corrected images path

Author: hadiparsianNIH

AWS/Submodule_00_background copy.ipynb

@@ -175,7 +175,7 @@
     "- Removal of known functional RNA\n",
     "\n",
     "#### Sequence Assembly\n",
-    "<img  src=\"images/deBruijnGraph.png\" width=600 alt=\"Conceptual design of a de Bruijn Graph\">\n",
+    "<img  src=\"../images/deBruijnGraph.png\" width=600 alt=\"Conceptual design of a de Bruijn Graph\">\n",
     "\n",
     "**Figure 1:** Conceptual diagram of a sequence-defined [de Bruijn graph](https://en.wikipedia.org/wiki/De_Bruijn_graph). (A) Each sequence in an RNA-seq is broken into overlapping *k*-mers. (B) Each *k*-mer becomes a node in the graph, shown in the example with *k*=6. Edges are drawn between nodes that match *k*-1 contiguous nucleotides. (C) Putative transcripts (shown in distinct colors) are represented as traversals of one of the many connected components of the graph generated by the starting sequence set.</p>\n",
     "\n",
@@ -444,7 +444,11 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 5
 }

AWS/Submodule_00_background.ipynb

@@ -292,7 +292,7 @@
     "\n",
     ">Consider the following file structure and you are currently in the directory `toDo`: \n",
     ">\n",
-    "> <img src=\"images/fileDemo.png\" width=\"1200\">\n",
+    "> <img src=\"../images/fileDemo.png\" width=\"1200\">\n",
     ">\n",
     ">- If you were to type `!ls ./`, it would return the contents of your current directory, so it would return `nextWeek`, `Today.txt`, `Tomorrow.txt`, `Yesterday.txt`.\n",
     ">     - The `./` path points to your current directory.\n",
@@ -401,7 +401,11 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 5
 }

AWS/Submodule_01_prog_setup.ipynb

@@ -20,7 +20,7 @@
     "- Annotation of the final transcriptome using alignment to known proteins (using DIAMOND/BLAST) and assignment to probable protein domains (using HMMER/Pfam).\n",
     "- Generation of output reports.\n",
     "\n",
-    "> <img src=\"images/TransPiWorkflow.png\" width=\"1500\">\n",
+    "> <img src=\"../images/TransPiWorkflow.png\" width=\"1500\">\n",
     ">\n",
     "> **Figure 1:** TransPi workflow for a basic transcriptome assembly run."
    ]
@@ -168,7 +168,7 @@
     "</div>\n",
     "\n",
     "\n",
-    "> <img src=\"images/jupyterRuntime.png\" width=\"500\">\n",
+    "> <img src=\"../images/jupyterRuntime.png\" width=\"500\">\n",
     ">\n",
     "> Remember that you can tell if the cell is still running by referring to the contents inside the `[ ]:` that sits to the left of the code cell. Or you can check the top right of the screen for the circle."
    ]

AWS/Submodule_02_basic_assembly.ipynb

@@ -84,7 +84,7 @@
    "id": "dc4cd97f-fc62-40ab-badc-ba0bc6f092e4",
    "metadata": {},
    "source": [
-    "> <img src=\"images/AnnotationProcess.png\" width=\"800\">\n",
+    "> <img src=\"../images/AnnotationProcess.png\" width=\"800\">\n",
     ">\n",
     "> **Figure 1:** Annotation workflow for a new, unannotated transcriptome. \n",
     "\n",
@@ -156,7 +156,7 @@
     "\n",
     "> The Oncorhynchus mykiss is commonly known as the **Rainbow Trout**. Here is what they look like:\n",
     ">\n",
-    "> <img src=\"images/rainbowTrout.jpeg\"  width=\"500\" >\n",
+    "> <img src=\"../images/rainbowTrout.jpeg\"  width=\"500\" >\n",
     "> \n",
     ">> Image Source: https://www.ndow.org/species/rainbow-trout/"
    ]
@@ -542,7 +542,11 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 5
 }

AWS/Submodule_03_annotation_only.ipynb

@@ -25,7 +25,7 @@
     "Fortunately, Batch and Nextflow are compatible with each other allowing for any Nextflow workflow, including the TransPi workflow that we have been using, to be executable on Batch.\n",
     "\n",
     "\n",
-    "> <img src=\"images/gcbDiagram.jpg\" width=\"1200\">\n",
+    "> <img src=\"../images/gcbDiagram.jpg\" width=\"1200\">\n",
     ">\n",
     "> **Figure 1:** Diagram illustrating the interactions between the components used for the Google Batch run. \n",
     "\n",
@@ -99,7 +99,7 @@
     "**Step 1:** Downsize the VM instance.\n",
     "> Consider downloading or taking a screenshot of the following image as the downsizing process will involve briefly stopping this VM instance.\n",
     ">\n",
-    "> <img src=\"images/VMdownsize.jpg\" width=\"1200\">"
+    "> <img src=\"../images/VMdownsize.jpg\" width=\"1200\">"
    ]
   },
   {

AWS/Submodule_04_google_batch_assembly.ipynb

@@ -175,7 +175,7 @@
     "- Removal of known functional RNA\n",
     "\n",
     "#### Sequence Assembly\n",
-    "<img  src=\"images/deBruijnGraph.png\" width=600 alt=\"Conceptual design of a de Bruijn Graph\">\n",
+    "<img  src=\"../images/deBruijnGraph.png\" width=600 alt=\"Conceptual design of a de Bruijn Graph\">\n",
     "\n",
     "**Figure 1:** Conceptual diagram of a sequence-defined [de Bruijn graph](https://en.wikipedia.org/wiki/De_Bruijn_graph). (A) Each sequence in an RNA-seq is broken into overlapping *k*-mers. (B) Each *k*-mer becomes a node in the graph, shown in the example with *k*=6. Edges are drawn between nodes that match *k*-1 contiguous nucleotides. (C) Putative transcripts (shown in distinct colors) are represented as traversals of one of the many connected components of the graph generated by the starting sequence set.</p>\n",
     "\n",
@@ -225,11 +225,11 @@
     "\n",
     "It is standard practice in modern biotechnology, bioinformatics, and computational biology that most complex analyses are carried out not by a single comprehensive program, but are instead carried out in a defined sequence of multiple programs. The process of running through these steps in the proper order is collectively called a ***workflow*** or ***pipeline***.\n",
     "\n",
-    "<img align=\"right\" src=\"images/workflow_concept.png\" width=400>\n",
+    "<img align=\"right\" src=\"../images/workflow_concept.png\" width=400>\n",
     "\n",
     "Workflow management systems, *e.g.*, Nextflow, provide a syntax for defining the order of steps and the associated flow of information between steps, while also providing management/control software that can read and carry out these workflows. The workflow control systems (which are generally platform-specific) are responsible for allocating resources, activating analysis steps, and also making sure that all steps occur in the proper order (e.g., only activating a sequence alignment program after the sequence quality control has been performed).\n",
     "\n",
-    "<img align=\"left\" src=\"images/module_concept.png\" width=250>\n",
+    "<img align=\"left\" src=\"../images/module_concept.png\" width=250>\n",
     "\n",
     "Workflows can be conceptually broken up into steps or modules (see the figure at left), which formalize the flow of information as inputs and outputs. A workflow conceptually ties the steps/modules together and enforces the dependencies (see the figure above), specifically in that if the output from one step is the input for a later step, the later step is blocked until the earlier step completes."
    ]
@@ -295,7 +295,7 @@
     "\n",
     "Each cell has options as to how it is executed. For example, the text that you are reading right now in this cell is in the `Markdown` cell type, but there are also `code`, and `raw` cell types. In these modules, you will primarily be seeing `Markdown` and `code` cells. *You can choose what each cell type is by using the drop-down menu at the top of the notebook.*\n",
     "\n",
-    "> <img src=\"images/cellMenu.png\" width=\"500\">\n",
+    "> <img src=\"../images/cellMenu.png\" width=\"500\">\n",
     "\n",
     "For the code cells, information carries over between cells, but in execution order. This is important because when looking at a series of cells you may be expecting a specific output, but receive a different output due to the order of execution."
    ]
@@ -357,7 +357,7 @@
     "1. The first way to check is to look to the left of the code cell. There will be an indication that looks like this: `[ ]:` If it is empty, then the cell has never been executed yet. If it looks like this: `[*]:`, that means that it is actively executing. And if it looks like this `[53]:`, that means that it has completed executing.\n",
     "2. The second way, which will check to see if anything in the entire notebook is executing is in the top right of the notebook (Image Below). If the circle is empty, then nothing is actively executing. If the circle is grayed out, then there is something executing.\n",
     "\n",
-    "> <img src=\"images/jupyterRuntimeCircle.png\" width=\"500\">"
+    "> <img src=\"../images/jupyterRuntimeCircle.png\" width=\"500\">"
    ]
   },
   {
@@ -444,7 +444,11 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 5
 }

GoogleCloud/Submodule_00_background.ipynb

@@ -292,7 +292,7 @@
     "\n",
     ">Consider the following file structure and you are currently in the directory `toDo`: \n",
     ">\n",
-    "> <img src=\"images/fileDemo.png\" width=\"1200\">\n",
+    "> <img src=\"../images/fileDemo.png\" width=\"1200\">\n",
     ">\n",
     ">- If you were to type `!ls ./`, it would return the contents of your current directory, so it would return `nextWeek`, `Today.txt`, `Tomorrow.txt`, `Yesterday.txt`.\n",
     ">     - The `./` path points to your current directory.\n",
@@ -401,7 +401,11 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 5
 }

GoogleCloud/Submodule_01_prog_setup.ipynb

@@ -20,7 +20,7 @@
     "- Annotation of the final transcriptome using alignment to known proteins (using DIAMOND/BLAST) and assignment to probable protein domains (using HMMER/Pfam).\n",
     "- Generation of output reports.\n",
     "\n",
-    "> <img src=\"images/TransPiWorkflow.png\" width=\"1500\">\n",
+    "> <img src=\"../images/TransPiWorkflow.png\" width=\"1500\">\n",
     ">\n",
     "> **Figure 1:** TransPi workflow for a basic transcriptome assembly run."
    ]
@@ -168,7 +168,7 @@
     "</div>\n",
     "\n",
     "\n",
-    "> <img src=\"images/jupyterRuntime.png\" width=\"500\">\n",
+    "> <img src=\"../images/jupyterRuntime.png\" width=\"500\">\n",
     ">\n",
     "> Remember that you can tell if the cell is still running by referring to the contents inside the `[ ]:` that sits to the left of the code cell. Or you can check the top right of the screen for the circle."
    ]

GoogleCloud/Submodule_02_basic_assembly.ipynb

@@ -84,7 +84,7 @@
    "id": "dc4cd97f-fc62-40ab-badc-ba0bc6f092e4",
    "metadata": {},
    "source": [
-    "> <img src=\"images/AnnotationProcess.png\" width=\"800\">\n",
+    "> <img src=\"../images/AnnotationProcess.png\" width=\"800\">\n",
     ">\n",
     "> **Figure 1:** Annotation workflow for a new, unannotated transcriptome. \n",
     "\n",
@@ -156,7 +156,7 @@
     "\n",
     "> The Oncorhynchus mykiss is commonly known as the **Rainbow Trout**. Here is what they look like:\n",
     ">\n",
-    "> <img src=\"images/rainbowTrout.jpeg\"  width=\"500\" >\n",
+    "> <img src=\"../images/rainbowTrout.jpeg\"  width=\"500\" >\n",
     "> \n",
     ">> Image Source: https://www.ndow.org/species/rainbow-trout/"
    ]
@@ -542,7 +542,11 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 5
 }