, synchronized to this server (synch loop) or outrageous synchronization distance.
- x falsetick
- The peer is discarded by the intersection algorithm as a falseticker.
- [char46] excess
- The peer is discarded as not among the first ten peers sorted by synchronization distance and so is probably a poor candidate for further consideration.
- - outlyer
- The peer is discarded by the clustering algorithm as an outlyer.
- + candidat
- The peer is a survivor and a candidate for the combining algorithm.
- # selected
- The peer is a survivor, but not among the first six peers sorted by synchronization distance. If the association is ephemeral, it may be demobilized to conserve resources.
- * sys.peer
- The peer has been declared the system peer and lends its variables to the system variables.
- o pps.peer
- The peer has been declared the system peer and lends its variables to the system variables. However, the actual system synchronization is derived from a pulse-per-second (PPS) signal, either indirectly via the PPS reference clock driver or directly via kernel interface.
SYSTEM VARIABLES
The status, leap, stratum, precision, rootdelay, rootdispersion, refid, reftime, poll, offset, and frequency variables are described in RFC-1305 specification. Additional NTPv4 system variables include the following.
-
- version
- Everything you might need to know about the software version and generation time.
- processor
- The processor and kernel identification string.
- system
- The operating system version and release identifier.
- state
- The state of the clock discipline state machine. The values are described in the architecture briefing on the NTP Project page linked from www.ntp.org.
- peer
- The internal integer used to identify the association currently designated the system peer.
- jitter
- The estimated time error of the system clock measured as an exponential average of RMS time differences.
- stability
- The estimated frequency stability of the system clock measured as an exponential average of RMS frequency differences.
When the NTPv4 daemon is compiled with the OpenSSL software library, additional system variables are displayed, including some or all of the following, depending on the particular dance:
-
- flags
-
The current flags word bits and message digest algorithm identifier (NID) in hex format. The high order 16 bits of the four-byte word contain the NID from the OpenSSL ligrary, while the low-order bits are interpreted as follows:
-
- 0x01
- autokey enabled
- 0x02
- NIST leapseconds file loaded
- 0x10
- PC identity scheme
- 0x20
- IFF identity scheme
- 0x40
- GQ identity scheme
-
- hostname
- The name of the host as returned by the Unix gethostname() library function.
- hostkey
- The NTP filestamp of the host key file.
- cert
-
A list of certificates held by the host. Each entry includes the subject, issuer, flags and NTP filestamp in order. The bits are interpreted as follows:
-
- 0x01
- certificate has been signed by the server
- 0x02
- certificate is trusted
- 0x04
- certificate is private
- 0x08
- certificate contains errors and should not be trusted
-
- leapseconds
- The NTP filestamp of the NIST leapseconds file.
- refresh
- The NTP timestamp when the host public cryptographic values were refreshed and signed.
- signature
- The host digest/signature scheme name from the OpenSSL library.
- tai
- The TAI-UTC offset in seconds obtained from the NIST leapseconds table.
PEER VARIABLES
The status, srcadr, srcport, dstadr, dstport, leap, stratum, precision, rootdelay, rootdispersion, readh, hmode, pmode, hpoll, ppoll, offset, delay, dspersion, reftime variables are described in the RFC-1305 specification, as are the timestamps org, rec and xmt[char46] Additional NTPv4 system variables include the following.
-
- flash
- The flash code for the most recent packet received. The encoding and meaning of these codes is given later in this page.
- jitter
- The estimated time error of the peer clock measured as an exponential average of RMS time differences.
- unreach
- The value of the counter which records the number of poll intervals since the last valid packet was received.
When the NTPv4 daemon is compiled with the OpenSSL software library, additional peer variables are displayed, including the following:
-
- flags
- The current flag bits. This word is the server host status word with additional bits used by the Autokey state machine. See the source code for the bit encoding.
- hostname
- The server host name.
- initkey key
- The initial key used by the key list generator in the Autokey protocol.
- initsequence index
- The initial index used by the key list generator in the Autokey protocol.
- signature
- The server message digest/signature scheme name from the OpenSSL software library.
- timestamp time
- The NTP timestamp when the last Autokey key list was generated and signed.
FLASH CODES
The flash code is a valuable debugging aid displayed in the peer variables list. It shows the results of the original sanity checks defined in the NTP specification RFC-1305 and additional ones added in NTPv4. There are 12 tests designated TEST1 through TEST12[char46] The tests are performed in a certain order designed to gain maximum diagnostic information while protecting against accidental or malicious errors. The flash variable is initialized to zero as each packet is received. If after each set of tests one or more bits are set, the packet is discarded.
Tests TEST1 through TEST3 check the packet timestamps from which the offset and delay are calculated. If any bits are set, the packet is discarded; otherwise, the packet header variables are saved. TEST4 and TEST5 are associated with access control and cryptographic authentication. If any bits are set, the packet is discarded immediately with nothing changed.
Tests TEST6 through TEST8 check the health of the server. If any bits are set, the packet is discarded; otherwise, the offset and delay relative to the server are calculated and saved. TEST9 checks the health of the association itself. If any bits are set, the packet is discarded; otherwise, the saved variables are passed to the clock filter and mitigation algorithms.
Tests TEST10 through TEST12 check the authentication state using Autokey public-key cryptography, as described in the Authentication Options page. If any bits are set and the association has previously been marked reachable, the packet is discarded; otherwise, the originate and receive timestamps are saved, as required by the NTP protocol, and processing continues.
The flash bits for each test are defined as follows.
-
- 0x001 TEST1
- Duplicate packet. The packet is at best a casual retransmission and at worst a malicious replay.
- 0x002 TEST2
- Bogus packet. The packet is not a reply to a message previously sent. This can happen when the NTP daemon is restarted and before somebody else notices.
- 0x004 TEST3
- Unsynchronized. One or more timestamp fields are invalid. This normally happens when the first packet from a peer is received.
- 0x008 TEST4
- Access is denied. See the Access Control Options page.
- 0x010 TEST5
- Cryptographic authentication fails. See the Authentication Options page.
- 0x020 TEST6
- The server is unsynchronized. Wind up its clock first.
- 0x040 TEST7
- The server stratum is at the maximum than 15. It is probably unsynchronized and its clock needs to be wound up.
- 0x080 TEST8
- Either the root delay or dispersion is greater than one second, which is highly unlikely unless the peer is unsynchronized to Mars.
- 0x100 TEST9
- Either the peer delay or dispersion is greater than one second, which is highly unlikely unless the peer is on Mars.
- 0x200 TEST10
- The autokey protocol has detected an authentication failure. See the Authentication Options page.
- 0x400 TEST11
- The autokey protocol has not verified the server or peer is proventic and has valid public key credentials. See the Authentication Options page.
- 0x800 TEST12
- A protocol or configuration error has occurred in the public key algorithms or a possible intrusion event has been detected. See the Authentication Options page.
BUGS
The peers command is non-atomic and may occasionally result in spurious error messages about invalid associations occurring and terminating the command. The timeout time is a fixed constant, which means you wait a long time for timeouts since it assumes sort of a worst case. The program should improve the timeout estimate as it sends queries to a particular host, but doesn't.
SEE ALSO
Primary source of documentation: /usr/share/doc/ntp-*
This file was automatically generated from HTML source.
Index
- NAME
- SYNOPSIS
- DESCRIPTION
- INTERNAL COMMANDS
- CONTROL MESSAGE COMMANDS
- TALLY CODES
- SYSTEM VARIABLES
- PEER VARIABLES
- FLASH CODES
- BUGS
- SEE ALSO
This document was created by man2html, using the manual pages.
Time: 05:34:28 GMT, December 24, 2015


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SLEEPY HOLLOW
STARRING: Johnny Depp, Christina Ricci, Miranda Richardson, Michael Gambon, Casper Van Dien, Jeffrey Jones, Ian McDiarmid, Christopher Lee DIRECTOR: Tim Burton WRITTEN BY: Kevin Yagher, Andrew Kevin Walker (based on "The Legend of Sleepy Hollow" by Washington Irving)
By now, after Beetlejuice, two Batman movies, and Edward Scissorhands (also starring Depp), one might conclude that the sky in weirdo/wunderkind Tim Burton's world is decidedly black. Yet, his bleak Gothic imagery has always been tempered by a childlike wonder (perhaps best realized in the truly marvelous musical fantasy The Nightmare Before Christmas, which he produced and co-wrote.) Underlined with strange and sublime music from constant collaborator Danny Elfman, Burton's films have a unique, fairy-tale-like quality that has often endeared him to both critics and audiences in a rare synergy of art and commerce (although not always; 1996's Mars Attacks! was just plain dreadful, while 1994's critical favorite Ed Wood was box-office anathema.) These same artistic and commercial elements appear in Sleepy Hollow, but blend less smoothly thanks to writing flaws that complicate what should have been a simple and straightforward tale.
The film's plot bears only a passing resemblance to Irving's short story. Ichabod Crane is now a constable and forensic scientist instead of a schoolmaster. This allows the writers to cook up an unnecessarily convoluted murder mystery involving conspiracy and witchcraft, a whodunit that in its resolution makes even the origin of the Headless Horseman seem completely plausible in comparison. Thrown in for good measure is some uncalled-for subtext involving Ichabod's Puritan childhood. In fact, Sleepy Hollow is even less faithful to its source than the short but memorable Disney cartoon (the last half of 1949's Ichabod and Mr. Toad) that is, to my mind, still the best-- and scariest-- film version of 'em all (so memorable, in fact, that Burton includes several bits of hommage to it, like the toads that croak Ichabod's name as he nervously guides his old horse across a covered bridge at night.)
This is not to say that the film is a waste of time. On the contrary, it's worth ponying up the bucks just to see the patented Burton visuals (accomplished this time by cinematographer Emmanuel Lubezki) married to Elfman's magical music. Pastoral vistas of upstate New York are as beautifully rendered as oil paintings, but the real treats are the gloomy little township of Sleepy Hollow and the gnarled, leaf-strewn forest surrounding it. They're like an Edward Gorey drawing come to ominous life. Even the few daylight sequences have a dreamlike, dark-at-the-fringes feel, and the characters all share an unhealthy-looking pallor that suits the grim (and often gruesome) proceedings. Depp's Ichabod Crane, with his constantly pursed lips and stiff, vaguely effeminate demeanor, matches Irving's conception in character if not appearance (in this respect, the Disney version is bang-on.) Ricci, on the other hand, matches Irving's physical description of Katrina Van Tassel letter for letter, but is neither coquettish nor fickle enough to be considered anything but a goody-goody. Thanks to the demands of a script that requires obligatory plot twists and action scenes, we are expected to believe things about both characters that simply don't add up. Worse, the villain is made to explain the whole messy mystery near the end, with the immediate and unfortunate result that we are suddenly yanked out of Tim Burton's darkly imaginative world and left sitting in a theater, watching something no more real than a Headless Horseman.
GRADE: **1/2
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|
AZX (AppZone eXtensions) documentation
1.1.9-CxL
A set of companion utilities that make AZ development easier
|
gnu definition More...
Go to the source code of this file.
Macros | |
| #define | stdout (void*)(0x88888888) |
| #define | stderr (void*)(0x99999999) |
| #define | fopen m2mb_fs_fopen |
| #define | fread m2mb_fs_fread |
| #define | fwrite m2mb_fs_fwrite |
| #define | fclose m2mb_fs_fclose |
| #define | fputs m2mb_fs_fputs |
| #define | fgets m2mb_fs_fgets |
| #define | fflush m2mb_fs_fflush |
| #define | fileno m2mb_fs_fileno |
| #define | unlink m2mb_fs_remove |
| #define | FILE M2MB_FILE_T |
| #define | m2m_fputc m2mb_fs_fputc |
| #define | m2m_fgetc m2mb_fs_fgetc |
| #define | fseek m2mb_fs_fseek |
| #define | rewind(a) (void)fseek(a, 0L, SEEK_SET) |
| #define | fprintf azx_gnu_fprintf |
| #define | truncate azx_gnu_truncate |
Functions | |
| int | azx_gnu_fprintf (void *f, const char *format,...) |
| Prints a autput. More... | |
| int | azx_gnu_truncate (const char *path, off_t length) |
| Truncate file. More... | |
gnu definition
Porting from gnu to azx
| int azx_gnu_fprintf | ( | void * | f, |
| const char * | format, | ||
| ... | |||
| ) |
Prints a autput.
Prints on the defined stream (UART or USB channel)
| [in] | f | void* pointer |
| [in] | format | const char* pointer |
Example
| int azx_gnu_truncate | ( | const char * | path, |
| off_t | length | ||
| ) |
Truncate file.
The function effect is that the regular file named by path will have a size which will be equal to length bytes.
| [in] | path | Name of file to be truncated. |
| [in] | length | New size of the file. |
Example


I design to improve user experience wich make remarkable products, services and brands.
Graphic Design
Online and offline expertise. I develop brands, stationary, brochures, exhibitions, invitations, and every possible aspect to make the message visual.
Web Design (UX | UI)
Using user-centered design, I develop user experience in websites, landing pages, emails and campaign assets, wich follows UI/UX and web best practices.
Marketing Design
With a depth knowledge of the consumer, I help to develop strategies that deliver the right message, in the right place for the right user.
Portfolio
Glacê - Easter Social Campaign
Art direction | Mar-Apr.2017
ContaAzul - New website
UX, UI | Feb.2017
Personal project - Wedding
Visual Identity | Jan.2017
ContaAzul - LP Academy
UX, UI | Nov.2016
ContaAzul - LP GeraNFe
UX, UI | Sep.2016
ContaAzul - Assets Campaigns
Art direction | Jul. 2016
Glacê - Easter Social Campaign
Art direction | Mar-Apr.2017
Glacê Gourmet is a small home confectionery, who offered homemade Chocolate Eggs and a Box of Sweets on last Easter.All the selling of the products were by social network messaging, so I helped to create a campaign to exhibit the products.
Exactly one month before the Easter date, we publish a poster remembering that Easter was coming. The aim of this post was to give a sense of urgency, stimulate the public to think about what they would buy as a gift for their family and friends and invite them to talk to Glacê to see the great options of Chocolate Eggs and the Box of Sweets.
The second post os focused on the sweets and the possibility of personalization. Glacê made it possible to the client choosing all the flavors that would fit into the Box of Sweets. Therefore the post was showing the picture of the box, and the flavors available.
A cover to the Box of Sweets was made, to highlit this option of the product.
A consistency of the communication was maintained in the box of the Chocolate Egg, wich it took a sticker with the same visual appeal and wishing Happy Easter.
ContaAzul - New website
UX, UI | February 2017
ContaAzul is one of the largest startups in Brazil that develops a financial system for small companies and accountants. Your website is one of the most important channels for converting visitors to leads, which increases the importance of this project, that aimed to improve the conversion rate through a better user experience.
It was known that the site had some broken points in the user's journey, so the first step was to map all the available content in an inventory, to find and fix the unlinked pages, making a new flow. When the inventory was ready, we realized that the site had 8 different navigation menu and 8 different footers, and this was making the user confused, it was difficult to find where to go, or how to get back, to find the content that was seen before.
So, in the second stage, a rearrangement of the content, a new Architectural Information of the site was made. ContaAzul has two distinct audiences, the entrepreneurs, and the accountants, so that was necessary clearly identify which content was being shown at every time. The best hypothesis found was fixing a content category filter - 'entrepreneur', 'accountants' and 'about the company' - before the main navigation, making easier for the user realize how to find their space, and more important than that, where login in the system.
Thinking of a better user experience, the Jobs To Be Done methodology was applied, to make the content organization feel more natural, having the problems that ContaAzul helps users solve in mind. To find the Jobs To Be Done that has fit with the ContaAzul public, we did a survey with the current clients at that time, asking what were the problems that were solved with the help of ContaAzul's features. As result of this survey, we find some common problems to all users, that could be applied as Jobs to Be Done. We filtered the most relevant in the number of choices, or in the strategy of business, and we applied a new research, an online Card Sorting method, to find and validate how to organize the features in those Jobs To Be Done.
With the new content hierarchy and the final Jobs to Be Done, the next step consisted in re-layout the main page of the site, and for that we use storytelling.
In the header, we wanted to show a confident entrepreneur, showing how does it feel using ContaAzul, how his business life is calmer, and his company is more effective. ContaAzul has a guideline based on illustrations, so we use a character, making him look to the main email input and call to action button, which is a nice conversion practice.
After showing the ContaAzul successful client, we present how ContaAzul helped him to get there, showing the features related with their Job's To Be Done. We focus on showing the screen of the system that represents better the problem solving of which job.
Beyond the helpful features, ContaAzul has the purpose of helping the entrepreneurs' success, and they do this through an Online University with a free educational material. So a section dedicated to showing the main categories of the University, such as webinars, courses, and guides.
Some current clients, that have being using ContaAzul, confirm their efficiency and tell how it improve their business. As social proof, this section centralized some small videos of clients reporting their experience using ContaAzul. The ideia was display the deppoiments as a carrossel and show the videos only when the user decide to, clicking on the play button.
To end the story of the site, we invite the user to join the currently numerous entrepreneurs that have been improving their business with ContaAzul. This Call to Action intend to have a great conversion rate, and we use two growth hacking good practices as the urgency sentence "start now" and the idea of no commitment with the sentence "Your card number is not asked".
I had the opportunity to be the main designer conducting this project and define some points of direction but was really amazing working with all areas of the company, researching clients, to get rich insights and develop best hypothesis. Unfortunately, I couldn't follow the validation and the develop implementation because I had to left the company to move to another country with my husband. But it is still ongoing with ContaAzul team.
Personal Project - Wedding
Visual Identity | Jan.2017
This project has a special meaning because it was the communication of my wedding. Our wedding party was a farewell too because we were moving to another country, so we used this context plus our love for traveling in the concept of the wedding visual identity. We did everything on the travel theme.
The invitation was a passport with a boarding pass
The tables had names of cities that we had already visited. And the sign of the table's names had pictures of our travels.
The wedding souvenir was a Craft Beer - made for my husband - and the label follows the rest of the Wedding ID.
We had little time to prepare the event - not much more than one month, - which means that I have had a week to develop the wedding concept, invitation, and communication. Even with the short time to do it, I enjoyed the result.
ContaAzul - LP Academy
UX, UI | November 2016
ContaAzul is a startup that develops a financial and accountant system. Their marketing strategy is hugely based on inbound marketing which provides educative materials, - like ebooks, guides, infographics, - about some subject for the users, but in their case, always related to entrepreneurship. The free materials were shared in emails or posts on the social networks, and through them, the user was directed to a download Landing Page.
A page with all materials had existed, but it was outdated regarding layout, which had the old visual style guide of the brand, and bad usability (it was not working on mobile devices). A technical structure issue was considered too, which the old page had been located in an old directory, and it had to be moved to new one, in Hubspot.
So the project briefing was re-layout the Landing Page of Materials, considering some points:
It had to follow the existent structure of pages built in Hubspot;
The assets of the materials couldn't be changes, it had to follow that dimension;
It had to be simple to update - it was all manually;
It had to be easy to find the categories of the materials;
It had to be ready in one week (the layout)- at the end, I have had 3 or 4 days to do it.
What I like about this project is the structure of the filter which makes all the information of the materials archive been available in the same time. You just need to interact with the filter to see the in-depth of materials.
Considering the limitations of the scope of the project and the tight deadline, I was satisfied to provide an objective and clear user experience and solve the project goals.
ContaAzul - LP GeraNFe
UX, UI | September 2016
Targeted landing page for lead capture
ContaAzul - Campaign assets
Art Direction | July 2016
Assets for Google Analytics and Facebook campaigns


Chapter 2 Daily journal
2.1 2021-10-07
Working on collaborative workflow for FIMS I found this training for workflows on GitHub. They advocate for Git Flow in all workflows.
2.2 2021-10-06
Trevor Riley of the NOAA library and I talked about 508 compliance and NOAA citations. Typically, when a NOAA librarian helps you with a document they recommend Cite While You Write combined with EndNote. The NOAA library is working on getting a single, integrated Endnote library but this is not currently available. Instead, they have Endnote libraries from individual projects.
2.2.1 Institutional Repository
All NOAA funded and NOAA published documents are supposed to be entered into the Institutional Repository The goal is to get all entries starting from 2015 to current year. They will accept entries from any year though.
The Institutional Repository uses NOAA resources to check metadata and assign a DOI. Assigning a DOI to all stock assessment documents would facilitate cataloging them. RIS file could be batch downloaded and converted to a bib file.
Everything in the repository should be 508 compliant and is checked internally using a standard. Jamie works on compliance issues every day and Jennifer has a good handle on it. Their guidance is summarized in the Quick Start Big 5 list.
- send .bib file to Trevor
- look at the link that Trevor sent to find how many assessments are actually in the institutional repository
2.2.2 EndNote library
- 200 projects
- 60 species and projects outside of species research
- all archived libraries from different projects
- goal is to bring it into a single repository that could be shared
- starting with Endangered Species Act work
- do not manually check information from a publisher or tell publishers when information is incorrect
<IP_ADDRESS> Import of bib file to EndNote
Trevor tried importing the Lingcod.bib file from the 2021 assessment and no metadata was found. I did a quick google search and found that Imperial College London has advice on LaTeX with EndNote with filters that are needed to import .bib entries. Even with these filters, the ability of EndNote to recognize metadata is not great.
2.3 2021-09-17
2.3.1 Z{"o}ller et al. 2020
As the workforce turns more towards remote work, decisions are becoming more local (Capra and Luisi, 2016). FLOSS-based groups are becoming more like a bazaar, structured horizontally and maintained by modular self-organized teams without central management, rather than a cathedral, e.g., Linux and Fetchmail. Schrape (2018) suggest that with corporate influence in FLOSS there are four types of open source projects,
- Corporate-led collaboration projects characterized by clear hierarchies,
- Hierarchical infrastructure projects that are largely run by nonprofits with horizontal structures,
- Elite-centered project communities that are hierarchical centered around a few core developers, and
- Egalitarian oriented peer production communities that maintain horizontal structure.
The ‘onion’ model suggests that newcomers move through the ranks by
- Contributing to bug fixes, documentation, small feature improvements, and discussion;
- Eventually becoming a core developer and contributing to pull requests.
Pull requests dictate the groups hierarchy. Small groups (3-7) are the primary settings for socialization, skill transfer, and the delegation of duties (Snow et al., 1986). Medium-sized groups (8-20) allow complex interdependent coordination. Decentralized groups perform better on complex tasks than centralized groups. More centralized communication patterns developed in groups that performed simple discrete tasks.
Goal settings and quality control are important group functions that require establishing a decision process. Resilient projects have complex structure with more than one person accepting pull requests. These complex groups maintained contributors and were more productive than star-shaped groups with a single person designated to accept pull requests.
Sharing information publicly reduces the burden of coordination creating less logistical overhead.
2.4 2021-08-16
2.4.1 Thesis Chapter 1
https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.12188 https://academic.oup.com/icesjms/article/77/7-8/2529/5912155#223391660 https://www.semanticscholar.org/paper/Estimation-and-classification-of-temporal-trends-to-Solvang-Planque/5f5727f6f2b3512ee5d9dc2e1258a7c75ed02ded https://www.semanticscholar.org/paper/A-simulation-study-of-trend-detection-methods-for-Hardison-Perretti/c679d003c94b70d587fa9be62f8a11911dc7944b#citing-papers https://github.com/nwfsc-timeseries/tvvarss::simTVVAR.R https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/arima.sim https://github.com/seanhardison1/soe_simulations/blob/master/R/sim_function.R https://github.com/kellijohnson-NOAA/tsrelation/blob/master/R/tvvarss_simTVVAR.R https://github.com/fate-ewi/bayesdfa::sim.R https://journal.r-project.org/archive/2019/RJ-2019-007/index.html
2.4.2 Hake recruitment
https://github.com/seanhardison1/soe_simulations/blob/master/R/sim_function.R
2.5 2021-06-10
2.5.1 Rstudio community talk - Building Effective Data Science Teams
<IP_ADDRESS> Prioritization
You will only ever have time to do 10% of the work. Therefore, it is important to have a list of tasks that are clearly defined and when a new task comes in it must be prioritized against the current list. Looking at a new task relative to the current list is important because if you want to work on the newly added task, then something else will need to be moved down the list.
2.6 2021-06-03
2.6.1 utils::file_test
Check if a file is a directory or file and if it exists or not. You can also test if a file is newer than or older than another file.
I found this function while perusing the bookdown::render_book function. It is used inside of an if statement, where the check is saved to an object, something I did not know how to do. I always thought you had to save it outside and then test it. For example,
if (!all(exist <- file_test("-f", input))) {
stop("Some files were not found: ", paste(input[!exist], collapse = ' '))
}
2.6.2 Openscapes
The openscapes training that Eric Ward set up helped to validate my workflow, which has been a great productivity generator for me because it often seemed like I was wasting time organizing and using such rigid standards. It is NOT a waste of time. Helping my future self not hate my job is legitimate.
Yesterday, I got feedback from PEP on my talk about sa4ss for the L-team. The previous day I got feedback from KM on the same talk. Both experiences were helpful. I learned that the more organized you are and the better the story of your first and last slides are, the better the information will be received.
2.6.3 R desc
The desc
package helps to read, parse, and edit DESCRIPTION files.
desc::desc_get_dps(file = "")
provides a list of all dependencies in the
DESCRIPTION file for a given package passed to file.
2.6.4 Pacific hake otolith exchange
Exchange of 100 otoliths with DFO
<IP_ADDRESS> Timing
Exchange fish from a single year.
Fish from early in the year are harder to age because the annulus isn’t as defined. Age readers often do fine when they know when the fish was landed because they can correct their read for the timing.
Survey ages will be coming to the lab later this year because of covid protocols that delay the timing of things.
<IP_ADDRESS> Bottom trawl survey are harder to read
The ages from the bottom trawl survey for hake are hard to read. They are patchy and faint. Not recommended for a beginning reader.
- genetic testing of hake fin clips from the two different surveys, midwater versus bottom trawl.
<IP_ADDRESS> Alternative methods for younger fish
Fish length, otolith weight, spectroscopy, …
Large year classes are hard to age when there are lots of little fish.
- Plot length distribution of age reads across years to see how consistent they are.
2.7 2021-05-29
2.7.1 Confidence intervals
When working with R, you can find the confidence interval of an estimate that is assumed to have a normal distribution using the stats package.
<- stats::qnorm(
crit p = 1 - (1 - 0.95) / 2,
mean = 0,
sd = 1,
lower.tail = TRUE,
log.p = FALSE
)print(crit)
## [1] 1.959964
will find the z score that is associated with a 95% confidence interval. One can change the value of 0.95 to any value between zero and one. This z-score is then multiplied by the standard error and both subtracted and added to the estimate to give a confidence interval. You can also multiply it by the standard deviation, but for small sample sizes the standard deviation needs to be corrected for sample size.
2.7.2 keywords
confidence interval statistics
2.8 2021-05-27
2.8.1 Lingcod CARE
- Mark Terwilliger (California): they do not age their own lingcod fins but they do
process them
- WDFW ages commercial samples, just under 1200 fins
- Laurel Lam aged sport samples, 260 samples per year,
- Mark Terwilliger is also currently ageing more sport fishery samples as we speak, he taught himself from looking at Laurel’s; also doing a second read on some structures that Laurel read
- black rockfish at the SWFSC is their bread and butter and there is no way that the SWFSC could age both lingcod and black rockfish at the same time
- Josie Thompson started looking into using otoliths in 2009 and 2010 (n = 100) to do double reads but nothing came of the study
- Nikki Paige (Newport)
- 2008 and back 100 percent aged, since then 2009 only half are aged
- 300 paired otolith samples, 2016 and 2017 survey data, they will be scanned as well as aged via break and burn,
- 2020 was 2000 fins
- doesn’t use the metal mesh binder clips, instead they use foam mats and pins
- Andrew Claiborne (WDFW)
- started production ageing in 2000
- port-samples do the fin-ray prep
- considered otoliths 3-4 years ago (n = 119), surface age on otolith because the otoliths get noisy as you go south, underageing relative to fin rays for the older fish, 5 year old fins appear as 10 year old otolith fish, older fish were fine, another couple hundred of pairs are available; like sablefish, if you only look at break and burn reads will be off but surface reads will help guide break and burn reads;
- Stephen Wischniowski
- 400-450 per year, 2021 == 1500 b/c they are behind, only age fin rays
- currently sampling oldest and youngest fish to do a comparison study
- Kevin McNeel (SE Alaska)
- fishers only return sampled fish
- getting sex data along with otolith data is important
- Chris Hinds (ADF&G ADU)
- use otoliths
- must use nail laqeur b/c they cannot get toxic material b/c there are no roads
2.9 2021-05-26
2.9.1 Steering committee
Mix of federal and external participants.
2.9.2 Cole Monnahan
Regarding how prioritizing is going to happen? Should we have a spreadsheet with each stock and their requirements. Rick responded with there is a start to that in SIS because it records basic information such as what model it is using. Christine responded with Stock SMART or peer-reviewed manuscripts could be helpful. Stock Smart has information on any stock that has an FMP.
As of 2019, 50 assessments are in SIS are VPA and 62 are SCAA according to StockSMART.
2.10 2021-05-26
2.10.1 Rethink Reporting with Automation by Claudio Rebelo and RStudio presentation
<IP_ADDRESS> Abstract
Companies struggle with reporting. Specifically, they’re caught in a cycle of inefficient and error-prone workflows that:
- Place a burden on individual data scientists when reports need to be repeated, updated, or shared.
- Prevent decision-makers and business users from getting important, accurate insights in a timely manner.
Resulting in enormous amounts of resources (people, tools, time) are invested into delivering a mediocre product to stakeholders, reports that are uninspiring to consume, slow to produce, and potentially not accurate.
On May 26th, we invite you to join Claudio Rebelo, Actuary at Swiss Re, to learn about how companies in every industry, but especially in insurance, can revolutionize their reporting capabilities with automation.
You’ll learn about his team’s journey transitioning from a reporting frankenstack, involving SAS, Excel, and SQL, to a more effective way with free, open-source tools like R Markdown.
The goal is to inspire you to think about what could be possible when it comes to reporting within your own organization, with just a little bit of effort. You’ll get a high-level overview of Claudio and Swiss Re’s journey, along with concrete tactical tips on how to use tools like R Markdown more effectively.
If you’re a team-lead or business user without much experience with R, you’ll learn:
- The consequences associated with traditional, messy reporting workflows.
- The benefits of automation when it comes to reporting.
- How to incorporate open-source tools like R Markdown into a corporate environment.
If you’re a data scientists already experienced with R and R Markdown you’ll learn:
- How to enhance your reporting with Shiny and parameterized reports.
- How to automate QA and collaboration tasks, like commenting.
- About new packages for specific tasks.
If you’re a data scientists already experienced with R, but not automating reports with tools like R Markdown
We hope this presentation inspires you to start ASAP!
<IP_ADDRESS> About the speaker
Claudio Rebelo / Actuary at Swiss Re Claudio Rebelo is an Actuary at Swiss Re in Zurich, Switzerland, where he has worked in reserving, pricing and currently model validation, having over 12 years of experience in the insurance industry. With a keen interest in insurance data visualization he is also involved, at Swiss Re, in the implementation of automated reporting solutions with R Markdown.
<IP_ADDRESS> R packages
- DT: searchable tables
- glue
- kable
- plotly
- officer
<IP_ADDRESS> Bookdown
- Can create word documents.
- Sentence structure
- Create sentences using ifelse statements
- Paramaterized reports
- Use the yaml header with param:
- Special characters can be escaped.
- Spell checker: word provides a lot of options, but so does RStudio. you can even load your own dictionary.
2.11 Acronyms
- FLOSS - Free/Libre Open Source Software


Abstract model providing information about rows of a table. More...
#include <rdb/abstracttablemodel.h>
Abstract model providing information about rows of a table.
One or more table models can be added to a TableItemModel in order to populate a list or tree view.
Inherited classes must implement at least the columnName() an text() methods.
| AbstractTableModel | ( | QObject * | parent | ) |
Constructor.
| parent | The parent object. |
| ~AbstractTableModel | ( | ) |
Destructor.
| virtual QString columnName | ( | int | column | ) | const [pure virtual] |
Return the header text of the given column.
| virtual QString text | ( | int | id, | |
| int | column | |||
| ) | const [pure virtual] |
Return the text of a given column of a row.
This method must be implemented in the inherited class.
| QPixmap icon | ( | int | id, | |
| int | column | |||
| ) | const [virtual] |
Return the icon of a given column of a row.
The default implementation returns an empty pixmap.
| QString toolTip | ( | int | id, | |
| int | column | |||
| ) | const [virtual] |
Return the tool tip of a given row.
The default implementation returns an empty string.
| int compare | ( | int | id1, | |
| int | id2, | |||
| int | column | |||
| ) | const [virtual] |
Compare two rows using given column.
The default implementation compares the texts using QString::localeAwareCompare().
| void dataChanged | ( | ) | [signal] |
Emit this signal when the model needs to be updated.
This signal is automatically connected to TableItemModel::updateData().


Ingredients: 4 OZ Dried Rice Noodle (1/4 - 1/2 inch)
2 TBSP Sugar
2 TBSP Fish Sauce
2 TBSP White Vinegar
3 TBSP Vegetable Oil
1/4 LB Chicken Breast (sliced thin, can sub fried tofu)
1 Egg
1 CUP Bean Sprouts
2 Stalk Green Onion (cut 2 inch slices)
2 TBSP Crushed Peanut
1 TSP Chile Powder
1 Lime
Preperation: 1. Soak the noodles in warm water for 30 minutes, until pliable enough to bend around a finger. (If you’re not using them immediately, you can drain the noodles and keep them in the fridge until ready to use.)
2. In a small bowl, stir together the sugar, fish sauce, and vinegar to make a sauce.
3. Heat an empty wok over high heat until it begins to smoke, then swirl in the oil. Once the oil is shimmering, add the chicken or tofu and stir-fry until the meat turns opaque but isn’t fully cooked, which should take about a minute (less time for shrimp—they will cook a little more quickly). Add the noodles and sauce, then continue to stir-fry, constantly stirring, until the noodles absorb the sauce, about another minute.
4. Use your spatula to push aside the noodles and leave them there, making an empty space in the center of the wok. Crack the egg into the empty space and let it cook until the edges start to set, 15 to 20 seconds. Use the edge of your spatula to break up and roughly scramble the egg, then toss it back in with the noodles while the egg is still soft. Once the egg looks mostly cooked, remove from the heat and throw in the bean sprouts and green onions, tossing thoroughly to combine. Transfer to a plate and garnish with the peanuts, chile powder, and lime wedge.


|
TP 2.5
1.0.0
Projeto Prático da Unidade Curricular AEDA
|
#include <graph.h>
Public Member Functions | |
| Graph & | addNode (const N &inf) |
| Graph & | addEdge (const N &begin, const N &end, const E &val) |
| Graph & | removeEdge (const N &begin, const N &end) |
| E & | edgeValue (const N &begin, const N &end) |
| unsigned | numEdges () const |
| unsigned | numNodes () const |
| void | print (std::ostream &os) const |
Private Attributes | |
| vector< Node< N, E > * > | nodes |
Graph Class - Contains every node and manages them
| N | - Type of the nodes of the graph |
| E | - Type of the edges of the graph |
| Graph< N, E > & Graph< N, E >::addEdge | ( | const N & | begin, |
| const N & | end, | ||
| const E & | val | ||
| ) |
Adds an edge betweeen two nodes
| begin | - Origin node |
| end | - Receptor node |
| val | - The value of the edge |
| E & Graph< N, E >::edgeValue | ( | const N & | begin, |
| const N & | end | ||
| ) |
Info about the edge value between two nodes
| begin | - First node's info |
| end | - Second node's info |
| unsigned Graph< N, E >::numEdges |
Number of edges in graph
| unsigned Graph< N, E >::numNodes |
Number of nodes in graph
| void Graph< N, E >::print | ( | std::ostream & | os | ) | const |
Function to send the info about the graph to a stream
| os | - Correspondent stream |
| Graph< N, E > & Graph< N, E >::removeEdge | ( | const N & | begin, |
| const N & | end | ||
| ) |
Removes an edge from the graph
| begin | - First node's info |
| end | - Final node's info |
Vector of nodes (allocated in memory - must be freed)


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Determines when the battery state changes.
More...
Determines when the battery state changes.
The BatteryStateService API lets you know when the battery state changes, that is, its current charge level, whether it is plugged and charging. It uses the BatteryChargeState structure to describe the current power state of Pebble.
Refer to the classio-battery-connection example, which demonstrates using the battery state service in a watchface.
◆ BatteryStateHandler [1/2]
Callback type for battery state change events
- Parameters
-
◆ BatteryStateHandler [2/2]
Callback type for battery state change events
- Parameters
-
◆ battery_state_service_peek()
Peek at the last known battery state.
- Returns
- a BatteryChargeState containing the last known data
◆ battery_state_service_subscribe()
Subscribe to the battery state event service. Once subscribed, the handler gets called on every battery state change
- Parameters
-
| handler | A callback to be executed on battery state change event |
◆ battery_state_service_unsubscribe()
| void battery_state_service_unsubscribe |
( |
void |
| ) |
|
Unsubscribe from the battery state event service. Once unsubscribed, the previously registered handler will no longer be called.


The DBManager class manages core methods used to access the data stored in the data base.
More...
#include <dbmanager.h>
The DBManager class manages core methods used to access the data stored in the data base.
◆ DBManager()
◆ AddFood()
| void DBManager::AddFood |
( |
const QString & |
city, |
|
|
const QString & |
food, |
|
|
const QString & |
price |
|
) |
| |
AddFood items to the DB.
- Parameters
-
| city; | name of city your adding a food item to |
| food; | name of the item |
| price; | items cost |
◆ CityToFoodNames()
| void DBManager::CityToFoodNames |
( |
const QString & |
city, |
|
|
QStringList & |
foods |
|
) |
| |
CityToFoodNames populates QStringList type with food items for a particular city.
- Parameters
-
| city; | city name |
| foods; | food name |
◆ DeleteFood()
| void DBManager::DeleteFood |
( |
const QString & |
foodName | ) |
|
◆ FoodNameToPrice()
| QString DBManager::FoodNameToPrice |
( |
const QString & |
food | ) |
|
FoodNameToPrice.
- Parameters
-
- Returns
- price for the passed in food item
◆ GetCities()
| void DBManager::GetCities |
( |
QStringList & |
cities | ) |
|
GetCities.
- Parameters
-
| cities; | container that holds all the cities in DB |
◆ GetDistances()
| int DBManager::GetDistances |
( |
const QString & |
city1, |
|
|
const QString & |
city2 |
|
) |
| |
GetDistances.
- Parameters
-
- Returns
- distance between two cities
◆ ImportCities()
| void DBManager::ImportCities |
( |
QWidget * |
parent = nullptr | ) |
|
ImportCities.
- Parameters
-
| parent; | access to QWidget class |
◆ instance()
creats one instance of the data base
- Returns
- pointer the the instance of the data base class
◆ operator=()
◆ UpdateFoodPrice()
| void DBManager::UpdateFoodPrice |
( |
const QString & |
foodName, |
|
|
const QString & |
price |
|
) |
| |
UpdateFoodPrice.
- Parameters
-
The documentation for this class was generated from the following files:
- /home/kord/Documents/source/cs1d/european-vacation/qt/app/dbmanager.h
- /home/kord/Documents/source/cs1d/european-vacation/qt/app/dbmanager.cpp


International text will be supported, but only via UTF-8. It has become the only sensible encoding, being plain-text compatible, supporting all human languages, and allowing documents with mixed languages. There is no reliable way to detect what encoding is used in a file, making it impossible to support other encodings in a fully automatic way. In any case, supporting other encodings would delay the desirable adoption of UTF-8 everywhere. So files must be converted to UTF-8 where necessary before being edited by Snipe.
When a new file is created, its filename is requested straight away, instead of creating an anonymous buffer. This is partly to be compatible with the no buffer convention. But it is also because otherwise the editor doesn't know the file extension and so can't do syntax highlighting of the text etc.
A separate settings file, perhaps .snipe
is supported in any
directory. A search is made in ancestor directories, so that a single settings
file can apply to a multi-directory project. A check is made that the file is
within the user's home area, to guard against security threats.
Conventional double clicks are time-dependent.  They are also inaccessible to people who have difficulty in clicking fast enough. So in Snipe a double click means exactly the same as two single clicks.
The common effect of double or triple clicking to select a word or line can still be achieved. A click at the same place as the existing cursor causes a word to be selected. A click within an existing selection causes it to be extended to the whole line. Within a directory listing, a click on a file name which is already selected causes the file to be opened.
Semicolons are inserted or corrected automatically on every edit, in a similar fashion to indenting. This is more language-dependent than indenting, and requires some support from language scanning.
Multiple cursors are too cool to leave out of Snipe. They are coming soon.
On pressing CTRL+S
for example, the file is saved, and a
pre-defined command or command sequence issued to compile and/or run the
program. This should be within an existing terminal window that the programmer
is already using, with a preferred environment, and which Snipe was
started up from.
Scrolling by grabbing a bar with the mouse, and some kind of equivalent using the keyboard, will be implemented. This will probably use a (semi-)transparent overlayed bar rather than permanently stealing space from the text, and much larger than usual to make an easy target for the mouse. Line numbers should also be visible as an overlay.
To go straight to a specific line number, the CTRL key is held down while the digits are typed. A line number overlay, and perhaps scrolling overlay, is displayed during the operation.


Weather Dashboard
Temprature:
Humidity:
Wind Speed:
UV index:
5-Day Forecast:
Temp:
Humidity:
Temp:
Humidity:
Temp:
Humidity:
Temp:
Humidity:
Temp:
Humidity:


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BILLY series
With its seamless customization options that make it the perfect addition to rooms of
any
size, it’s no wonder IKEA’s BILLY bookcase series has become a beloved classic around the world.
BILLY
bookcases are built with a stackable design that allows you to attach new units whenever you need
additional storage, just decide on what height suits your space best. Every model in the BILLY
series
also features adjustable shelves so you can fit anything from books to trophies, and everything in
between.