Chapter 14 Introduction to Bacteremia
To demonstrate the workflow and content of IDA, we created a hypothetical research aim and corresponding statistical analysis plan, which is described in more detail in the section Bact_SAP.Rmd.
Hypothetical research aim for IDA is to develop a multivariable diagnostic model for bacteremia using 49 continuous laboratory blood parameters, age and gender with the primary aim of prediction and a secondary aim of describing the association of each variable with the outcome (‘explaining’ the multivariable model).
A diagnostic prediction model was developed based on this data set and validated in “A Risk Prediction Model for Screening Bacteremic Patients: A Cross Sectional Study” Ratzinger et al, PLoS One 2014. The assumed research aim is in line with this diagnostic prediction model.
14.1 Dataset Description
Ratzinger et al (2014) performed a diagnostic study in which age, sex and 49 laboratory variables can be used to diagnose bacteremia status of a blood sample using a multivariable model. Between January 2006 and December 2010, patients with the clinical suspicion to suffer from bacteraemia were included if blood culture analysis was requested by the responsible physician and blood was sampled for assessment of haematology and biochemistry. The data consists of 14,691 observations from different patients.
Our version of this data was slightly modified compared to original version, and this modified version was cleared by the Medical University of Vienna for public use (DC 2019-0054). Variable names have been kept as they were (partly German abbreviations). A data dictionary is available in the misc folder of the project directory (‘bacteremia-DataDictionary.csv’).
In the original paper describing the study (Ratzinger et al, PLoS One 2014), a machine learning approach was taken to diagnose a positive status of blood culture. The true status was determined for all blood samples by blood culture analysis, which is the gold standard. Here we will make use of a multivariable logistic regression model.
14.2 Bacteremia dataset contents
14.2.1 Source dataset
We refer to the source data set as the dataset available in this repository.
Display the source dataset contents. This dataset is in the data folder of the project directory.
Data frame:bact
14691 observations and 53 variables, maximum # NAs:7114| Name | Storage | NAs |
|---|---|---|
| ID | integer | 0 |
| sex | integer | 0 |
| Alter | integer | 0 |
| MCV | double | 42 |
| HGB | double | 41 |
| HCT | double | 42 |
| PLT | integer | 42 |
| MCH | double | 42 |
| MCHC | double | 42 |
| RDW | double | 56 |
| MPV | double | 702 |
| LYM | double | 262 |
| MONO | double | 246 |
| EOS | double | 135 |
| BASO | double | 146 |
| NT | integer | 2467 |
| APTT | double | 2549 |
| FIB | integer | 2567 |
| NA. | integer | 1282 |
| K | double | 2008 |
| CA | double | 1276 |
| PHOS | double | 1242 |
| MG | double | 1869 |
| KREA | double | 159 |
| BUN | double | 172 |
| HS | double | 3061 |
| GBIL | double | 1441 |
| TP | double | 1583 |
| ALB | double | 1676 |
| AMY | integer | 3913 |
| PAMY | integer | 7114 |
| LIP | integer | 3699 |
| CHE | double | 2447 |
| AP | integer | 1400 |
| ASAT | integer | 1154 |
| ALAT | integer | 987 |
| GGT | integer | 1262 |
| LDH | integer | 1714 |
| CK | integer | 2080 |
| GLU | integer | 4192 |
| TRIG | integer | 5061 |
| CHOL | integer | 5045 |
| CRP | double | 155 |
| BASOR | double | 732 |
| EOSR | double | 732 |
| LYMR | double | 732 |
| MONOR | double | 732 |
| NEU | double | 728 |
| NEUR | double | 732 |
| PDW | double | 1102 |
| RBC | double | 461 |
| WBC | double | 462 |
| BloodCulture | character | 0 |
14.2.2 Updated analysis dataset
Additional meta-data is added to the original source data set. We write this new modified (annotated) data set back to the data folder after adding additional meta-data for all variables. The meta-data is taken from the data dictionary.
At the stage we could select the variables of interest to take in to the IDA phase by dropping variables we do not check in IDA.
As a cross check we display the contents again to ensure the additional data is added, and then write the changes to the data folder in the file “data/a_bact.rda”.
Input object size: 5119632 bytes; 53 variables 14691 observations New object size: 5159904 bytes; 53 variables 14691 observations Input object size: 5277552 bytes; 54 variables 14691 observations New object size: 5219544 bytes; 54 variables 14691 observations
Data frame:a_bact
14691 observations and 54 variables, maximum # NAs:7114| Name | Labels | Units | Class | Storage | NAs |
|---|---|---|---|---|---|
| ID | Patient Identification | 1-14691 | integer | integer | 0 |
| sex | Patient Sex | 1=male, 2=female | integer | integer | 0 |
| Alter | Patient Age | years | integer | integer | 0 |
| MCV | Mean corpuscular volume | pg | numeric | double | 42 |
| HGB | Haemoglobin | G/L | numeric | double | 41 |
| HCT | Haematocrit | % | numeric | double | 42 |
| PLT | Blood platelets | G/L | integer | integer | 42 |
| MCH | Mean corpuscular hemoglobin | fl | numeric | double | 42 |
| MCHC | Mean corpuscular hemoglobin concentration | g/dl | numeric | double | 42 |
| RDW | Red blood cell distribution width | % | numeric | double | 56 |
| MPV | Mean platelet volume | fl | numeric | double | 702 |
| LYM | Lymphocytes | G/L | numeric | double | 262 |
| MONO | Monocytes | G/L | numeric | double | 246 |
| EOS | Eosinophils | G/L | numeric | double | 135 |
| BASO | Basophiles | G/L | numeric | double | 146 |
| NT | Normotest | % | integer | integer | 2467 |
| APTT | Activated partial thromboplastin time | sec | numeric | double | 2549 |
| FIB | Fibrinogen | mg/dl | integer | integer | 2567 |
| NA. | Sodium | mmol/L | integer | integer | 1282 |
| K | Potassium | mmol/L | numeric | double | 2008 |
| CA | Calcium | mmol/L | numeric | double | 1276 |
| PHOS | Phosphate | mmol/L | numeric | double | 1242 |
| MG | Magnesium | mmol/L | numeric | double | 1869 |
| KREA | Creatinine | mg/dl | numeric | double | 159 |
| BUN | Blood urea nitrogen | mg/dl | numeric | double | 172 |
| HS | Uric acid | mg/dl | numeric | double | 3061 |
| GBIL | Bilirubin | mg/dl | numeric | double | 1441 |
| TP | Total protein | G/L | numeric | double | 1583 |
| ALB | Albumin | G/L | numeric | double | 1676 |
| AMY | Amylase | U/L | integer | integer | 3913 |
| PAMY | Pancreas amylase | U/L | integer | integer | 7114 |
| LIP | Lipases | U/L | integer | integer | 3699 |
| CHE | Cholinesterase | kU/L | numeric | double | 2447 |
| AP | Alkaline phosphatase | U/L | integer | integer | 1400 |
| ASAT | Aspartate transaminase | U/L | integer | integer | 1154 |
| ALAT | Alanin transaminase | U/L | integer | integer | 987 |
| GGT | Gamma-glutamyl transpeptidase | G/L | integer | integer | 1262 |
| LDH | Lactate dehydrogenase | U/L | integer | integer | 1714 |
| CK | Creatinine kinases | U/L | integer | integer | 2080 |
| GLU | Glucoses | mg/dl | integer | integer | 4192 |
| TRIG | Triclyceride | mg/dl | integer | integer | 5061 |
| CHOL | Cholesterol | mg/dl | integer | integer | 5045 |
| CRP | C-reactive protein | mg/dl | numeric | double | 155 |
| BASOR | Basophile ratio | % | numeric | double | 732 |
| EOSR | Eosinophil ratio | % | numeric | double | 732 |
| LYMR | Lymphocyte ratio | % (mg/dl) | numeric | double | 732 |
| MONOR | Monocyte ratio | % | numeric | double | 732 |
| NEU | Neutrophiles | G/L | numeric | double | 728 |
| NEUR | Neutrophile ratio | % | numeric | double | 732 |
| PDW | Platelet distribution width | % | numeric | double | 1102 |
| RBC | Red blood count | T/L | numeric | double | 461 |
| WBC | White blood count | G/L | numeric | double | 462 |
| BloodCulture | Blood culture result for bacteremia | no, yes | character | character | 0 |
| BC | bacteremia | 0/1 | integer | integer | 0 |
14.3 Section session info
## R version 4.1.3 (2022-03-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 17763)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_Austria.1252 LC_CTYPE=English_Austria.1252
## [3] LC_MONETARY=English_Austria.1252 LC_NUMERIC=C
## [5] LC_TIME=English_Austria.1252
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] Hmisc_4.6-0 Formula_1.2-4 survival_3.2-13 lattice_0.20-45
## [5] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.8 purrr_0.3.4
## [9] readr_2.1.2 tidyr_1.2.0 tibble_3.1.6 ggplot2_3.3.5
## [13] tidyverse_1.3.1 here_1.0.1
##
## loaded via a namespace (and not attached):
## [1] httr_1.4.2 sass_0.4.1 jsonlite_1.8.0
## [4] splines_4.1.3 modelr_0.1.8 bslib_0.3.1
## [7] assertthat_0.2.1 latticeExtra_0.6-29 cellranger_1.1.0
## [10] yaml_2.3.5 pillar_1.7.0 backports_1.4.1
## [13] glue_1.6.2 digest_0.6.29 checkmate_2.0.0
## [16] RColorBrewer_1.1-2 rvest_1.0.2 colorspace_2.0-3
## [19] htmltools_0.5.2 Matrix_1.4-0 pkgconfig_2.0.3
## [22] broom_0.7.12 haven_2.4.3 bookdown_0.25
## [25] scales_1.1.1 jpeg_0.1-9 tzdb_0.2.0
## [28] htmlTable_2.4.0 generics_0.1.2 ellipsis_0.3.2
## [31] withr_2.5.0 nnet_7.3-17 cli_3.2.0
## [34] magrittr_2.0.2 crayon_1.5.1 readxl_1.3.1
## [37] evaluate_0.15 fs_1.5.2 fansi_1.0.3
## [40] xml2_1.3.3 foreign_0.8-82 data.table_1.14.2
## [43] tools_4.1.3 hms_1.1.1 lifecycle_1.0.1
## [46] munsell_0.5.0 reprex_2.0.1 cluster_2.1.2
## [49] compiler_4.1.3 jquerylib_0.1.4 rlang_1.0.2
## [52] grid_4.1.3 rstudioapi_0.13 htmlwidgets_1.5.4
## [55] base64enc_0.1-3 rmarkdown_2.13 gtable_0.3.0
## [58] DBI_1.1.2 R6_2.5.1 gridExtra_2.3
## [61] lubridate_1.8.0 knitr_1.38 fastmap_1.1.0
## [64] utf8_1.2.2 rprojroot_2.0.2 stringi_1.7.6
## [67] Rcpp_<IP_ADDRESS> vctrs_0.3.8 rpart_4.1.16
## [70] png_0.1-7 dbplyr_2.1.1 tidyselect_1.1.2
## [73] xfun_0.30


Mat3 Class
A 3x3 matrix.
Constructor
Mat3
(
-
array
Parameters:
-
array
Objectelements Array of nine elements. Optional.
Item Index
Methods
Properties
Methods
copy
(
Mat3
-
source
Copy another matrix into this matrix object.
Parameters:
-
source
Mat3
Returns:
Mat3:
this
e
(
Number
-
row
-
column
-
value
Get an element in the matrix by index. Index starts at 0, not 1!!!
Parameters:
-
row
Number -
column
Number -
value
NumberOptional. If provided, the matrix element will be set to this value.
Returns:
Number:
identity
()
Sets the matrix to identity
mmult
(
Mat3
-
m
Matrix multiplication
Parameters:
-
m
Mat3Matrix to multiply with from left side.
Returns:
Mat3:
The result.
reverse
(
Mat3
-
target
reverse the matrix
Parameters:
-
target
Mat3Optional. Target matrix to save in.
Returns:
Mat3:
The solution x
setZero
()
Set all elements to zero
smult
(
-
s
Matrix-scalar multiplication
Parameters:
-
s
Number
toString
()
Returns a string representation of the matrix.
Returns:
string
Properties
elements
Array
A vector of length 9, containing all matrix elements


 They are described here to facilitate debugging and
extending the library. They are not to be used by applications.
typedef struct bignum_st BIGNUM;
struct bignum_st
{
BN_ULONG *d; /* Pointer to an array of 'BN_BITS2' bit chunks. */
int top; /* Index of last used d +1. */
/* The next are internal book keeping for bn_expand. */
int dmax; /* Size of the d array. */
int neg; /* one if the number is negative */
int flags;
};
The integer value is stored in d, a malloc()ed array of words (BN_ULONG), least significant word first. A BN_ULONG can be either 16, 32 or 64 bits in size, depending on the 'number of bits'
(BITS2) specified in
openssl/bn.h .
dmax is the size of the d array that has been allocated. top
is the number of words being used, so for a value of 4, bn.d[0]=4 and
bn.top=1. neg is 1 if the number is negative. When a BIGNUM is
0, the d field can be NULL and top == 0.
flags is a bit field of flags which are defined in openssl/bn.h . The flags begin with BN_FLG_. The macros BN_set_flags(b,n) and
BN_get_flags(b,n) exist to enable or fetch
flag(s) n from BIGNUM
structure b.
Various routines in this library require the use of temporary
BIGNUM variables during their execution. Since dynamic memory allocation to create BIGNUMs is rather expensive when used in conjunction with repeated subroutine
calls, the BN_CTX structure is used. This structure contains BN_CTX_NUM BIGNUMs, see
BN_CTX_start(3).
These functions are implemented in C and for several platforms in assembly
language:
bn_mul_words( rp, ap, num, w) operates on the num word arrays rp and ap. It computes ap * w, places the result in rp, and returns the high word (carry).
bn_mul_add_words( rp, ap, num, w) operates on the num
word arrays rp and ap. It computes ap * w + rp, places the result in rp, and returns the high word (carry).
bn_sqr_words( rp, ap, n) operates on the num word array
ap and the 2*num word array ap. It computes ap * ap
word-wise, and places the low and high bytes of the result in rp.
bn_div_words( h, l, d) divides the two word number (h,l) by d and returns the result.
bn_add_words( rp, ap, bp, num) operates on the num word arrays ap, bp and rp. It computes ap + bp, places the result in rp, and returns the high word (carry).
bn_sub_words( rp, ap, bp, num) operates on the num word arrays ap, bp and rp. It computes ap - bp, places the result in rp, and returns the carry (1 if bp > ap, 0 otherwise).
bn_mul_comba4( r, a, b) operates on the 4 word arrays a and
b and the 8 word array r. It computes a*b and places the result in r.
bn_mul_comba8( r, a, b) operates on the 8 word arrays a and
b and the 16 word array r. It computes a*b and places the result in r.
bn_sqr_comba4( r, a, b) operates on the 4 word arrays a and
b and the 8 word array r.
bn_sqr_comba8( r, a, b) operates on the 8 word arrays a and
b and the 16 word array r.
The following functions are implemented in C:
bn_cmp_words( a, b, n) operates on the n word arrays a
and b. It returns 1, 0 and -1 if a is greater than, equal and less than b.
bn_mul_normal( r, a, na, b, nb) operates on the na
word array a, the nb word array b and the na+nb word array r. It computes a*b and places the result in r.
bn_mul_low_normal( r, a, b, n) operates on the n word arrays r, a and b. It computes the n low words of
a*b and places the result in r.
bn_mul_recursive( r, a, b, n2, dna, dnb, t) operates on the word arrays a and b of length n2+dna and n2+dnb
(dna and dnb are currently allowed to be 0 or negative) and the 2*n2
word arrays r and t. n2 must be a power of 2. It computes
a*b and places the result in r.
bn_mul_part_recursive( r, a, b, n, tna, tnb, tmp) operates on the word arrays a and b of length n+tna and
n+tnb and the 4*n word arrays r and tmp.
bn_mul_low_recursive( r, a, b, n2, tmp) operates on the
n2 word arrays r and tmp and the n2/2 word arrays a
and b.
bn_mul_high( r, a, b, l, n2, tmp) operates on the
n2 word arrays r, a, b and l (?) and the 3*n2 word array tmp.
BN_mul() calls bn_mul_normal(), or an optimized
implementation if the factors have the same size:
bn_mul_comba8() is used if they are 8 words long,
bn_mul_recursive() if they are larger than
BN_MULL_SIZE_NORMAL and the size is an exact multiple of the word size, and
bn_mul_part_recursive() for others that are larger than
BN_MULL_SIZE_NORMAL.
bn_sqr_normal( r, a, n, tmp) operates on the n word array
a and the 2*n word arrays tmp and r.
The implementations use the following macros which, depending on the
architecture, may use ``long long'' C operations or inline assembler. They
are defined in bn_lcl.h .
mul( r, a, w, c) computes w*a+c and places the low word of the result in r and the high word in c.
mul_add( r, a, w, c) computes w*a+r+c and places the low word of the result in r and the high word in c.
sqr( r0, r1, a) computes a*a and places the low word of the result in r0 and the high word in r1.
bn_expand() ensures that b has enough space for a bits bit number. bn_wexpand() ensures that b has enough space for an
n word number. If the number has to be expanded, both macros call
bn_expand2(), which allocates a new d array and copies the data. They return NULL on error, b otherwise.
The bn_fix_top() macro reduces a->top to point to the most significant non-zero word plus one when a has shrunk.
bn_check_top() verifies that ((a)->top >= 0 && (a)->top
<= (a)->dmax) . A violation will cause the program to abort.
bn_print() prints a to stderr. bn_dump() prints n words at d
(in reverse order, i.e. most significant word first) to stderr.
bn_set_max() makes a a static number with a dmax of its current size. This is used by bn_set_low() and
bn_set_high() to make r a read-only
BIGNUM that contains the n low or high words of a.
If BN_DEBUG is not defined, bn_check_top(), bn_print(),
bn_dump() and bn_set_max() are defined as empty
macros.
bn(3)
| | |


GeoMesa Blob Store¶
The GeoMesa Blob Store is found in geomesa-blobstore
in the source distribution.
The GeoMesaIndexedBlobStore
is an interface that describes the
function of a GeoMesa BlobStore, which is to store and retrieve files
that have spatio-temporal data associated with them. A GeoMesa Blobstore
is created by combining a geotools data store and a backing blob store
which will contain the blobs separated from the geo index. The
BlobStore
interface can be used to implement compatibility with
other databases or distributed file systems.
During ingest of a file into a GeoMesa BlobStore, a pluggable system of
FileHandler
s examines the files (and associated maps of
parameters) and creates SimpleFeature
s which are the written to a
GeoMesa data store while the blobs are persisted using a class that
implements the BlobStore
interface.
File retrieval is a two-step process. First a query is made to the
GeoMesa FeatureStore
. The returned SimpleFeature
s will contain
a URI field. That URI points to the desired file stored in Accumulo, and
can be retrieved by the GeoMesaIndexedBlobStore
API or by the REST
interface.
FileHandler Interface¶
The FileHandler interface is designed to allow file handling in the
Blobstore to be pluggable. Implementors should implement
org.locationtech.geomesa.blob.api.handlers.FileHandler
or extend the
abstract implementation
org.locationtech.geomesa.blob.api.handlers.AbstractFileHandler
. The
class WKTFileHandler
serves as an example of that latter approach.
FileHandler
implementations are loaded at runtime by the Java
ServiceLoader. As such, available implementations should have their
classname registered in
META-INF/services/org.locationtech.geomesa.blob.api.FileHandler
.
BlobStore Interface¶
The BlobStore
interface is designed to allow the backing blob store
of a GeoMesaIndexedBlobStore
to be pluggable. Implementors should
implement org.locationtech.geomesa.blob.api.BlobStore
interface. The
AccumuloBlobStoreImpl
serves as an example implementation of a
BlobStore
.
As of this time the BlobStore
interface does not yet use the Service
Provider Interface.
Provided File Handlers¶
The BlobStore API contains by default the WKTFileHandler
and
ByteArrayHandler
handlers. The WKTFileHandler
allows users to
ingest any file by associating a WKT geometry to a file. Similarly the
ByteArrayHandler
allows users to ingest arbitrary byte arrays
accompanied with spatio-temporal attributes.
Along with these included handlers, the GeoMesa BlobStore has two sub modules of additional handlers in the geomesa-blobstore-handlers module.
GeoMesa-BlobStore-EXIF¶
The EXIF module contains the MetadataFileHandler
which can parse
EXIF metadata to retrieve geolocation information. This enables ingest
of large collections of geotagged images into a GeoMesa BlobStore.
GeoMesa-BlobStore-GDAL¶
The GDAL module contains the GDALFileHandler
which utilizes GDAL to
extract geolocation information and time from raster/imagery files
supported by GDAL 2.0.0. For a complete list of GDAL supported file
formats please refer to: GDAL formats list.
To utilize this handler the user must have compiled GDAL Java bindings and have placed relevant JNI libraries in the LD_LIBRARY_PATH environment variable. To build GDAL and the JNI libraries, follow the instructions here: GDAL JNI build instructions.
GeoMesa-BlobStore-Accumulo¶
The BlobStore-Accumulo module contains concrete implementations of the
GeoMesaIndexedBlobStore
interface for Accumulo as well as an
implementation of the BlobStore
interface for Accumulo, the
AccumuloBlobStoreImpl
class. The GeoMesaAccumuloBlobStore
utilizes a GeoMesa Accumulo DataStore as well as the
AccumuloBlobStoreImpl
for the Blob persistance layer.
File retrieval is a two-step process. First a query is made to the
GeoMesa FeatureStore
. The returned SimpleFeature
s will contain
a URI field. That URI points to the desired file stored in Accumulo, and
can be retrieved by the GeoMesaIndexedBlobStore
API or by the REST
interface.
REST API¶
The GeoMesa BlobStore comes with a RESTful web interface servlet that can be used in place of more direct programmatic access via the Java and Scala classes. As of now the the BlobStore only provides an interface to an Accumulo backed DataStore and BlobStore. Once the servlet is deployed the RESTful api for the Blobstore can be easily utilized via cURL.
DataStores are managed by assigning them to aliases, this allows users to connect to multiple blobstores. To Register a GeoMesa Blob Store to an alias (in this case myBlobStore):
curl -d 'instanceId=myCloud' -d 'zookeepers=zoo1,zoo2,zoo3' -d 'tableName=myBlobStore' -d 'user=user' -d 'password=password' http://localhost:8080/geoserver/geomesa/blobstore/ds/myBlobStore
Other Blob Store commands:
- DELETE /ds/:alias - Delete a previously registered GeoMesa data store
- GET /ds/:alias - Display a registered GeoMesa data store
- GET /ds/ - Display all registered BlobStores
To ingest a file:
curl -X POST -F<EMAIL_ADDRESS>http://localhost:8080/geoserver/geomesa/blobstore/blob/:alias
To GET a file with the original filename preserved via id, run:
curl -JO http://localhost:8080/geoserver/geomesa/blobstore/blob/:alias/some-id/
The Blobstore servlet also has optional GZip support which can be used
by adding the --compressed
cURL parameter.
curl --compressed -JO http://localhost:8080/geoserver/geomesa/blobstore/blob/:alias/some-id
To DELETE a file from the blobstore, you must do so by id:
curl -X "DELETE" http://localhost:8080/geoserver/geomesa/blobstore/blob/:alias/some-id
Servlet Configuration Options¶
File upload constraints for the BlobstoreServlet
can be configured with
the following system properties:
org.locationtech.geomesa.blob.api.maxFileSizeMB (defaults to 50MB)
org.locationtech.geomesa.blob.api.maxRequestSizeMB (defaults to 100MB)
The expected unit for these properties is in MB, so setting
org.locationtech.geomesa.blob.api.maxFileSizeMB=10
will result in a
10MB maxFileSize.


|
FANTOM is an international research consortium established by Dr. Hayashizaki and his colleagues in 2000 to assign functional annotations to the full-length cDNAs that were collected during the Mouse Encyclopedia Project at RIKEN.
FANTOM1-3 focused on identifying the transcribed components of mammalian cells, improving gene identification and alternative transcript isoforms in both human and mouse, and revealed that a large fraction of the transcriptome is non-coding. FANTOM4 focused on the dynamics of transcription start site (TSS) usage via deepCAGE monitoring during a time course of monocytic differentiation in the acute myeloid leukemia cell line THP-1 helping to identifying key factors that determine cell fates. FANTOM5 focused on systematically investigating transciptional expression in virtually all cell types across the human body and mice. We aim to use this information to build transcriptional regulatory models for every primary cell type that makes up a human. All FANTOM5 views in data explorer |
||
| Basic annotation views | ||
| If you do not see your genome of interest, please search for a view configuration in the data explorer |
ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data processing and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files.
Please check our documentation wiki for details on how to use the system, or check out some of the views above.
Please check our documentation wiki for details on how to use the system, or check out some of the views above.
The ZENBU system is compatible with the majority of web browsers : Google Chrome, Firefox, Safari, Opera.
currently ZENBU does not support InternetExplorer for lack of sufficient HTML5/SVG/XML support.


Natalie and Tristan met in late November of 2011 when he was next in line at the Starbucks register Natalie was working behind. Tristan had recently begun working across the street at a menswear boutique and would soon become a regular at Natalie’s store, seeing her for his daily Double Tall Americano. Natalie found Tristan handsome and endearing, which is way more than she could say for any other customer who came into her Starbucks because they were all horrible and the worst.
A month or so went by and Tristan’s daily coffee trip turned into TRIPS stopping in before and after his shift--this fact was not lost on Natalie. Finally after holding up too many lines and Natalie giving Tristan too many free Double Tall Americanos, Tristan asked Natalie out on a date and they have been going on dates ever since.
Natalie and Tristan live together in Chicago with their “doghter” (like “daughter”, but she’s a dog), Holiday. Natalie works as a manufacturer’s representative and Tristan is in web development. Tristan had worked as a commercial diver and traveled often all over the world for the majority of their relationship, so they very much appreciate their time at home together. Natalie likes to cook food and Tristan enjoys eating it. Tristan likes to make cocktails and Natalie enjoys drinking them. Natalie loves to love Tristan and Tristan loves to love Natalie. They cannot put into words how excited they are to be married and to celebrate with their dearest friends and family!


D-PLACE is open source software. Source code is available on GitHub under an MIT License.
D-PLACE uses Travis CI for continuous integration. Automated tests are run with each commit to the repository, build status is reported at travis-ci.org/D-PLACE/dplace.
Please report issues using the GitHub Issue Tracker.


{% extends "base.html" %} {% block body %}
coming in future blog posts. One thing to note right now: data comes back in a bunch of 7kB base64 encoded chunks.
| Command | Information |
| shell {command} | This runs {command} in a terminal by leveraging JXA's Application.doShellScript({command}) |
| js {command} | This runs the JavaScript command, {command}, and returns its output |
| jsb {command} | This runs the ObjectiveC bridge JavaScript command, {command}, and returns its output. This will call deepunwrap on the output to convert the ObjectiveC objects to normal strings to be returned |
| shell_elevated | This creates two popup dialogs prompting for a command to run and a prompt to give the user. The command will use your prompt to pop a dialog box for the user asking for them to input their password so that the command you entered will be executed in an elevated context |
| shell_api | This creates two popup dialogs prompting for a full binpath and then arguments for that binary. The command uses the ObjectiveC bridge to spawn that process with those arguments on the computer and get your output back. It is not interactive. |
| launchapp {bundle name} | This uses the Objective C bridge to launch the specified app asynchronously and 'hidden' (it'll still show up in the dock for now). An example of the bundle name is 'com.apple.itunes' for launching iTunes. |
| clipboard | This will return the current clipboard contents on the target machine. |
| clipboard [data] | This will set the clipboard data to [data] |
| list_apps [verbose] | This uses JXA to list the currently running processes on the sytem and provides some information about them. To get a lot of information, use the verbose optional parameter |
| list_users [method] | This uses JXA to list the non-service user accounts on the system. In the future you can specify a [method] to do this via the ObjectiveC bridge or other methods. |
| current_user [method] | This uses JXA to list information about the current user. In the future you can specify a [method] to do this via the ObjectiveC bridge or other methods. |
| security_info [method] | This uses JXA to list some security information about the system. In the future you can specify a [method] to do this via the ObjectiveC bridge or other methods. |
| chrome_tabs | This uses JXA to list information about all of the open tabs in all of the open Chrome instances. If Chrome is not currently running, this will launch Chrome (potential OPSEC issue) and might have a conflict with trying to access Chrome tabs as Chrome is starting. It's recommended to not use this unless Chrome is already running. Use the list_apps function to check if Chrome is running. |
| chrome_bookmarks | This uses JXA to list information about all of the bookmarks in Chrome. If Chrome is not currently running, this will launch Chrome (potential OPSEC issue) and might have a conflict with trying to access Chrome's bookmarks as Chrome is starting. It's recommended to not use this unless Chrome is already running. Use the list_apps function to check if Chrome is running. |
| js_chrome {window ID number} {tab ID number} {JavaScript} | This uses JXA to execute the specified JavaScript code into a specific browser tab. The chrome_tabs function will specify for each tab the window/tab numbers that you can use for this function. |
| system_info [method] | This uses JXA to get some system information. In the future you can specify a [method] to do this via the ObjectiveC bridge or other methods. |
| terminals read [history] [contents] | This uses JXA to read information about open instances of Apple's Terminal.app. The contents flag allows you to see exactly what the user can see at that moment on the screen. The history flag allows you to see everything that's in that tab's scroll history. This can be a lot of information, so keep that in mind. This function will also give you the window/tab information for each open session and a bunch of other information. |
| terminals send {window ID number} {tab ID number} {command} | This uses JXA to inject the shell command, {command}, into the specified terminal shell as if the user typed it from the keyboard. This is pretty powerful. Consider the instance where the user is SSH-ed into another machine via terminal - with this you can inject commands to run on the remote host. Just remember, the user will be able to see the command, but you can always see what they see as well with the terminals read contents command. |
| spawn shell_api oneliner apfell-jxa {payload UUID} | This pulls down the payload specified by {payload UUID} and uses the shell_api to execute it in a sub-process. I'll look into spawning it in such a way that it doesn't end up being a subprocess, but you can still interact with each of them at the same time. |
| exit | This exits the current apfell-jxa instance by leveraging the ObjectiveC bridge's NSApplication terminate function. |


bearingsToRegister property
Bearings to register in this session
@note The number of faces to register is determined by the {@linkcode VerIDSessionSettings.numberOfResultsToCollect} parameter. If the number of results to collect exceeds the number of bearings to register the session will start take the next bearing from the beginning of the bearings array.
For example, a session with bearings to register set to [Bearing.STRAIGHT, Bearing.LEFT, Bearing.RIGHT]
and numberOfResultsToCollect
set to 2
will register faces with bearings: [Bearing.STRAIGHT, Bearing.LEFT]
.
A session with bearings to register set to ```Bearing.STRAIGHT, Bearing.LEFT, Bearing.RIGHT
and
numberOfResultsToCollectset to
2will register faces with bearings:
Bearing.STRAIGHT, Bearing.LEFT, Bearing.RIGHT, Bearing.STRAIGHT
`.
Implementation
List<Bearing> bearingsToRegister = [
Bearing.STRAIGHT,
Bearing.LEFT,
Bearing.RIGHT
];


Purdue ROV competed in Houston, TX from June 23 - 25 at NASA's Neutral Buoyancy Lab! The team reached its largest size yet at 42 members with Kyle Rakos captaining the team first semester and for the competition while Sanay Shah took over for the second semester. At the international competition we had a wonderful technical presentation, an excellent poster, and great technical documentation. We had some electronics issues during the mission runs but were still able to place 13th internationally! Additionally, Kyle Rakos was awarded with the Flying Fish award for his passion and demonstrated leadership in the field!
The team faced its third change in captancy with Kyle Rakos taking over. The many new team members designed this polar oilfield service vehicle. The dedicated group of 20 students finished 15th out of 42 registered teams in St. John's, NL, Canada. The team is eager to use what they learned to finish in the top 5 next year.
This was the first year in the team's history that they failed to qualify for the international competition. The marine sanctuary vehicle designed to identify shipwrecks and study marine ecology could not be built. Plagued with thruster issues throughout the season, the team still managed to construct a prototype vehicle and train members on both electrical and mechanical design. The prototype vehicle, affectionately dubbed ROV Incompetence, would be improved upon for future practice missions in order to prepare for next season.
After Seth led the team for four years, the team faced its first change in captaincy. Michael Hayashi led the charge to ensure the team's legacy continued with a new seafloor networking vehicle. This resulted in the creation of ROV Model N. The team finished 17th in the Explorer class in Seattle, WA.
The Purdue Offshore Tanker Assessment and Tactical Operations Submersible finished 2nd Place in Orlando, FL. Seth Baklor was one of sixteen team members that made this shipwreck study and fuel oil extraction vehicle.
Seth Baklor led a team of nine people to finish 2nd in the Explorer class in Houston, TX. ROV Hybris was a specific-purpose ROV built to solve the challenges of the Deepwater Horizons oil spill.
The eight team members, including Captain Seth Baklor, finished 4th in the Explorer class in Hilo, HI. ROV Competence was a volcanic seamount exploration vehicle.
Seth Baklor and a small, yet dedicated group of four other students founded the team in 2008. Despite it being the first year, the team finished 5th in the Explorer class in Buzzards Bay, MA. ROV Osprey was a submarine rescue vehicle.
Seth Baklor, Joe Pellettiere, and Dustin Mitchell met before the formation of the committee itself to create a practice vehicle. Intended as a learning platform for the fledgling team, ROV Sugrak, with her simple manipulator and PVC frame, was never finished.


Codehaus XFire
DocumentationQuicklinksDevelopers
Sponsors |
Logging SystemXFire uses Commons Logging to provide you with debugging information. If you are having problems probably the first thing you'll want to do is turn up the debugging to DEBUG level. Here's a sample log4j.properties file which will do that: # Set root logger level to DEBUG and its only appender to A1. log4j.rootLogger=DEBUG, A1 # A1 is set to be a ConsoleAppender. log4j.appender.A1=org.apache.log4j.ConsoleAppender # A1 uses PatternLayout. log4j.appender.A1.layout=org.apache.log4j.PatternLayout log4j.appender.A1.layout.ConversionPattern=MIT: %-4r [%t] %-5p %c %x - %m%n log4j.category.org.codehaus.xfire = DEBUG log4j.category.org.apache.commons.httpclient = WARN log4j.category.httpclient.wire = WARN You may want to tweak the httpclient categories to actually see the message. Logging the messagesBy virtue of XFire being stax based, it never caches the whole message in memory. However sometimes you need access to the whole message to debug. Turning it on is simple: Service service = ...; // Tell XFire to cache a DOM document for the various in/out/fault flows service.addInHandler(new org.codehaus.xfire.util.dom.DOMInHandler()); service.addOutHandler(new org.codehaus.xfire.util.dom.DOMOutHandler()); service.addFaultHandler(new org.codehaus.xfire.util.dom.DOMOutHandler()); // Add a logging handler to each flow service.addInHandler(new org.codehaus.xfire.util.LoggingHandler()); service.addOutHandler(new org.codehaus.xfire.util.LoggingHandler()); service.addFaultHandler(new org.codehaus.xfire.util.LoggingHandler()); |


--- title: Comments Upgrade with Avatars layout: post tags: [meta] uuid: 3de1f1d8-9649-38b9-4efe-b3f7a0f731ad ---
Update: This is refering to my old, hand-written comment system, before I changed web hosts and switched to external comment hosting.
I started getting Asian spam in my comments in the last couple days. If you are subscribed to the comments feed you probably noticed this. The spammer was manually filling out captchas, so this wasn't a bot but rather a patient human being. Getting tired of removing these, I set up some filters to silently drop messages that fit certain criteria. By "silently" I mean the server tells the client everything went fine but the comment never actually gets written to the database.
The spammer gained nothing except annoying us because all links in
comments get a rel="nofollow"
attribute, which tells
search engines to ignore it.
Well anyway, while I had my sleeves rolled up and my hands on the code I decided to make some upgrades I have been wanting to do. The e-mail address is no longer displayed (stupid idea in the first place) but instead used for a Gravatar image. You can also specify a home URL, which will be linked from your name. This makes my comment system work very similarly to what you find around the web, except that I don't require anything from you but a captcha and a comment.
I also fixed a small usability issue: when you preview a comment now it takes you right down to the form rather than leaving you at the top of the page. The back-end database was also adjusted from the original pollxn design to scale better as the website grows.
Now, Gravatar is a neat concept but I have two complaints. One, I don't like centralized systems. It's a single point of failure and a single point of control. It has privacy issues. It's anti-web. It's inelegant. Decentralized systems built around self-enforcing protocols are more robust and democratic.
Luckily, a decentralized version does exist! It's a specification called Pavatar. The avatar is tied to a URL rather than an e-mail address. However, it's a bit less flexible, since it needs to remain simple on the server side. It's harder to set up and I doubt 99% of the users on the web would be capable of doing it. What would help Pavatar gain a wider audience would be Pavatar provider services. Hmmm...
So, I think might switch it to Pavatar sometime, with a possible fall-back to Gravatar. That takes significantly more work to set up than Gravatar does, so it's a future project. And, well, no one uses it yet either. I actually thought the project was dead until just now because their website was down the first time I visited it a couple months ago.
My second complaint is that Gravatar incorrectly assumes e-mail addresses are not case-sensitive. The domain part is, but the alias part is not. These two addresses could technically arrive to two different e-mail inboxes,
<EMAIL_ADDRESS><EMAIL_ADDRESS>Pretty much every e-mail server will treat these as the same address
as a convenience, because treating these differently would just be
confusing, but it's not necessarily the case. Gravatar specifically
says to hash the e-mail in lowercase form, so the unique address
<EMAIL_ADDRESS>can't be used with the service.
So, go ahead and play in the comments a bit.


WITNESS LIST Pensions & Investments Committee May 2, 2001-9:00A HB 783 For: Bresnen, Steve (First American Pension Services) Fickle, Ann (Texas Classroom Teachers Association) Kouri, Richard (Texas State Teachers Association) Lara, Rene (Texas Federation Of Teachers) Romo, Joel (Association Of Texas Professional Educators) On: Massey, Doug (Self) Payne, Tyson (Texas Association Of Insurance and Financial Advisors) Registering, but not testifying: For: Baker, Mary (Self) Coffey, Jeanie (Self) Dahlberg, Warner (Self) Gregg, Aleene (Self) Hise, Zora (Self) Jordan, Cheryl (Self) Lehr, Mike (Texas Retired Teachers Association) Mellenbruch, Julia (Self) Rogers, Tom (Self) Sayers, DeEtta (Self) Sayers, Russell (Self) Scholtz, Annie (Self) Sweat, Flossie (Self) Wallace, Chester (Self) Wallace, Margaret (Self) Wiley, Novella (Self) Wynn, Jimmy (Harris County Department Of Education)


This page demonstrates the use of the "fit" extension for deck.js.
Use left/right arrow keys to browse the presentation.
Getting started with deck.js:
fit extension
use right arrow to move on
“fit”: What It Does
-
Before anything
please resize the slides by dragging the bottom right corner of the dark-red frame
-
More on the next slide
Designing for “fit”
- You decide on a design dimension
(default: 800x600)
- You write all your slides
as if they were exactly of this size
- You put your slides in a container of any size
- You decide how they should adapt (e.g., center)
- And “fit” handles it!
Playing with “fit” demo
- Resize the red box
- Change the “fitMode”
with the select on the top-right of this page
- Press the 's' key to make the slides fit to the window
Browser support
- Did it work for you? :)
- Should be ok on good browsers
Notes about the demo
- The 8 yellow boxes are to test background elements. You may use them into your slides, e.g., for footer, logos, …
- The red border just helps understanding where the “deck-container” is
- The white border just helps understanding where each “slide” is
- The white border also illustrates the “fitMarginX” and “fitMarginY” options that can be used for adding a margin around the slides


Pustike EventBus is a fork of Guava EventBus, which is probably the most commonly known event bus for Java. Most of the documentation here and test cases are from Guava itself.
The Guava Project contains several core libraries and is distributed as a single module that has a size of ~2.2MB (as of v19.0). So an application using only the EventBus will also need to include the full Guava dependency.
Pustike EventBus is an effort to extract only the event bus library from Guava project without any other dependencies. And it also provides few additional features / changes, like:
@Subscribe(threadSafe = true)
instead of @AllowConcurrentEvents
The project is available on GitHub.
An event bus is a library providing publisher/subscriber pattern for loose coupling between components(event senders and receivers), by sending messages to each other indirectly. Some objects register with the bus to be notified when certain events of interest occur. And some publish events on the bus. The bus notifies each of the registrants when the event is published. So the registrant objects and the event-source objects need not know about each other directly. Each may join or depart the bus at any time. Thus it enables central communication between components, simplifies the code and removes direct dependencies.
To create an instance of event bus with a default identifier and using a per thread dispatch queue and a direct executor which publishes events in the same thread:
EventBus bus = new EventBus();
Dispatcher is used for dispatching events to subscribers, providing different event ordering guarantees that make sense for different situations. Please note that the dispatcher controls the order in which events are dispatched, while the executor controls how (i.e. on which thread) the subscriber is actually called when an event is dispatched to it. Two types of dispatchers are supported:
Subscribe to events by registering listeners to the bus. Subscriber methods in a listener should be annotated with @Subscribe
and the method should take only a single parameter, the type of which will be the event to subscribe to. The registry will traverse the listener class hierarchy and add methods from base classes or interfaces that are annotated.
Object listener = new Object() {
@Subscribe
public void onMessageEvent(String message) {
// process the message here...
}
};
bus.register(listener);
Here internally weak references to listener objects are maintained instead of strong references, as in Gauava.
@Subscribe(threadSafe = true)
. It indicates that the bus may invoke this event subscriber simultaneously from multiple threads.Publish events on the bus which dispatches it to all listeners subscribing to this event type. An instance of any class may be published and it will only be dispatched to subscribers for that type.
String messageEvent = "Hello!";
bus.publish(messageEvent);
String
and Integer
type events are published, the subscriber to Comparable
will be called on both the events. This can be used to create more generic listeners listening for a broader range of events and more detailed ones for specific purposes.Listeners can be unregistered from the bus using
bus.unregister(listener);
CustomerEvent
, VendorEvent
, etc, the TypedEvent<Customer>
, TypedEvent<Vendor>
can be used. The context information can be useful in communicating the state of the object, like new TypedEvent<>(customer, "MODIFIED");
@Subscribe
public void onTypedStringEvent(TypedEvent<String> event) {
// event.getSource();// the object of the event.
// event.getType();// the type of the object.
// event.getContext();// the event context if available, can be null.
}
// ... and publish the event as following
bus.publish(new TypedEvent<>("Hello!"));// note that this will not be matched to TypedEvent<Integer> subscriber!
@Subscribe
public void onDeadEvent(DeadEvent deadEvent) {
// deadEvent.getEvent(); // the event that could not be delivered.
}
@Subscribe
public void onException(ExceptionEvent exceptionEvent) {
// process the exception info here...
}
By default, the event bus will use a ConcurrentMap internally to cache Subscriber methods identified on registering listener objects. To use an external cache like Caffeine for loading & storing subscriber methods in a listener class and type hierarchy of event classes, the following approach can be used:
public class CaffeineSubscriberLoader extends DefaultSubscriberLoader {
private final LoadingCache<Class<?>, List<Method>> subscriberMethodCache;
private final LoadingCache<Class<?>, Set<Class<?>>> typeHierarchyCache;
public CaffeineSubscriberLoader() {
this.subscriberMethodCache = Caffeine.newBuilder().weakKeys()
.build(super::findAnnotatedMethodsNotCached);
this.typeHierarchyCache = Caffeine.newBuilder().weakKeys().weakValues()
.build(super::flattenHierarchyNotCached);
}
@Override
public List<Method> findSubscriberMethods(Class<?> clazz) {
return subscriberMethodCache.get(clazz);
}
@Override
public Set<Class<?>> flattenHierarchy(Class<?> clazz) {
return typeHierarchyCache.get(clazz);
}
@Override
public void invalidateAll() {
subscribeMethodsCache.invalidateAll();
typeHierarchyCache.invalidateAll();
}
}
// and create the event bus using this cache
CaffeineSubscriberLoader subscriberLoader = new CaffeineSubscriberLoader();
Executor executor = Runnable::run; // a simple direct executor!
EventBus eventBus = new EventBus("default", Dispatcher.perThreadDispatchQueue(),
executor, subscriberLoader);
Guava EventBus allows publish-subscribe-style event communication
Square’s Otto: An enhanced event bus with emphasis on Android support.
GreenRobot Event Bus: Android optimized event bus that simplifies communication between Activities, Fragments, Threads, Services, etc. Less code, better quality.
MBassador is a light-weight, high-performance message (event) bus implementation based on the publish subscribe pattern.
Mycila PubSub is a new powerful event framework for in-memory event management.
Spring Framework Application Event publishing support using spring context.
This library is published under the Apache License, Version 2.0
Copyright (C) 2016 the original author or authors.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.


Select a date in the line chart on the bottom by clicking a column; the TreeMap chart at the top of the file presents the cost breakdown for the selected date.
Select a product or sku from the treemap to show charges for just the selected product or sku in the line chart.
Go back up by right clicking the treemap chart.
Show or hide lines in the line chart by selecting a series in the chart legend.
"Flush Caches" button is only needed if object change notifications aren't configured, it will take time when a large number of objects exist in the bucket


This presentation shows the implementation of a multiplayer AR experience. In this case through a game similar to Whack-a-Mole.
Click by hovering the cursor over an object, then pressing the cursor with your finger.


{% extends 'base_registration.html' %} {% block title %}Password reset sent{% endblock %} {% block form_title %}Password reset sent{% endblock %} {% block cardBody %}
We've emailed you instructions for setting your password, if an account exists with the email you entered. You should receive them shortly.
If you don't receive an email, please make sure you've entered the address you registered with, and check your spam folder.
Go back {% endblock %}


{%- extends 'base.template.html' -%}
{%- block body %}
{% block shortDescription %}
{$ doc.shortDescription | marked $}
{%- if doc.description %}
See more...
{% endif %}
{% endblock %}
{%- include "includes/security-notes.html" -%}
{%- include "includes/deprecation.html" -%}
{%- block overview %}{% endblock -%}
{%- include "includes/see-also.html" -%}
{%- block details %}{% endblock -%}
{%- block endNotes %}{% include "includes/usageNotes.html" %}{% endblock -%}
{%- endblock -%}


if you have the heartbeat message producer running, you should see messages in the console...
- step 1: start the message hub (bin/start.js)
- step 2: start the heartbeat (examples/heartbeat.js)
- step 3: launch the index page and observe messages in the browser console.


select API:
window.requestIdleCallback
@livelybone/request-idle-callback
requestidlecallback
input run times:
run
Now you can:
1. do some interaction to verify whether the browser is blocked,
like input here:
2. see the behavior logs in dev-tool


ETLBox video
This example will give you a brief overview of the basic concepts of ETLBox.
See the video
There is also a video demonstrating this example.
Environment
For this demo you can use Visual Studio for Mac and Sql Server for linux running in a docker image. An User interface for managing sql server on Mac would be the Azure Data Studio.
First, we need to start a docker image running sql server on ubuntu. Run the following command line statement in the terminal to start up the container.
docker run -d --name sql_server_demo -e 'ACCEPT_EULA=Y' -e 'SA_PASSWORD=reallyStrongPwd123' -p 1433:1433 microsoft/mssql-server-linux
With the command docker ps
we can see the container is up and running.
Now create a new dotnet core console application. Do this either with your GUI or execute the following command:
dotnet new console
Add the current version of ETLBox as a package to your project.
dotnet add package ETLBox
Now you will be able to use the full set of tools coming with ETLBox
Start coding
Now we are in the static main method.
We need to store a connection string in the static Control Flow object.
ControlFlow.CurrentDbConnection = new SqlConnectionManager(new ConnectionString
("Data Source=.;Integrated Security=false;User=sa;password=reallyStrongPwd123"));
With CreateDatabaseTask we will create a new Database.
CreateDatabaseTask.Create("demo");
Also we would like to change the connection to the database we just created and create a table in there using the CreateTableTask.
ControlFlow.CurrentDbConnection = new SqlConnectionManager(new ConnectionString
("Data Source=.;Integrated Security=false;User=sa;password=reallyStrongPwd123;Initial Catalog=demo"));
CreateTableTask.Create("dbo.table1", new List<TableColumn>()
{
new TableColumn("ID","int",allowNulls:false, isPrimaryKey:true, isIdentity:true),
new TableColumn("Col1","nvarchar(100)",allowNulls:true),
new TableColumn("Col2","smallint",allowNulls:true)
});
Adding nlog.config
Before we test our demo project, we want to have some logging output displayed. ETLBox logging is build on nlog. On the etlbox website you will find examples how to configure logging with nlog. Add the following lines as nlog.config to your project root. Make sure it is copied into the output directory.
<?xml version="1.0" encoding="utf-8"?>
<nlog xmlns="http://www.nlog-project.org/schemas/NLog.xsd"
xsi:schemaLocation="NLog NLog.xsd"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<rules>
<logger name="*" minlevel="Debug" writeTo="console" />
</rules>
<targets>
<target name="console" xsi:type="Console" />
</targets>
</nlog>
Running the project
Now build and run the project. A terminal window will pop up and display the logging output. As the logging level is set to debug, you will see all SQL code which is executed against the database. Check if the database and the table was created.
A simple etl pipeline
Next we want to create a simple etl pipeline. First we create a demo csv file named input.csv
. The input file contains header information and some value. Also we need to copy it into the output directory.
Col1,Col2
Value,1
Value2,2
Value3,3
Now we create a CSVSource pointing to the newly created input file.
CSVSource source = new CSVSource("input.csv");
Before we continue, we will need an object that can hold our data. Let's call it MyData.
public class MyData
{
public string Col1 { get; set; }
public string Col2 { get; set; }
}
Now we add a row transformation. The row transformation will receive a string array from the source and transform it in our Mydata object.
RowTransformation<string[], MyData> row = new RowTransformation<string[], MyData>
(
input => new MyData()
{ Col1 = input[0], Col2 = input[1] }
);
Next we add a database destination pointing to our table.
DBDestination<MyData> dest = new DBDestination<MyData>("dbo.table1");
Now we need to link the components of our dataflow.
source.LinkTo(row);
row.LinkTo(dest);
After linking the components, we want to have the source reading the input data. The destination should wait until it received all data.
source.Execute();
dest.Wait();
Finlly, we check if the data was successfully loaded into the table and write it into the console output. We use the SQLTask for this.
SqlTask.ExecuteReader("Read all data from table1",
"select Col1, Col2 from dbo.table1",
col1 => Console.WriteLine(col1.ToString() + ","),
col2 => Console.WriteLine(col2.ToString())
);
Run again
Let's run the project again and see the output.
You'll see that the data was successfully copied into the database table.
Whole code
Here is the whole example code.
File Program.cs
using System;
using System.Collections.Generic;
using ALE.ETLBox;
using ALE.ETLBox.ConnectionManager;
using ALE.ETLBox.ControlFlow;
using ALE.ETLBox.DataFlow;
namespace Demo
{
class Program
{
static void Main(string[] args)
{
Console.WriteLine("Hello World!");
ControlFlow.CurrentDbConnection = new SqlConnectionManager(new ConnectionString
("Data Source=.;Integrated Security=false;User=sa;password=reallyStrongPwd123"));
CreateDatabaseTask.Create("demo");
ControlFlow.CurrentDbConnection = new SqlConnectionManager(new ConnectionString
("Data Source=.;Integrated Security=false;User=sa;password=reallyStrongPwd123;Initial Catalog=demo"));
CreateTableTask.Create("dbo.table1", new List<TableColumn>()
{
new TableColumn("ID","int",allowNulls:false, isPrimaryKey:true, isIdentity:true),
new TableColumn("Col1","nvarchar(100)",allowNulls:true),
new TableColumn("Col2","smallint",allowNulls:true)
});
CSVSource source = new CSVSource("input.csv");
RowTransformation<string[], MyData> row = new RowTransformation<string[], MyData>(
input => new MyData() { Col1 = input[0], Col2 = input[1] });
DBDestination<MyData> dest = new DBDestination<MyData>("dbo.table1");
source.LinkTo(row);
row.LinkTo(dest);
source.Execute();
dest.Wait();
SqlTask.ExecuteReader("Read all data from table1",
"select Col1, Col2 from dbo.table1",
col1 => Console.WriteLine(col1.ToString() + ","),
col2 => Console.WriteLine(col2.ToString()));
}
public class MyData
{
public string Col1 { get; set; }
public string Col2 { get; set; }
}
}
}
nlog.config
<?xml version="1.0" encoding="utf-8"?>
<nlog xmlns="http://www.nlog-project.org/schemas/NLog.xsd"
xsi:schemaLocation="NLog NLog.xsd"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<rules>
<logger name="*" minlevel="Debug" writeTo="console" />
</rules>
<targets>
<target name="console" xsi:type="Console" />
</targets>
</nlog>
input.csv
Col1,Col2
Value,1
Value2,2
Value3,3


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Welcome to the Brain Trust, New Age Liberty's think tank and economic vehicle. New Age Liberty was born on 08 April 2016 with the vision of creating a free, united and prosperous Afrika by 2063.
Below are our organisational documents for all members to get acquainted with our organisation, our thinking, our culture and our goals.
New Age Liberty founding manifesto
{% include "Home/proverb/p69.html" %} {% endblock %}


Welcome to my website. I am a tech hobbyist who enjoys learning about cybersecurity, computer vision, machine learning, and software engineering. In the past few years I have worked on may independent projects alongside my formal education. My goal is to leverage technology solutions to improve the quality of life of individuals and organizations. I have advance knowledge in C and Python, experience developing various sites, and tend to focus my projects around making life easier through the use of technology.
2 years of experience including webscraping, python spark bot dev, and general data manipulation
Class Picker | View All Projects
2 years of experience including webscraping, python spark bot dev, and general data manipulation
Class Picker | View All Projects
2 years of experience including webscraping, python spark bot dev, and general data manipulation
Class Picker | View All Projects
2 years of experience including webscraping, python spark bot dev, and general data manipulation
Class Picker | View All Projects


Texas death row inmate Rodney Reed seeks stay
New evidence draws national attention
BASTROP, Texas - - The Innocence Project, celebrities and others work for an execution stay for Rodney Reed, amid serious questions over his conviction.
BASTROP, Texas - - The Innocence Project, celebrities and others work for an execution stay for Rodney Reed, amid serious questions over his conviction.


Package org.apache.sis.referencing.cs
Coordinate System (CS) definitions as the set of coordinate system axes that spans the coordinate space.
An explanation for this package is provided in the OpenGIS® javadoc.
The remaining discussion on this page is specific to the SIS implementation.
The root class in this package is AbstractCS
.
Various subclasses are defined for various kinds of mathematical rules that determine
how coordinates are associated to quantities such as angles and distances.
Those SIS subclasses provide additional methods that are not part of OGC/ISO specifications:
CoordinateSystems
utility class
with static methods for estimating an angle between two axes, determining the change of axis directions
and units between two coordinate systems, or filtering axes.- Since:
- 0.4
Defined in the sis-referencing
module
-
Interface Summary Interface Description AxisFilter Modifications to apply on the axes of a coordinate system in order to produce a new coordinate system. -
Class Summary Class Description AbstractCS The set of coordinate system axes that spans a given coordinate space.CoordinateSystems Utility methods working onCoordinateSystem
objects and their axes.DefaultAffineCS A 2- or 3-dimensional coordinate system with straight axes that are not necessarily orthogonal.DefaultCartesianCS A 2- or 3-dimensional Cartesian coordinate system made of straight orthogonal axes.DefaultCompoundCS A coordinate system made of two or more independent coordinate systems.DefaultCoordinateSystemAxis Coordinate system axis name, direction, unit and range of values.DefaultCylindricalCS A 3-dimensional coordinate system made of a polar coordinate system extended by a straight perpendicular axis.DefaultEllipsoidalCS A 2- or 3-dimensional coordinate system for geodetic latitude and longitude, optionally with ellipsoidal height.DefaultLinearCS A 1-dimensional coordinate system for points that lie on a single axis (not necessarily a straight line).DefaultParametricCS A 1-dimensional coordinate system for parametric values or functions.DefaultPolarCS A 2-dimensional coordinate system for coordinates represented by a distance from the origin and an angle from a fixed direction.DefaultSphericalCS A 3-dimensional coordinate system with one distance measured from the origin and two angular coordinates.DefaultTimeCS A 1-dimensional coordinate system for time elapsed in the specified time units from a specified time origin.DefaultUserDefinedCS A 2- or 3-dimensional coordinate system for any combination of coordinate axes not covered by other CS types.DefaultVerticalCS A 1-dimensional coordinate system for heights or depths of points. -
Enum Summary Enum Description AxesConvention High-level characteristics about the axes of a coordinate system.


Wallet Generator
Wallet Type
P2PKH - Pay to Public Key Hash (legacy)
P2WPKH - Pay to Witness Public Key Hash (segwit)
P2SH - Pay to Script Hash
P2WSH - Pay to Witness Script Hash
Network
Bitcoin Mainnet
Bitcoin Testnet
Create Wallet
Address
Private Key
Print Wallet


--- description: Framework JavaScript bundle sizes templateLanguage: liquid templateEngineOverride: html orientation: vertical typing: - 64-580 # As of October 8, 2020 --- {% layout "./layouts/liquid-layout.html" %} {% block content %}
52.9
KiB: Gatsby.js Hello World59.6
KiB: Next.js Starter (Static Export)66.9
KiB: Gridsome Starter77.1
KiB: Nuxt.js Starter (Full Static)(Compressed)
{% endblock %}


|
Talking Clock
1.0
Talking clock for Cypress PSoC Analog Coprocessor kit
|
Project independent LPC audio decoder implementation. More...
Functions | |
| static void | synth_core (void) |
| Read LPC coefficients from bitstream. More... | |
| static uint8_t | reverse_bit_order (uint8_t byte) |
| Reverse bit order (LSB/MSB) in given byte. More... | |
| static uint8_t | get_bits (uint8_t bit_count) |
| Read given number of bits from LPC bitstream. More... | |
| static int16_t | generate_sample (void) |
| Generate single LPC audio sample based on global coefficients. More... | |
| static void | synth_dma_set_config (void) |
| Configure DMA parameters. More... | |
| static void | synth_dma_isr (void) |
| DMA ISR - prepares DMA buffer data. More... | |
| void | synth_hw_init (void) |
| Initialize synthesizer hardware components. More... | |
| void | synth_say (const uint8_t *p_lpc_data) |
| Generate speech audio based on LPC encoded bitstream. More... | |
Variables | |
| static const int8_t | CHIRP [CHIRP_SIZE] |
| LPC 'chirp' sample array. More... | |
| static const uint8_t | ENERGY [0x10] |
| LPC energy lookup array. More... | |
| static const uint8_t | PITCH [0x40] |
| LPC pitch lookup array. More... | |
| static const int16_t | K1 [0x20] |
| LPC coefficient K1 lookup array. More... | |
| static const int16_t | K2 [0x20] |
| LPC coefficient K2 lookup array. More... | |
| static const int8_t | K3 [0x10] |
| LPC coefficient K3 lookup array. More... | |
| static const int8_t | K4 [0x10] |
| LPC coefficient K4 lookup array. More... | |
| static const int8_t | K5 [0x10] |
| LPC coefficient K5 lookup array. More... | |
| static const int8_t | K6 [0x10] |
| LPC coefficient K6 lookup array. More... | |
| static const int8_t | K7 [0x10] |
| LPC coefficient K7 lookup array. More... | |
| static const int8_t | K8 [0x08] |
| LPC coefficient K8 lookup array. More... | |
| static const int8_t | K9 [0x08] |
| LPC coefficient K9 lookup array. More... | |
| static const int8_t | K10 [0x08] |
| LPC coefficient K10 lookup array. More... | |
| static uint8_t * | gp_byte |
| LPC bitstream byte pointer. | |
| static uint8_t | g_bit_pointer |
| LPC bitstream bit pointer. | |
| static uint8_t | g_byte_1 |
| LPC bitstream current read byte. | |
| static uint8_t | g_byte_2 |
| LPC bitstream next read byte. | |
| static uint8_t | gb_using_fram |
| Boolean flag whether FRAM is being used as LPC bitstream source. | |
| static uint8_t | g_synth_pitch |
| LPC synthesizer current pitch. | |
| static uint16_t | g_synth_energy |
| LPC synthesizer current energy. | |
| static int32_t | g_synth_k1 |
| LPC synthesizer current coefficient k1. | |
| static int32_t | g_synth_k2 |
| LPC synthesizer current coefficient k2. | |
| static int16_t | g_synth_k3 |
| LPC synthesizer current coefficient k3. | |
| static int16_t | g_synth_k4 |
| LPC synthesizer current coefficient k4. | |
| static int16_t | g_synth_k5 |
| LPC synthesizer current coefficient k5. | |
| static int16_t | g_synth_k6 |
| LPC synthesizer current coefficient k6. | |
| static int16_t | g_synth_k7 |
| LPC synthesizer current coefficient k7. | |
| static int16_t | g_synth_k8 |
| LPC synthesizer current coefficient k8. | |
| static int16_t | g_synth_k9 |
| LPC synthesizer current coefficient k9. | |
| static int16_t | g_synth_k10 |
| LPC synthesizer current coefficient k10. | |
| static int16_t | g_synth_buffer_0 [DMA_BUFFER_SIZE] |
| DMA buffer 0. | |
| static int16_t | g_synth_buffer_1 [DMA_BUFFER_SIZE] |
| DMA buffer 1. | |
| int16_t *const | gp_buffer_addr [] = {g_synth_buffer_0, g_synth_buffer_1} |
| DMA buffer pointer lookup table. | |
| int16_t volatile * | gp_buffer |
| Pointer to currently used DMA buffer. | |
| uint8_t volatile | g_buffer_sel |
| DMA buffer selector. | |
| uint8_t volatile | g_elem_idx |
| DMA buffer element index. | |
Project independent LPC audio decoder implementation.
|
static |
Generate single LPC audio sample based on global coefficients.
|
static |
Read given number of bits from LPC bitstream.
| bit_count | Number of bits to read. |
|
static |
Reverse bit order (LSB/MSB) in given byte.
| byte | Byte to reverse bits from. |
|
static |
Read LPC coefficients from bitstream.
|
static |
DMA ISR - prepares DMA buffer data.
|
static |
Configure DMA parameters.
| void synth_hw_init | ( | void | ) |
Initialize synthesizer hardware components.
| void synth_say | ( | const uint8_t * | p_lpc_data | ) |
Generate speech audio based on LPC encoded bitstream.
|
static |
LPC 'chirp' sample array.
|
static |
LPC energy lookup array.
|
static |
LPC coefficient K1 lookup array.
|
static |
LPC coefficient K10 lookup array.
|
static |
LPC coefficient K2 lookup array.
|
static |
LPC coefficient K3 lookup array.
|
static |
LPC coefficient K4 lookup array.
|
static |
LPC coefficient K5 lookup array.
|
static |
LPC coefficient K6 lookup array.
|
static |
LPC coefficient K7 lookup array.
|
static |
LPC coefficient K8 lookup array.
|
static |
LPC coefficient K9 lookup array.
|
static |
LPC pitch lookup array.


As lead partner you must choose a Project Manager who will be responsible for setting up your project. We need this information now so that your Monitoring Officer can contact the Project Manager.
As lead partner you must choose a Project Manager who will be responsible for setting up your project. We need this information now so that your Monitoring Officer can contact the Project Manager.


{% extends 'base.html' %} {% load crispy_forms_tags %} {% load i18n %} {% block content %}
{% trans "Send a message to everyone in your learning circle. If any of the participants provided a mobile number when they signed up, you should also provide a text message to be sent. Your email address will be included in the reminder as the 'reply to' address." %}


I'm considering this as possible but low probability scenario where before stock market crash whales with good connections switch to BTC / alts and to take good position they could make some good FUD. Then they would initialize some exit pumpts as after stock market collapse crypto will follow sooner or later, but if someone with power and connection used it properly he could exit well from stock , move through crypto / BTC and make 10x or so before the long comming crisis that will last some years...


Examples
- 3D Model
- A 3D model that tracks the orientation of the IMU.
- 3D Example
- A simpler version of the 3D model code.
- Bar Chart
- Bar charts of all the sensor values.
- Sketch
- An example p5.js sketch.
- Dashboard
- List connected devices and sample rate.
- 3D Model
- A list of connected devices.
- D3 Graph
- Uses D3 to graph sensor values over time.
- Highcharts Chart
- Uses Highcharts to chart sensor values over time.


Step 1: If you are using Stanz' K2 Script Editor, load your map with the Script Editor and create a new trigger called "K2". Then copy and paste the code below into the "K2" trigger. If you don't have the Script editor, you can do the same using the Map Editor instead. If you are upgrading your project, just replace the code in the existing "K2" trigger.
{code1}
Step 2: If you are updating your project you can skip this step. Switch to the trigger called "maploaded" and add the following code:
// Initialize the K2 framework Set __K2_INI 0; ExecScript K2;
Step 3: The script is now installed and ready to use. Happy coding!
Step 1: Open your map with a file archiver (such as Winzip, 7zip etc.) and extract the file called "triggerlist". Open this file with a text editor and replace the entire content of the file with the code below.
{code2}
Step 2: Save the file and put it back into the map archive (overwrite the existing file). Please note that by doing this, you are deleting any existing script code in this map - unless it is stored in separate cfg files.
Step 3: The script is now installed and ready to use. Happy coding!


--- layout: post title: "Linux Gaming" date: 2007-08-02 14:48:45 +0000 permalink: /2007/08/02/linux-gaming/ category: Linux redirect_from: - /blog/linux-gaming/ ---
The Micahville blog has an excellent article on why Linux should not be dismissed as a serious gaming platform. It lists 17 awesome games for Linux, many of which I have not even heard of. I'm going to give some of them a try later. I'd really like to hook up a joystick to my computer again to hit up FlightGear.


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{{copy.contribute_to}}
{{address}}
{{votes}}
{{copy.votes}}
{{contributions}}
{{copy.contributions}}
{{points}}
{{copy.points}}
{{copy.home}}
{{copy.address}}
{{copy.share}}
{{{details}}}
{{/issue}} {{^issue}}
INVALID OR CLOSED ISSUE
{{/issue}}


Born in Nairobi, grew up in one of it's famous suburb places with only two wish ("Invent and Be Great!") I had to brave up through the uncertainities of a complex society with the help of strict rules enacted by my parents. My ties with my past though, remains as strong like yesterday.  My lifestyle and the hobbies are a reflection of that. You can say i am a godly and a cool guy, but not tasty the majority.
I am a graduate of medical studies in Public Health and Sanitation and an alumni of St. Peters Mumias Boys high school. Learnt my primary at Olympic primary school.
My first job was in Barclays Bank of Kenya. I later left for my practise in my medical field as a volunteer public health officer. Finished my term last year and later engaged myself with the church activities. Early this year, I went for volunteership in SHOFCO, specifically, in search for a job,and thanks heaven!! I am in an Exclusive International Computer School, Moringa Optimistic of becoming Great! After finishing the school.


Pros and Cons of NoSQL over Relational Databases
September 21, 2014
Databases have become a very important part of how businesses operate since the beginning of the digital era. The relational database management system (RDBMS) model has been the dominant model for database management since it was first described by E.F. Codd in 1970. Relational databases use a computer language called SQL (structured query language) to store data in a series of tables that are related to each other.
A simple example of a relational database model is a doctor's office that stores patient contact info in one table and the patient's health information in another table. The tables below are related because the patient's health information is linked to the patient id number.
Recently, NoSQL databases are gaining popularity as an alternative to the relational database model. NoSQL is a new class of data management designed to meet the increasing volume, velocity, and variety of business data organizations are collection. NoSQL is simply a database management system that does not use a tabular relation model.
Pros and Cons of using NoSQL:
Pros
- Better and cheaper scaling. As databases move into the cloud there is cost savings since you can spread your databases across multiple hosts rather than requiring more servers.
- Better for big data. The volume of data has increased massively in recent years. The sheer volume of data that can be practically managed by a relational database system is becoming too much to bear for many enterprises. NoSQL systems can handle the volumes of 'big data' much better than the largest relational database systems.
- Requires less labor costs for design and maintenance of data management system compared to RDMBS.
- NoSQL databases have far more relaxed data model restrictions than RDMBS. For example, its much easier to add columns in NoSQL.
Cons
- NoSQL is relatively new and it is not as stable nor fully functional as a RDMBS.
- NoSQL support is not as good as RDMBS since most NoSQL is open source and RDBMS are supported by large established companies like Oracle, Microsoft, or IBM.
- It's far easier to find experienced RDMBS programmers than a NoSQL expert. NoSQL requires a lot of specialized skill to install and maintain.
Compared to relational databases NoSQL databases are more scalable and flexible, however NoSQL is still relatively new, does not have a great support, and is not as stable as an RDMBS. With the increasing importance of 'big data' and business intelligence, I believe NoSQL will grow in popularity and become a viable solution for database management.
Resources


We sell blockchain!
- streamline vertical applications
- strategize back-end e-commerce
- enable user-centric convergence
- envisioneer impactful partnerships
- generate strategic technologies
- integrate leading-edge supply-chains
- embrace turn-key channels
- generate mission-critical functionalities
- synergize value-added channels
- unleash visionary systems
- evolve B2B partnerships
- morph next-generation metrics
- disintermediate magnetic schemas
- transition wireless partnerships


{% extends 'base.html' %} {% block title %} Reset Your Password {% endblock title %} {% block content %}
Enter your email address and we will send you a link to reset your password.


class DateRangeSelectorHelper
A helper class to manage user inputs for a start date and end date. The user can each of these dates through a click then dialog, and the other date will update accordingly.
DateRangeSelectorHelper(startDateHelper: DateSelectorHelper, endDateHelper: DateSelectorHelper)
A helper class to manage user inputs for a start date and end date. The user can each of these dates through a click then dialog, and the other date will update accordingly. |
val endDateHelper: DateSelectorHelper
the DateSelectorHelper to manage inputs for the end date |
|
val startDateHelper: DateSelectorHelper
the DateSelectorHelper to manage inputs for the start date |
fun getEndDate(): LocalDate? |
|
fun getStartDate(): LocalDate? |
|
fun setDateRangePickerConstraints(): Unit
Sets the default minimum and maximum dates for two date pickers (for start and end dates). This is based on the current person, and selections made in other date pickers. |
|
fun setDates(startDate: LocalDate, endDate: LocalDate?): Unit
Sets the dates to be displayed on the date pickers, and updates the selectable date ranges of each of these accordingly (i.e. their "minimum" and "maximum" dates) |


The /etc/passwd file is a text file that describes user login accounts
for the system. It should have read permission allowed for all users (many
utilities, like ls(1) use it to map user IDs to usernames), but write
access only for the superuser.
In the good old days there was no great problem with this general
read permission. Everybody could read the encrypted passwords, but the
hardware was too slow to crack a well-chosen password, and moreover the
basic assumption used to be that of a friendly user-community. These days
many people run some version of the shadow password suite, where
/etc/passwd has an 'x' character in the password field, and the
encrypted passwords are in /etc/shadow, which is readable by the
superuser only.
If the encrypted password, whether in /etc/passwd or in
/etc/shadow, is an empty string, login is allowed without even asking
for a password. Note that this functionality may be intentionally disabled
in applications, or configurable (for example using the "nullok"
or "nonull" arguments to pam_unix.so).
If the encrypted password in /etc/passwd is
"*NP*" (without the quotes), the shadow record should be
obtained from an NIS+ server.
Regardless of whether shadow passwords are used, many system
administrators use an asterisk (*) in the encrypted password field to make
sure that this user can not authenticate themself using a password. (But see
NOTES below.)
If you create a new login, first put an asterisk (*) in the
password field, then use passwd(1) to set it.
Each line of the file describes a single user, and contains seven
colon-separated fields:
name:password:UID:GID:GECOS:directory:shell
The field are as follows:
- name
- This is the user's login name. It should not contain capital letters.
- password
- This is either the encrypted user password, an asterisk (*), or the letter
'x'. (See pwconv(8) for an explanation of 'x'.)
- UID
- The privileged root login account (superuser) has the user ID
0.
- GID
- This is the numeric primary group ID for this user. (Additional groups for
the user are defined in the system group file; see group(5)).
- GECOS
- This field (sometimes called the "comment field") is optional
and used only for informational purposes. Usually, it contains the full
username. Some programs (for example, finger(1)) display
information from this field.
- GECOS stands for "General Electric Comprehensive Operating
System", which was renamed to GCOS when GE's large systems division
was sold to Honeywell. Dennis Ritchie has reported: "Sometimes we
sent printer output or batch jobs to the GCOS machine. The gcos field in
the password file was a place to stash the information for the $IDENTcard.
Not elegant."
- directory
- This is the user's home directory: the initial directory where the user is
placed after logging in. The value in this field is used to set the
HOME environment variable.
- shell
- This is the program to run at login (if empty, use /bin/sh). If set
to a nonexistent executable, the user will be unable to login through
login(1). The value in this field is used to set the SHELL
environment variable.
If you want to create user groups, there must be an entry in /etc/group,
or no group will exist.
If the encrypted password is set to an asterisk (*), the user will
be unable to login using login(1), but may still login using
rlogin(1), run existing processes and initiate new ones through
rsh(1), cron(8), at(1), or mail filters, etc. Trying to
lock an account by simply changing the shell field yields the same result
and additionally allows the use of su(1).
chfn(1), chsh(1), login(1), passwd(1), su(1),
crypt(3), getpwent(3), getpwnam(3), group(5),
shadow(5), vipw(8)
This page is part of release 5.05 of the Linux man-pages project. A
description of the project, information about reporting bugs, and the latest
version of this page, can be found at https://www.kernel.org/doc/man-pages/.


Name : Student Name
Roll Number : Student Roll No
| Sel | Course | Credits | Professor |
|---|---|---|---|
| Theory Of Computation | 4 | Dr Viswanath | |
| Concepts Of DOTA | 2 | Dr Navi Dendi | |
| ITS | 4 | Dr Nagesh Kolgani | |
| Introduction to DOTA | 4 | Dr Sajas Pandit | |
| Advanced Carry Theory (DOTA) | 4 | Dr Rajeev xSmart |


Ghosts and Dark Matter Detection Tweet
How do you catch a ghost?
How do you actually catch neutrinos? In CMS, the detector really can’t detect their signals so they’re only interpreted as “missing energy”. Since they can hardly be stopped by anything along its path, they can be “messenger particles” that send “unadulterated messages” from farflung parts of the universe.
The highest energy neutrinos ( MeV) are produced in super high-energy collisions that cannot be done in the LHC. These collisions could happen deep in outer space nuclei where a start collapses for example. These produce cosmic rays with pions and muons which subsequently decay into neutrinos. These neutrinos don’t really get bent by magnetic fields nor do they interact with material outerspace. So how do we detect them?
Down in Antartica, a cubic kilometer of super clear ice has been setup. These have also been drilled with holes to put some detectors that capture any trace of neutrinos. But how? If the neutrino energy is high enough and if this hits an ice molecule it then smashes it into pieces. These pieces travel faster through the ice than light does. These then leave behind a cone of blue light called Cerenkov radiation just like how supersonic jets leaves a sonic boom cone when it travels faster than the speed of sound in air. The signals are picked up by the detectors with photomultiplier tubes. Just like in CMS, the information is then stored and analyzed by scientists. This cool experiment is called IceCube.
There are other cool experiments that operate with the same principle. There’s one in Japan called Super Kamiokande. But I won’t talk about them here anymore.
Neutrino beams
It’s kind of interesting that neutrino beams can even be made by man. They hardly interact with anything so they’re hard to control. We first need highly energetic protons that are accelerated and smashed onto a target. When a proton gets smashed, its constituents, gluons, quarks then hadronize and form other particles like pions. Pions could be positively charged, negatively charged or neutral. Neutral pions could decay into a pair of photons. Charged pions are more unstable and decay into a muon plus a neutrino.
So if neutrinos are uncontrollable, how do you make them go in a relatively thin beam? Well you can’t control them. But you can control their charged parents, the pions. Powerful magnetic fields could be used to redirect the pions to travel roughly in the same direction. And then when they decay into neutrinos, they’d just travel along in the same direction. But this isn’t yet a pure neutrino beam! What do we do with the muons? We need to put some material that would absorb them. Neutrinos would just go through these block absorbers like GHOSTS!
These neutrino beams are used for different particle physics experiments that answer questions on neutrino oscillations, neutrino mass hierarchy and new neutrino types.
The Neutrinoless double beta decay
I’ll talk about the Neutrinoless double beta decay relatively quickly. I don’t know much about it to be honest but I’m trying to learn it. If the neutrino is a Majorana particle or it is the antineutrino of itself, and there is at least a type of neutrino which are not massless, then could occur.
Experiments that search for this phenomenon use a bunch of decaying isotopes with low background. They look for electrons that come out of neutrons decaying into two protons. I’m not into this, but a friend of mine is and he’s been one of the first few people who’ve been using convolutional neural network on this type of search. Pretty cool!
Particle Nature of Dark Matter
So we know by now that the Standard Model only explains 4% of the universe. Right now, we’re trying to figure out the 21% which is made of some mysterious thing called dark matter. It could be made of entirely something else. But their are constraints as to which kind of particles they could be.
First, we know that these guys do not interact strongly with ordinary matter and hence they should be “non-baryonic”. It’s not made up of quarks and gluons that are confined in a baryon.
Second, it should be “non-visible”. Duh! Well, we can’t see it! But we can see its effects on visible matter though. If we can’t see it then it does not interact electromagnetically. Third, it is stable over cosmological time scales, otherwise it wouldn’t be keeping galaxies together today. They are also “cold”, i.e. non-relativistic and should explain the Dark matter relic abundance.
Last of the Series
I think this would be the last article on particle physics review series. I would still write some more particle physics in the future but not as intensely. I hope to be writing some more interesting stuff on other things I like and hopefully get started on more programming projects!
Was fun!


To become a Berserker, you must be higher than level 40 and have obtained a letter of recommendation.
You have reached an acceptable level, so find Master Orkurus in the Old Castle village and win his approval.


TABLE OF INTERACTIONS WITH
RIFABUTIN
See also: enzymatic inducers
From the French ANSM drug interactions document of September2016, p. 190
RIFABUTIN RxNorm: 55672 ATC: J04AB04 |
ATOVAQUONE RxNorm: 60212 ATC: P01AX06 |
Moderate decrease of the plasma concentrations of atovaquone by the enzymatic inducer |
Take into account |
RIFABUTIN RxNorm: 55672 ATC: J04AB04 |
CLARITHROMYCIN RxNorm: 21212 ATC: J01FA09 |
Risk of increase of the undesirable effects of the rifabutin (uveitis) due to increase of its concentrations and of those of its active metabolite by the clarithromycin. In addition, increase of the metabolism of the clarithromycin by the rifabutin, with increase of the concentrations of its active metabolite |
Precaution for use Regular clinical and biological monitoring, especially at the beginning of the administration of the two medications together. |
RIFABUTIN RxNorm: 55672 ATC: J04AB04 |
COBICISTAT RxNorm: 1306284 ATC: V03AX03 J05AR09 |
Very large increase of the metabolite of the rifabutin, with risk of increase of its toxicity (uveitis, neutropenia). Furthermore, possible decrease of the concentrations of cobicistat |
Precaution for use Adjustment of the dosage of the rifabutin (in principle, reduction of the doses by half). |
RIFABUTIN RxNorm: 55672 ATC: J04AB04 |
EFAVIRENZ RxNorm: 195085 ATC: J05AG03 J05AR06 |
Decrease of the concentrations of rifabutin by about half, due to increase of its hepatic metabolism by the efavirenz |
Precaution for use Adjustment of the dosage of the rifabutin during the treatment with efavirenz. |
RIFABUTIN RxNorm: 55672 ATC: J04AB04 |
ELVITEGRAVIR RxNorm: 1306286 ATC: J05AX11 J05AR09 |
Decrease of the minimal concentrations of elvitegravir |
Take into account |
RIFABUTIN RxNorm: 55672 ATC: J04AB04 |
FLUCONAZOLE RxNorm: 4450 ATC: D01AC15 J02AC01 |
Risk of increase of the undesirable effects of the rifabutin (uveitis), due to increase of its concentrations and of those of its active metabolite |
Precaution for use Regular clinical and biological monitoring, especially at the beginning of the treatment with the two medications together. |
RIFABUTIN RxNorm: 55672 ATC: J04AB04 |
THYROID HORMONES CLASS CODE: H03AA |
Described for phenytoin, rifampicin, and carbamazepine. Risk of clinical hypothyroidism in patients with low thyroid, due to increase of the metabolism of the T3 and T4 |
Precaution for use Monitoring of serum concentrations of T3 and of T4 and adjustment, if needed, of the dosage of the thyroid hormones during the treatment with rifabutin and after it is stopped. |
RIFABUTIN RxNorm: 55672 ATC: J04AB04 |
RITONAVIR BOOSTED PROTEASE INHIBITORS CLASS CODE: J05AE-002 |
Risk of reduction of the effectiveness of the protease inhibitor (even more so when the dosage of the rifabutin is large) for one thing, and risk of increase of the undesirable effects (uveitis) of the rifabutin for another. |
Precaution for use Regular clinical and biological monitoring, especially at the beginning of the administration of the substances together. |
RIFABUTIN RxNorm: 55672 ATC: J04AB04 |
POSACONAZOLE RxNorm: 282446 ATC: J02AC04 |
Risk of increase of the undesirable effects of the rifabutin (uveitis), due to increase of its concentrations and of those of its active metabolite |
Not recommended Regular clinical and biological monitoring, especially at the beginning of the administration of the medications together. |
RIFABUTIN RxNorm: 55672 ATC: J04AB04 |
VORICONAZOLE RxNorm: 121243 ATC: J02AC03 |
Decrease of the plasma concentrations of the voriconazole with risk of loss of effectiveness, due to increase of its hepatic metabolism by the rifabutin for one thing; and risk of increase of the undesirable effects (uveitis) of the rifabutin for another |
Not recommended If the administration of these substances together is judged necessary, clinical monitoring and adjustment of the dosage of the voriconazole (generally doubled) during the treatment with the rifabutin. |


| 1 | package fr.sii.ogham.spring.email; | |
| 2 | ||
| 3 | import java.net.URL; | |
| 4 | ||
| 5 | import org.springframework.boot.context.properties.ConfigurationProperties; | |
| 6 | ||
| 7 | @ConfigurationProperties("ogham.email.sendgrid") | |
| 8 | public class OghamSendGridProperties { | |
| 9 | /** | |
| 10 | * Set SendGrid API key.
 | |
| 11 | *
 | |
| 12 | * | |
| 13 | * /!\ In Spring Boot application: if you provide a value for | |
| 14 | * spring.sendgrid.api-key, this property is not used. This is because | |
| 15 | * Spring Boot provides its own SendGrid client. | |
| 16 | */ | |
| 17 | private String apiKey; | |
| 18 | /** | |
| 19 | * Set SendGrid API base URL.
 | |
| 20 | *
 | |
| 21 | * | |
| 22 | * Changing the URL may be useful in tests.
 | |
| 23 | *
 | |
| 24 | * | |
| 25 | * /!\ In Spring Boot application: if you provide a value for | |
| 26 | * spring.sendgrid.api-key, this property is not used. This is because | |
| 27 | * Spring Boot provides its own SendGrid client. | |
| 28 | */ | |
| 29 | private URL url; | |
| 30 | /** | |
| 31 | * Set username for SendGrid HTTP API.
 | |
| 32 | *
 | |
| 33 | * | |
| 34 | * @deprecated since version 3 of SendGrid Java library. Use API key instead | |
| 35 | */ | |
| 36 | @Deprecated | |
| 37 | private String username; | |
| 38 | /** | |
| 39 | * Set password for SendGrid HTTP API.
 | |
| 40 | *
 | |
| 41 | * | |
| 42 | * @deprecated since version 3 of SendGrid Java library. Use API key instead | |
| 43 | */ | |
| 44 | @Deprecated | |
| 45 | private String password; | |
| 46 | /** | |
| 47 | * Configure SendGrid Client to run in unit tests. Only available since | |
| 48 | * version 3 of SendGrid Java library | |
| 49 | */ | |
| 50 | private boolean unitTesting; | |
| 51 | ||
| 52 | public String getApiKey() { | |
| 53 |
1
1. getApiKey : replaced return value with "" for fr/sii/ogham/spring/email/OghamSendGridProperties::getApiKey → RUN_ERROR |
return apiKey; |
| 54 | } | |
| 55 | ||
| 56 | public void setApiKey(String apiKey) { | |
| 57 | this.apiKey = apiKey; | |
| 58 | } | |
| 59 | ||
| 60 | /** | |
| 61 | * @deprecated Spring Boot uses SendGrid Java library v4 since Spring Boot | |
| 62 | * 2. Use API keys instead. | |
| 63 | * | |
| 64 | * @return the username | |
| 65 | */ | |
| 66 | @Deprecated | |
| 67 | public String getUsername() { | |
| 68 |
1
1. getUsername : replaced return value with "" for fr/sii/ogham/spring/email/OghamSendGridProperties::getUsername → RUN_ERROR |
return username; |
| 69 | } | |
| 70 | ||
| 71 | /** | |
| 72 | * @deprecated Spring Boot uses SendGrid Java library v4 since Spring Boot | |
| 73 | * 2. Use API keys instead. | |
| 74 | * | |
| 75 | * @param username | |
| 76 | * the username | |
| 77 | */ | |
| 78 | @Deprecated | |
| 79 | public void setUsername(String username) { | |
| 80 | this.username = username; | |
| 81 | } | |
| 82 | ||
| 83 | /** | |
| 84 | * @deprecated Spring Boot uses SendGrid Java library v4 since Spring Boot | |
| 85 | * 2. Use API keys instead. | |
| 86 | * | |
| 87 | * @return the password | |
| 88 | */ | |
| 89 | @Deprecated | |
| 90 | public String getPassword() { | |
| 91 |
1
1. getPassword : replaced return value with "" for fr/sii/ogham/spring/email/OghamSendGridProperties::getPassword → RUN_ERROR |
return password; |
| 92 | } | |
| 93 | ||
| 94 | /** | |
| 95 | * @deprecated Spring Boot uses SendGrid Java library v4 since Spring Boot | |
| 96 | * 2. Use API keys instead. | |
| 97 | * | |
| 98 | * @param password | |
| 99 | * the password | |
| 100 | */ | |
| 101 | @Deprecated | |
| 102 | public void setPassword(String password) { | |
| 103 | this.password = password; | |
| 104 | } | |
| 105 | ||
| 106 | public URL getUrl() { | |
| 107 |
1
1. getUrl : replaced return value with null for fr/sii/ogham/spring/email/OghamSendGridProperties::getUrl → RUN_ERROR |
return url; |
| 108 | } | |
| 109 | ||
| 110 | public void setUrl(URL url) { | |
| 111 | this.url = url; | |
| 112 | } | |
| 113 | ||
| 114 | public boolean isUnitTesting() { | |
| 115 |
2
1. isUnitTesting : replaced boolean return with true for fr/sii/ogham/spring/email/OghamSendGridProperties::isUnitTesting → RUN_ERROR 2. isUnitTesting : replaced boolean return with false for fr/sii/ogham/spring/email/OghamSendGridProperties::isUnitTesting → RUN_ERROR |
return unitTesting; |
| 116 | } | |
| 117 | ||
| 118 | public void setUnitTesting(boolean unitTesting) { | |
| 119 | this.unitTesting = unitTesting; | |
| 120 | } | |
| 121 | ||
| 122 | } | |
Mutations | ||
| 53 |
1.1 |
|
| 68 |
1.1 |
|
| 91 |
1.1 |
|
| 107 |
1.1 |
|
| 115 |
1.1 2.2 |


This field sets how long Slips7ream will wait for a response from an external process. Slips7ream makes calls to programs such as DISM frequently, and can be told to fail if these calls take too long.
By default, the Command Timeout feature is disabled (with a value of 0), which means that Slips7ream will wait until the program closes on its own before continuing.


Suite
Test
Method
Status
Execution Time(ms)
My test suite
numbersXML
givenNumberObjectFromDataProvider_ifEvenCheckOK_thenCorrect
PASSED
0


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