studium 0.9.383

data/lib/studium/ects/still_missing.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Studium::StillMissing
+#
+# This small class will just tell us, on the commandline, how many ECTS
+# points are still missing from a given curriculum.
+#
+# It will default to the bachelor-master curriculum "vektoren" if no
+# argument is provided.
+#
+# Usage example:
+#   Studium::StillMissing.new
+# =========================================================================== #
+# require 'studium/ects/still_missing.rb'
+# =========================================================================== #
+require 'studium/base/base.rb'
+
+module Studium
+
+class StillMissing < Base # === Studium::StillMissing
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === DEFAULT_CURRICULUM_TO_BE_USED
+  # ========================================================================= #
+  DEFAULT_CURRICULUM_TO_BE_USED = :bachelor_master_vektorx
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      i           = DEFAULT_CURRICULUM_TO_BE_USED,
+      run_already = true
+    )
+    reset
+    set_use_this_curriculum(i)
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    @n_ects_in_this_curriculum = 0
+    @n_ects_points_are_still_missing = 0
+  end
+
+  # ========================================================================= #
+  # === set_use_this_curriculum
+  # ========================================================================= #
+  def set_use_this_curriculum(
+      i = :default
+    )
+    i = i.first if i.is_a? Array
+    case i
+    when :default, nil
+      i = DEFAULT_CURRICULUM_TO_BE_USED
+    end
+    @use_this_curriculum = i
+  end
+
+  # ========================================================================= #
+  # === use_this_curriculum?
+  # ========================================================================= #
+  def use_this_curriculum?
+    @use_this_curriculum
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    # ======================================================================= #
+    # This is currently hardcoded to bachelor-master vektor - ought to
+    # be changed at a later time.
+    # ======================================================================= #
+    dataset_from_the_curriculum_file = return_dataset_from_this_curriculum_file(
+      @use_this_curriculum
+    )
+    dataset_from_the_curriculum_file.each {|name_of_the_lecture, inner_hash|
+      n_ects_points  = inner_hash[:ects]
+      already_solved = inner_hash[:already_solved]
+      @n_ects_in_this_curriculum += n_ects_points
+      unless already_solved
+        @n_ects_points_are_still_missing += n_ects_points
+      end
+    }
+    e
+    e 'This curriculum has a total of '+
+      sfancy(@n_ects_in_this_curriculum.to_s)+' ECTS points.'
+    n_percent_missing = (
+      @n_ects_points_are_still_missing * 100.0 / @n_ects_in_this_curriculum.to_f
+    )
+    n_percent_missing = n_percent_missing.round(2).to_s
+    # ======================================================================= #
+    # Also notify the user how many ECTS points are still missing.
+    # ======================================================================= #
+    e
+    e 'Still missing '+
+      gold(@n_ects_points_are_still_missing)+' ECTS '\
+      'points in this curriculum.'+
+      ' (=> '+crimson(n_percent_missing.to_s+'%')+
+      ')'
+    e
+  end
+
+  # ========================================================================= #
+  # === Studium::StillMissing[]
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i)
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Studium::StillMissing.new(ARGV)
+end # still_missing

data/lib/studium/ects/sum_of_ects.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Studium::SumOfEcts
+#
+# This class will calculate the sum of all ECTS points.
+#
+# Usage example:
+#   Studium::SumOfEcts.new
+# =========================================================================== #
+# require 'studium/utility_scripts/sum_of_ects.rb'
+# =========================================================================== #
+require 'studium/base/base.rb'
+
+module Studium
+
+class SumOfEcts < ::Studium::Base # === Studium::SumOfEcts.new
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      i           = nil,
+      run_already = true
+    )
+    reset
+    set_input(i)
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    @namespace = NAMESPACE
+  end
+
+  # ========================================================================= #
+  # === set_input
+  # ========================================================================= #
+  def set_input(i = '')
+    i = i.first if i.is_a? Array
+    i = i.to_s.dup
+    case i # case tag
+    when 'todo' # Todo file
+      i = FILE_TODO_BOKU
+      parse_todo_file(i)
+      exit
+    end unless File.exist? i
+    # ======================================================================= #
+    # If the file exist, read it and use it as the new dataset.
+    # ======================================================================= #
+    if File.exist? i
+      i = File.read(i)
+    end
+    @input = i
+  end
+
+  # ========================================================================= #
+  # === input?
+  # ========================================================================= #
+  def input?
+    @input
+  end
+
+  # ========================================================================= #
+  # === parse_input
+  # ========================================================================= #
+  def parse_input(i = @input)
+    i = i.split(N)
+    i.flatten! # Out with nil values.
+    i.reject!(&:empty?) # Get rid of empty lines.
+    i.reject! {|line|
+      line.strip.start_with? '==='
+    }
+    if i.any? {|entry| entry.include? '|' } # Work on | entries.
+      i.map! {|entry|
+        splitted = entry.split('|')
+        entry = splitted.last
+        entry
+      }
+    end
+    i.map! {|entry|
+      entry.gsub!(/ECTS/,'')
+      entry.gsub!(/ects/,'')
+      entry.strip.to_f
+    }
+  end
+
+  # ========================================================================= #
+  # === report_result
+  # ========================================================================= #
+  def report_result
+    opnn; e "The total sum is: #{simp(@sum.to_s)}"
+  end
+
+  # ========================================================================= #
+  # === calculate_total_sum
+  # ========================================================================= #
+  def calculate_total_sum(use_this_input = @input)
+    if use_this_input.is_a? Array
+      use_this_input.flatten!
+    end
+    @sum = use_this_input.inject(0) {|a,b| a.to_f+b.to_f }
+  end
+
+  # ========================================================================= #
+  # === parse_todo_file
+  #
+  # This is a simpler method which just parses the file.
+  # ========================================================================= #
+  def parse_todo_file(i)
+    data = File.read(i)
+    use_this_regex = /\((\d+.?\d+ ECTS)\)/ # See: http://rubular.com/r/1lTBn5wQZC
+    result = data.scan(use_this_regex)
+    calculate_total_sum(result)
+    report_result
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    parse_input
+    calculate_total_sum
+    report_result
+  end
+
+  # ========================================================================= #
+  # === []
+  # ========================================================================= #
+  def self.[](i = '')
+    new
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Studium::SumOfEcts.new(ARGV)
+end # sum_of_ects todo

data/lib/studium/encoding/encoding.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# This file is necessary so that we can easily use non-Unicode encodings.
+# =========================================================================== #
+# require 'studium/encoding/encoding.rb'
+# =========================================================================== #
+module Studium
+
+  require 'studium/requires/require_the_proper_yaml_engine.rb' # Load up the proper YAML engine here.
+  require 'studium/project/project.rb'
+  require 'studium/toplevel_methods/save_file.rb'
+
+  # ========================================================================= #
+  # === Studium::ENCODING_UTF
+  # ========================================================================= #
+  ENCODING_UTF = 'UTF-8'
+    UTF8 = ENCODING_UTF # === UTF8
+    UTF  = ENCODING_UTF # === UTF
+
+  # ========================================================================= #
+  # === Studium::ENCODING_ISO
+  # ========================================================================= #
+  ENCODING_ISO = 'ISO-8859-1'
+    ISO          = ENCODING_ISO # === ISO
+    ISO_ENCODING = ENCODING_ISO # === ISO_ENCODING
+
+  # ========================================================================= #
+  # === FILE_DEFAULT_ENCODING
+  #
+  # On my home system this file resides at:
+  #
+  #   bl $RSRC/studium/lib/studium/yaml/default_encoding.yml
+  #
+  # ========================================================================= #
+  FILE_DEFAULT_ENCODING = "#{yaml_directory?}default_encoding.yml"
+
+  # ========================================================================= #
+  # === Studium::USE_THIS_ENCODING
+  #
+  # Which encoding to use for this project is specified by this constant
+  # here, called USE_THIS_ENCODING.
+  #
+  # I primarily use the ISO encoding but we should remain flexible here,
+  # in the event that we wish to change to another encoding one day.
+  #
+  # As of January 2018, the yam file default_encoding.yml will determine
+  # which yaml file is to be used.
+  # ========================================================================= #
+  @use_this_encoding = YAML.load_file(FILE_DEFAULT_ENCODING)
+    USE_THIS_ENCODING = @use_this_encoding
+    MAIN_ENCODING    = @use_this_encoding
+
+  # ========================================================================= #
+  # === Studium.utf_encoding?
+  # ========================================================================= #
+  def self.utf_encoding?
+    ENCODING_UTF
+  end
+
+  # ========================================================================= #
+  # === Studium.encoding?
+  #
+  # The main encoding to use for this project.
+  # ========================================================================= #
+  def self.encoding?
+    @use_this_encoding
+  end; self.instance_eval { alias use_this_encoding? encoding? } # === Studium.use_this_encoding?
+       self.instance_eval { alias main_encoding?     encoding? } # === Studium.main_encoding?
+
+  # ========================================================================= #
+  # === Studium.use_this_new_encoding
+  # ========================================================================= #
+  def self.use_this_new_encoding(
+      i, also_save_the_new_encoding = true
+    )
+    case i # case tag
+    when 'iso1'
+      i = 'ISO-8859-1'
+    end
+    @use_this_encoding = i
+    if also_save_the_new_encoding
+      puts "Now storing this content #{i} into `#{into}`."
+      into = FILE_DEFAULT_ENCODING # Yup, this is the correct path.
+      write_what_into(i+"\n", into)
+    end
+  end
+
+  # ========================================================================= #
+  # === Studium.ensure_main_encoding
+  #
+  # This method will ensure the main encoding in use. This presently
+  # works for both Arrays and Strings.
+  # ========================================================================= #
+  def self.ensure_main_encoding(i)
+    copy = i
+    use_this_encoding = @use_this_encoding
+    # ======================================================================= #
+    # === Handle Array next
+    # ======================================================================= #
+    if copy.is_a? Array
+      copy = copy.map {|entry|
+        if entry.is_a? String
+          unless entry.encoding.to_s.include? use_this_encoding
+            entry = entry.force_encoding(use_this_encoding)
+          end
+        end
+        entry
+      }
+    # ======================================================================= #
+    # === Handle Hash next
+    # ======================================================================= #
+    elsif copy.is_a? Hash
+      new_hash = {}
+      copy.each_pair {|key, value|
+        unless key.encoding.to_s.include? use_this_encoding
+          key = key.dup if key.frozen?
+          unless key.is_a? Symbol
+            key = key.force_encoding(use_this_encoding)
+          end
+        end
+        if value.is_a? Array
+          array = Studium.ensure_main_encoding(array)
+        end
+        new_hash[key] = ensure_main_encoding(value)
+      }
+      copy = new_hash
+    # ======================================================================= #
+    # === Handle String next
+    # ======================================================================= #
+    elsif copy.is_a? String
+      unless copy.encoding.to_s.include? use_this_encoding
+        copy = copy.dup if copy.frozen?
+        copy = copy.force_encoding(use_this_encoding)
+      end
+    end
+    return copy
+  end
+
+end

data/lib/studium/exam_topics/RNAi_siRNA_and_miRNA

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+# =========================================================================== #
+# === RNAi, siRNA und miRNA
+#
+# Inkludiert auch Therapie-Formen mittels RNAi.
+# =========================================================================== #
+
+- For a <one>miRNA</one>: what has the <three>strongest influence on target regulation</three>, structurally? The "seed sequence", aka the seed region.
+- <one>1993</one> wurde die erste small RNA, eine miRNA, entdeckt. Wie heisst sie? <one>lin-4</one>
+- Welches Protein kommt normalerweise vor <one>Dicer</one>? <one>Drosha</one>. []
+- <one>RNAi</one> verändert die vorhandene Menge an ... ? <one>mRNA</one>.
+- What is the biggest hurdle of <one>RNAi therapeutics</one>? <one>Delivery</one> - that is, to get the RNA into the target tissue safely and effectively.
+- What was discovered first: <one>RNA interference</one> or <one>microRNAs</one>? <one>MicroRNAs</one>.
+- Was ist <one>miRNA</one>? A: Das sind "Transkripte zellulärer Gene".
+- What is the size of the <one>RISC</one> complex in Drosophila? <one>~500 kDa</one>.
+- Name the two general components of <one>the RISC complex</one>. A: (1) <one>Nuclease</one> (2) <one>small RNA</one>
+- Do viruses contain miRNA genes? Yes; viruses of the herpes virus family in particular.
+- miRNA precursors have a two nucleotide overhang at which end? At the 3' end.
+- Name two domains that can typically be found in an Ago (argonaute) protein. A: (1) <one>PIWI</one> (2) <one>PAZ</one>
+- Name a domain that can be found between the Argonaute-protein PAZ and PIWI domain. A: <one>MID</one>.
+- Which protein is typically associated with miRNAs? The <one>Argonaute protein</one>.
+- miRNA-protein complexes are often termed ... ? <one>RISC</one>. URL: https://en.wikipedia.org/wiki/RNA-induced_silencing_complex
+- <one>Drosha</one> is what kind of enzyme? Drosha is a <one>RNase III enzyme</one>.
+- Does the "seed sequence" of a <violet>miRNA</violet> have to be perfectly complementary? Yes.
+- In short, two words only, the effect of "siRNAs" is ... ? <one>Gene silencing</one>.
+- Within the genome: where can we typically find miRNAs? miRNAs are usually <one>located in introns of protein-coding genes</one>.
+- Are primary miRNA transcripts capped? Generally yes.
+- Bei miRNA: wie kennzeichnen wir den <violet>Gegenstrang</violet>? Via <one>*</one>, also zum Beispiel "miRNA*" oder "MIR*".
+- What is the seed sequence of a miRNA? The seed sequence, such as "AAAACCA", is "an essential and conserved heptametrical sequence", which is mostly situated at positions 2-7 from the miRNA 5'-end.
+- Was genau ist die "seed region" einer miRNA? Dies ist der Bereich der Nukleotide 2-7, die für die "mRNA Erkennung" relevant sind.
+- How long is a typical seed sequence of a miRNA? 7 nucleotides in length.
+- Name a <one>miRNA</one> that can be used to battle cancer. A: "miR-26A".
+- Nenne zwei "RISC Domänen". A: (1) "PIWI" (2) "PAZ" URL: http://smart.embl.de/smart/do_annotation.pl?DOMAIN=SM00949
+- What is the "trigger molecule" for RNAi? "dsRNA".
+- Was kann man mit "RNA-Interferenz" bewirken? A: Man kann quasi jedes Gen blockieren.
+- Kommt "RNA Editing" bei miRNAs vor? Ja.
+- Wenn wir "kurze 3'-UTRs" sehen, können wir daraus etwas über die miRNA Regulation folgern? Ja; in kurzen 3'-UTRs kommt es fast immer zu keiner miRNA Regulation.
+- The first miRNA, called "lin-4", was discovered in what year? "1993".
+- What may be the "evolutionary role of siRNA"? It "shuts off undesirable genetic elements" that insert into the genome.
+- Name a cause of (transcription of) "endo-siRNAs". A: "Transposons".
+- Name two characteristic features of "siRNAs". A: (1) They contain "phosphate groups" at their 5' ends. (2) They have a "two nucleotide overhang" on both 3' ends.
+- Was mögen wir beobachten wenn Dicer genetisch ausgeschalten wird? Die Zelle beziehungsweise der Organismus leiden öfters an Krebs.
+- Beim RISC Komplex, den Argonautenproteinen gibt es die "PIWI-Domäne". Was für eine Aktivität besitzt diese Domäne? SIe besitzt eine "Endonuclease-Aktivität".
+- miRNA will in general bind to which part of a mRNA? miRNA will bind to the 3'-UTR part of a mRNA.
+- Können "siRNA Oligonukleotide" die Blut-Hirn Schranke durch passive Diffusion überwinden? Nein.
+- Nenne einen "Algorithmus zur Vorhersage von miRNA-Zielen". A: "miranda".
+- Can pre-miRNAs, the "precursors of miRNA", be located within introns? Yes. URL: https://www.thermofisher.com/at/en/home/references/ambion-tech-support/microrna-studies/tech-notes/precursor-mirnas-for-successful-mirna-functional-studies.html
+- Bei RNAi-Therapien, wieso möchten wir die Stabilität der siRNAs erhöhen? Da dies die Zirkulationszeit im Blutkreislauf erhöhen mag; aber auch sonstwo die Halbwertszeit erhöht wird je stabiler eine siRNA ist.
+- Nenne zwei wichtige Unterschiede zwischen siRNA und miRNA. A: (1) siRNA leitet den Abbau der mRNA ein, miRNA hingegen verhindert die Translation. (2) miRNA ist toleranter und kann auch Fehlpaarungen eingehen, siRNA hingegen benötigt genaue Bindung.
+- Was ist das Ziel, also das Zielobjekt, einer miRNA? Eine mRNA.
+- Weshalb führt langkettige doppelsträngige RNA in Säugetierzellen nicht zum Gene-Silencing, wie zum Beispiel in "Drosophila"? Das es zu einer "Interferonantwort" und "Immunaktivierung" kommt, die den "sequenzspezifischen Effekt" überdeckt.
+- Winkler: Was ist das wichtigste Kriterium dafür, damit die Zelle "entscheiden" kann, welcher der beiden siRNA Stränge der Leitstrang (Antisensestrang) im RISC Komplex ausgewählt wird? Die "thermodynamische Stabilität am Strangende" - das labilere Ende wird das "5'-Ende des Leitstrangs".
+- Was meinen wir mit einer "komplexen Regulation" über miRNAs? Eine miRNA kann viele Gene regulieren; ein Gen kann von vielen miRNAs reguliert werden. (Yin/Yang)
+- Kann "RNAi" dazu benutzt werden herauszufinden welche Rolle ein Protein hat? Ja - zumindest während der Entwicklung eines Organismus (und des dazugehörigen Proteins).
+- In welchem Organismus beziehungsweise Organismusgruppe wurde RNAi zuerst entdeckt? In "Pflanzen".
+- Wie bezeichnen wir RNAi in Neurospora? "Quelling". URL: https://www.ncbi.nlm.nih.gov/pubmed/17395524
+- Welcher Strang verbleibt im RISC ("RNA-induced silencing complex")? Der als "Leitstrang bezeichnete "RNA-Einzelstrang" verbleibt im RISC-Komplex.
+- RNAi could be used to treat diseases. In particular against what kind of diseases, in general? Diseases that may arise due to any overproduction of a gene - this is an area where RNAi might be useful.
+- Name the two major components of the "processing machinery for RNAi". A: (1) "Dicer" (2) "Argonaute"
+- Warum können wir nicht längere dsRNA verwenden als Anwendung für den Menschen? Da die Interferon-Abwehr hier aktiv werden würde.
+- Nenne den wichtigsten Grund wieso wir siRNAs chemisch modifizieren möchten. A: Wir erhöhen damit die Stabilität dieser RNA.
+- Name a way how to deliver RNAi therapeutics into a patient. A: We could use "LNPs" aka "lipid nano particle".
+- Vergleiche die Kosten von siRNA zu Antisense-RNA, vom kommerziellen Standpunkt. A: siRNA ist etwa 10x so teuer wie Antisense-RNA.
+- Bei RNAi-Therapien, was meinen wir mit einem "transienten System"? Das meint das es zu keinem dauerhaften Ausschalten eines Gens kommt.
+- Wann wurde RNAi (RNA-Interferenz) entdeckt? Im Jahre "1983". URL: https://en.wikipedia.org/wiki/RNA_interference#Downregulation_of_genes
+- Eine miRNA ("microRNA") enthält etwa 22 Nukleotide. Das menschliche Genom kodiert für etwa wieviele verschiedene miRNAs? Für "etwas mehr als 1000 verschiedene miRNAs".
+- A miRNA is processed from a longer transcript, called ...? The "pri-miRNA" ("primary transcript").
+- "Miravirsen" is an inhibitor of which miRNA? "miR-122".
+- Wie lange sind miRNAs (von-bis)? 20-200 nucleotides.
+- When was the first microRNA ("miRNA") gene uncovered? In "1993".
+- Most miRNAs act how? They repress the expression of genes.
+- miRNA bindet an welchen mRNA Teil? A: An den "3'-UTR" Bereich der jeweiligen mRNA.
+- Haben miRNAs ein 5'-Cap? Ja, zumindest als "primary miRNA".
+- Nenne zwei miRNA in C. elegans! A: lin-4 und let-7
+- Was sind miRNAs? Kurze RNA Moleküle (22 nt).
+- Wie lange sind die miRNAs? 21-25 Nucleotide.
+- Grob formuliert, was ist der Unterschied zwischen miRNA und siRNA? (a) eine miRNA reguliert die Genexpression, indem es "die Translation hemmt" (b) eine siRNA reguliert die Genexpression, indem es "mRNA abbaut"
+- What are "miRNAs"? MicroRNAs are "ssRNA molecules" that "regulate gene expression".
+- The human genome produces n different miRNAs? "Over 1000 different miRNAs".
+- Wer entdeckte 1993 das miRNAs die Genexpression von C. elegans beeinflussen können? "Victor Ambros".